https://sourceforge.net/p/advants/activity/Recent activity for Advanced Normalization Tools ( ANTs )enSat, 22 May 2021 14:24:52 -0000https://sourceforge.net/p/advants/discussion/840261/thread/98b4838b/?limit=25#3fe7<REDACTED>Sat, 22 May 2021 14:24:52 -0000https://sourceforge.net/p/advants/discussion/840261/thread/98b4838b/?limit=25#3fe7https://sourceforge.net/p/advants/discussion/840261/thread/f591777c/?limit=25#2329<REDACTED>Sat, 22 May 2021 14:24:26 -0000https://sourceforge.net/p/advants/discussion/840261/thread/f591777c/?limit=25#2329https://sourceforge.net/p/advants/discussion/840261/thread/0570452b5f/?limit=25#1a29How to get help with ANTs ANTs wiki: https://github.com/ANTsX/ANTs/wiki Search issues or open a new one: https://github.com/ANTsX/ANTs/issues Please use the issue templates to ensure that you provide us with the information we need to help.Philip CookWed, 27 May 2020 15:49:01 -0000https://sourceforge.net/p/advants/discussion/840261/thread/0570452b5f/?limit=25#1a29https://sourceforge.net/p/advants/discussion/840260/thread/281b986d67/?limit=25#bccbHow to get help with ANTs ANTs wiki: https://github.com/ANTsX/ANTs/wiki Search issues or open a new one: https://github.com/ANTsX/ANTs/issues Please use the issue templates to ensure that you provide us with the information we need to help.Philip CookWed, 27 May 2020 15:45:37 -0000https://sourceforge.net/p/advants/discussion/840260/thread/281b986d67/?limit=25#bccbhttps://sourceforge.net/p/advants/discussion/840261/thread/0570452b5f/?limit=25#1a29How to get help with ANTs ANTs wiki: https://github.com/ANTsX/ANTs/wiki Search issues or open a new one https://github.com/ANTsX/ANTs/issues Please use the issue templates to ensure that you provide us with the information we need to help.Philip CookWed, 27 May 2020 15:43:10 -0000https://sourceforge.net/p/advants/discussion/840261/thread/0570452b5f/?limit=25#1a29https://sourceforge.net/p/advants/discussion/840261/thread/3f384cad06/?limit=25#afb4/ea0c/cff3okay, thank you!sahjiroWed, 27 May 2020 15:12:44 -0000https://sourceforge.net/p/advants/discussion/840261/thread/3f384cad06/?limit=25#afb4/ea0c/cff3https://sourceforge.net/p/advants/discussion/840261/thread/3f384cad06/?limit=25#afb4/ea0cPlease post this as an issue over at the ANTs github site.Nick TustisonWed, 27 May 2020 15:11:51 -0000https://sourceforge.net/p/advants/discussion/840261/thread/3f384cad06/?limit=25#afb4/ea0chttps://sourceforge.net/p/advants/discussion/840261/thread/3f384cad06/?limit=25#afb4Hi, I red the "Multivariate Analysis of Structural and Diffusion Imaging in Traumatic Brain Injuty, Avants et al" paper (https://pubmed.ncbi.nlm.nih.gov/18995188/). This paper is very interesting for my internship because I would like to do something similar. I was searching in the documentation of ANTs if there is an option for using SyNMN while doing registration but I can't find anything. Has someone an idea where I can find this option (if it actually exists)? Thank you in advance!!sahjiroWed, 27 May 2020 15:08:39 -0000https://sourceforge.net/p/advants/discussion/840261/thread/3f384cad06/?limit=25#afb4https://sourceforge.net/p/advants/discussion/840261/thread/496d67f5cb/?limit=25#dc5cDone: https://github.com/ANTsX/ANTs/issues/1007 .noah10Wed, 27 May 2020 13:59:22 -0000https://sourceforge.net/p/advants/discussion/840261/thread/496d67f5cb/?limit=25#dc5chttps://sourceforge.net/p/advants/discussion/840261/thread/828d1b71d3/?limit=25#ca7dHello, I am sending the V02_to_V01_Warped.nii.gz and the V02_to_V01_Using_trans.nii.gz in the link. https://drive.google.com/open?id=18ayG9b6DeF8Ui76uf9tKlcqn85x7OYp6mariem HAMZAOUIWed, 27 May 2020 11:53:58 -0000https://sourceforge.net/p/advants/discussion/840261/thread/828d1b71d3/?limit=25#ca7dhttps://sourceforge.net/p/advants/discussion/840261/thread/496d67f5cb/?limit=25#e150/20d0Please post this as an issue over at the ANTs github repo. We can continue the conversation over there.Nick TustisonWed, 27 May 2020 00:41:43 -0000https://sourceforge.net/p/advants/discussion/840261/thread/496d67f5cb/?limit=25#e150/20d0https://sourceforge.net/p/advants/discussion/840261/thread/496d67f5cb/?limit=25#e150We recently ran the following buildtemplateparallel command: /usr/lib/ants/buildtemplateparallel.sh -m 30x90x20 -r 1 -g 0.25 -i 4 -t GR -s CC -d 3 -o btp1_ -c 2 -n 1 -j 96 -z /flywheel/v0/input/template/btp_test_template.nii.gz subj-*-*_MPRAGE_reoriented_upsampled.nii.gz ...and found that it needed a little less than 3TB of disk space and took about 30 hours to run when given 10 scans. We want to run this same command on 245 scans. What are some reasonable estimates for the amount of disk space we...noah10Wed, 27 May 2020 00:14:18 -0000https://sourceforge.net/p/advants/discussion/840261/thread/496d67f5cb/?limit=25#e150https://sourceforge.net/p/advants/discussion/840261/thread/828d1b71d3/?limit=25#9acd/d031V02_to_V01_Using_trans.nii.gz is different than V02_to_V01_Warped.nii.gz How much different?Nick TustisonTue, 26 May 2020 15:14:10 -0000https://sourceforge.net/p/advants/discussion/840261/thread/828d1b71d3/?limit=25#9acd/d031https://sourceforge.net/p/advants/discussion/840261/thread/828d1b71d3/?limit=25#9acdHello, Thank you for your response so I did what you told me antsRegistration --verbose 1 --dimensionality 3 --float 1 --collapse-output-transforms 1 -o [V02_to_V01_,V02_to_V01_Warped.nii.gz,V02_to_V01_InverseWarped.nii.gz] --initial-fixed-transform V01_transform2.txt --initial-fixed-transform V01_transform1.mat --initial-moving-transform V02_transform3_0Warp.nii.gz --initial-moving-transform V02_transform2.txt --initial-moving-transform V02_transform1.mat -t SyN[ 0.5,3,0 ] --interpolation BSpline...mariem HAMZAOUITue, 26 May 2020 13:13:01 -0000https://sourceforge.net/p/advants/discussion/840261/thread/828d1b71d3/?limit=25#9acdhttps://sourceforge.net/p/advants/discussion/840261/thread/afe9caed26/?limit=25#a208done :) Thankssankalp tikooTue, 26 May 2020 04:03:36 -0000https://sourceforge.net/p/advants/discussion/840261/thread/afe9caed26/?limit=25#a208https://sourceforge.net/p/advants/discussion/840261/thread/afe9caed26/?limit=25#3e13/c5d8Please post your questions as an issue over at the ANTs GitHub repo.Nick TustisonMon, 25 May 2020 15:35:52 -0000https://sourceforge.net/p/advants/discussion/840261/thread/afe9caed26/?limit=25#3e13/c5d8https://sourceforge.net/p/advants/discussion/840261/thread/afe9caed26/?limit=25#3e13Dear All, I have a cohort of 55 pediatric subjects(age 7-14 years) and i want to calculate cortical thickness and gyrification index via ANTs. Can anyone suggest me how to create a pediatric template using ANTs which can be further used for brain extraction and calculation of cortical thickness and gyrification. Thank you.sankalp tikooMon, 25 May 2020 09:31:05 -0000https://sourceforge.net/p/advants/discussion/840261/thread/afe9caed26/?limit=25#3e13https://sourceforge.net/p/advants/discussion/840261/thread/828d1b71d3/?limit=25#44f8/dc12The flag needs to precede each transform: --initial-moving-transform $transform1 --initial-moving-transform $transform2 ...Nick TustisonFri, 22 May 2020 15:27:47 -0000https://sourceforge.net/p/advants/discussion/840261/thread/828d1b71d3/?limit=25#44f8/dc12https://sourceforge.net/p/advants/discussion/840261/thread/828d1b71d3/?limit=25#44f8Hello, I read in the antsRegistration help that I can do the registration while providing the transformation files for the fixed and the moving image using the --initial-fixed-transform & --initial-moving-transform flags instead of applying the transformation and registring the transformed volumes. This is my command: antsRegistration --verbose 1 --dimensionality 3 --float 1 --collapse-output-transforms 1 -o [V02_to_V01_,V02_to_V01_Warped.nii.gz,V02_to_V01_InverseWarped.nii.gz] --initial-fixed-transform...mariem HAMZAOUIFri, 22 May 2020 15:24:53 -0000https://sourceforge.net/p/advants/discussion/840261/thread/828d1b71d3/?limit=25#44f8https://sourceforge.net/p/advants/discussion/840261/thread/5572bee929/?limit=25#0c4f/8870/cc57/e9e3That would be great. On May 21, 2020, at 8:40 AM, Philip Cook cookpa@users.sourceforge.net wrote:  I have trouble getting Sourceforge emails consistently. We could set preferred support to Github rather than this forum? Problem when creating FA map after Warping and reorienting a DT image Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/advants/discussion/840261/ To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/Nick TustisonThu, 21 May 2020 16:41:00 -0000https://sourceforge.net/p/advants/discussion/840261/thread/5572bee929/?limit=25#0c4f/8870/cc57/e9e3https://sourceforge.net/p/advants/discussion/840261/thread/5572bee929/?limit=25#0c4f/8870/cc57I have trouble getting Sourceforge emails consistently. We could set preferred support to Github rather than this forum?Philip CookThu, 21 May 2020 15:40:40 -0000https://sourceforge.net/p/advants/discussion/840261/thread/5572bee929/?limit=25#0c4f/8870/cc57https://sourceforge.net/p/advants/discussion/840261/thread/5572bee929/?limit=25#0c4f/8870Please post this over at the ANTs GitHub site as an issue. SourceForge tends to be not as visible to the developers. Also, if you can, please post the actual data.Nick TustisonMon, 18 May 2020 17:02:40 -0000https://sourceforge.net/p/advants/discussion/840261/thread/5572bee929/?limit=25#0c4f/8870https://sourceforge.net/p/advants/discussion/840261/thread/5572bee929/?limit=25#0c4fHi, After reviewing literature on registration of diffusion MRI data, I've realized that registering the tensor image is better, as it allows to use orientational, as well as spatial, information during registration (I had previously applied registration on my FA and MD maps). I followed the steps outlined here: https://github.com/ANTsX/ANTs/wiki/Warp-and-reorient-a-diffusion-tensor-image, and I started by testing the deformation and reorientation with a simple affine transformation (so no warps...Stéfanie TremblayMon, 18 May 2020 16:33:17 -0000https://sourceforge.net/p/advants/discussion/840261/thread/5572bee929/?limit=25#0c4fhttps://sourceforge.net/p/advants/discussion/840261/thread/c2fc4a06e3/?limit=25#88f8Ok, sorry, I thought this would be the appropriate place, because it's also general question about the mathematics/implementation of the displacement transform, which probably is ITK. I don't expect it to be a bug.Maximilian HoffmannFri, 15 May 2020 14:52:49 -0000https://sourceforge.net/p/advants/discussion/840261/thread/c2fc4a06e3/?limit=25#88f8https://sourceforge.net/p/advants/discussion/840261/thread/c2fc4a06e3/?limit=25#3dab/a8a3Please post this over at the appropriate GitHub forum depending on the package you're using (e.g., ANTsPy or ANTs).Nick TustisonFri, 15 May 2020 14:49:51 -0000https://sourceforge.net/p/advants/discussion/840261/thread/c2fc4a06e3/?limit=25#3dab/a8a3https://sourceforge.net/p/advants/discussion/840261/thread/c2fc4a06e3/?limit=25#3dabI currently initialise a displacement transform from a numpy array. Do I get that right, that in principle effects of this transform should be more or less confined to a local environments within the limits of ~ px-coordinate + displacement ? Because I see different results if I compare a cut out of a volume and displacement field + transform versus a cutout of the transformed whole volume + displacement field. Thank you!Maximilian HoffmannFri, 15 May 2020 14:43:44 -0000https://sourceforge.net/p/advants/discussion/840261/thread/c2fc4a06e3/?limit=25#3dabhttps://sourceforge.net/p/advants/discussion/840261/thread/5e576edf93/?limit=25#3e06/ab66Please post this as an issue over at the ANTsPy github website.Nick TustisonTue, 12 May 2020 16:19:56 -0000https://sourceforge.net/p/advants/discussion/840261/thread/5e576edf93/?limit=25#3e06/ab66https://sourceforge.net/p/advants/discussion/840261/thread/5e576edf93/?limit=25#3e06Using antspy, when I supply images as numpyarrays which contain negative values I get the error above, is this expected?Maximilian HoffmannTue, 12 May 2020 16:15:21 -0000https://sourceforge.net/p/advants/discussion/840261/thread/5e576edf93/?limit=25#3e06https://sourceforge.net/p/advants/discussion/840261/thread/4daf9b78df/?limit=25#b969/4263/49c0/8f08/f6b9/e260Sorry, I can't make sense of the error log. It looks to be a system-specific issue for which is really difficult to debug using the help forum.Nick TustisonTue, 12 May 2020 14:56:04 -0000https://sourceforge.net/p/advants/discussion/840261/thread/4daf9b78df/?limit=25#b969/4263/49c0/8f08/f6b9/e260https://sourceforge.net/p/advants/discussion/840261/thread/4daf9b78df/?limit=25#b969/4263/49c0/8f08/f6b9Sorry, I re-send the files and the cmake error and output log files were attached. CMakeError.log https://docs.google.com/document/d/18GEfMkW211MJeujpcnMcMrJho8e_ViNaNnTy5NOFto4/edit?usp=drivesdk CMakeOutput.log https://docs.google.com/document/d/1FIQCdFbubf59k3uM2A5DLgR_rddQg8PzSY593pgEuv4/edit?usp=drivesdk Nick Tustison ntustison@users.sourceforge.net 于 2020年5月11日周一 下午10:28写道： Your second link is incomplete and I don't have permission to read the first link. ANTs installtion error https://sourceforge.net/p/advants/discussion/840261/thread/4daf9b78df/?limit=25#b969/4263/49c0/8f08...Yuxuan,ZhangTue, 12 May 2020 01:50:43 -0000https://sourceforge.net/p/advants/discussion/840261/thread/4daf9b78df/?limit=25#b969/4263/49c0/8f08/f6b9https://sourceforge.net/p/advants/discussion/840260/thread/4f63c753a3/?limit=25#4ba1/89a6Have you looked at the images?Nick TustisonMon, 11 May 2020 20:26:18 -0000https://sourceforge.net/p/advants/discussion/840260/thread/4f63c753a3/?limit=25#4ba1/89a6https://sourceforge.net/p/advants/discussion/840260/thread/4f63c753a3/?limit=25#4ba1Hi, I have a subject cohort of aphasic patients whose age range is between 50-90. I have applied an imputation method on the lesioned brains. I wanted to use the age-matched IXI template on the data but was confused about which template to use. I found this link reading through the forum. https://drive.google.com/drive/folders/0B4SvObeEfaRySUNDOE5DWksyQ0k In the IXI folder, there are three templates template0, 1, 2. I wasn't sure which one to use. There is also a AgeGender specific folder with different...Apoorva KelkarMon, 11 May 2020 20:14:40 -0000https://sourceforge.net/p/advants/discussion/840260/thread/4f63c753a3/?limit=25#4ba1https://sourceforge.net/p/advants/discussion/840261/thread/1bfa94f013/?limit=25#10b2/1673/ffd2/abfdIt sounds like a system-specific issuse which is obviously difficult to debug through a help forum. Know that all the main developers primarily use macs so you should be fine with respect to that issue.Nick TustisonMon, 11 May 2020 18:22:39 -0000https://sourceforge.net/p/advants/discussion/840261/thread/1bfa94f013/?limit=25#10b2/1673/ffd2/abfdhttps://sourceforge.net/p/advants/discussion/840261/thread/1bfa94f013/?limit=25#10b2/1673/ffd2Yes, as strange as it can be, the registration results look correct. However, I think that the problem comes from my setup. I was doing some testing of my preprocessing pipeline on my MacBook Pro (macOS Catalina 10.15.4, clang version 11.0.3). But when I run the same code on the computing cluster of my organization, the deformation maps look just fine. Thank you. KilianKilian HettMon, 11 May 2020 17:49:11 -0000https://sourceforge.net/p/advants/discussion/840261/thread/1bfa94f013/?limit=25#10b2/1673/ffd2https://sourceforge.net/p/advants/discussion/840261/thread/4daf9b78df/?limit=25#b969/4263/49c0/8f08Your second link is incomplete and I don't have permission to read the first link.Nick TustisonMon, 11 May 2020 14:28:28 -0000https://sourceforge.net/p/advants/discussion/840261/thread/4daf9b78df/?limit=25#b969/4263/49c0/8f08https://sourceforge.net/p/advants/discussion/840261/thread/4daf9b78df/?limit=25#b969/4263/49c0The cmake error log file and output log file were attached. CMakeOutput.log https://docs.google.com/document/d/10kV2TxrpaNwt98pE0_eGq21YyLs9IVwA6GXBzPEiwVc/edit?usp=drivesdk CMakeOutput.log https://docs.google.com/document/d/1FIQCdFbubf59k3uM2A5DLgR_rddQg8PzSY593pgEuv4/edit?usp=drivesdk Nick Tustison ntustison@users.sourceforge.net 于 2020年5月11日周一 上午11:29写道： Please include the entire error log file. Also, if you're compiling, I would recommend compiling from the latest source. ANTs installtion error...Yuxuan,ZhangMon, 11 May 2020 07:11:52 -0000https://sourceforge.net/p/advants/discussion/840261/thread/4daf9b78df/?limit=25#b969/4263/49c0https://sourceforge.net/p/advants/discussion/840261/thread/4daf9b78df/?limit=25#b969/4263Please include the entire error log file. Also, if you're compiling, I would recommend compiling from the latest source.Nick TustisonMon, 11 May 2020 03:29:23 -0000https://sourceforge.net/p/advants/discussion/840261/thread/4daf9b78df/?limit=25#b969/4263https://sourceforge.net/p/advants/discussion/840261/thread/4daf9b78df/?limit=25#b969Hi, I followed the instructions on website( https://brianavants.wordpress.com/2012/04/13/updated-ants-compile-instructions-april-12-2012/ ) to install ANTs version 2.1.0. However, after the command "make -j 4", it stopped with the following error. I have tried many times with different ANTs version(v2.1.0 to v2.1.rc1 to rc2 to rc3 to v2.2) but it always encountered with the error. So I want to inquire how to solve this problem.Yuxuan,ZhangMon, 11 May 2020 03:24:34 -0000https://sourceforge.net/p/advants/discussion/840261/thread/4daf9b78df/?limit=25#b969https://sourceforge.net/p/advants/discussion/840261/thread/1bfa94f013/?limit=25#10b2/1673Do the registration results look correct?Nick TustisonSat, 09 May 2020 00:10:27 -0000https://sourceforge.net/p/advants/discussion/840261/thread/1bfa94f013/?limit=25#10b2/1673https://sourceforge.net/p/advants/discussion/840261/thread/1bfa94f013/?limit=25#10b2Hello, I want to analyze the deformation fields produced by the non-rigid registration. However, I have a problem that I struggle to solve. When I’m looking at the jacobian's determinant, only a part of the brain is represented. It seems that the deformation field has been cropped. I don’t understand why (the same thing happens for InverseWarp or Warp). Can someone help me to understand what’s going on? In advance thanks. KilianKilian HettFri, 08 May 2020 22:21:07 -0000https://sourceforge.net/p/advants/discussion/840261/thread/1bfa94f013/?limit=25#10b2https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166e/5e2b/e7c1/fe92/b603/8069/722cOne other difference is I didn't use the mask. I suspect that would be more of a cause than the metric.Nick TustisonFri, 08 May 2020 20:32:26 -0000https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166e/5e2b/e7c1/fe92/b603/8069/722chttps://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166e/5e2b/e7c1/fe92/b603/8069That is so bizarre. That worked for me as well. Any thoughts on why SyNQuick vs SyN produced markedly different outcomes?Adam RaikesFri, 08 May 2020 20:23:25 -0000https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166e/5e2b/e7c1/fe92/b603/8069https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166e/5e2b/e7c1/fe92/b603Here's what I ran and the results look fine: $ antsRegistrationSyNQuick.sh -d 3 -f DSURQE_40micron_average.nii -m sub-apoe0084_acq-2avg_space-T2w_desc-brain_unbiased.nii -o templatexsub -n 4 $ antsApplyTransforms -d 3 -i DSURQE_40micron_labels.nii -r sub-apoe0084_acq-2avg_space-T2w_desc-brain_unbiased.nii -o sub-apoe0084_acq-2avg_space-T2w_desc-brain_unbiased_labels.nii.gz -n GenericLabel -t [ templatexsub0GenericAffine.mat , 1] -t templatexsub1InverseWarp.nii.gz -v 1Nick TustisonFri, 08 May 2020 15:18:29 -0000https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166e/5e2b/e7c1/fe92/b603https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166e/5e2b/e7c1/fe92/b603Here's what I ran and the results look fine: $ antsRegistrationSyNQuick.sh -d 3 -f DSURQE_40micron_average.nii -m sub-apoe0084_acq-2avg_space-T2w_desc-brain_unbiased.nii -o templatexsub -n 4 $ antsApplyTransforms -d 3 -i DSURQE_40micron_labels.nii -r sub-apoe0084_acq-2avg_space-T2w_desc-brain_unbiased.nii -o sub-apoe0084_acq-2avg_space-T2w_desc-brain_unbiased_labels.nii.gz -n GenericLabel -t [ templatexsub0GenericAffine.mat , 1] -t templatexsub1InverseWarp.nii.gz -v 1Nick TustisonFri, 08 May 2020 15:17:41 -0000https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166e/5e2b/e7c1/fe92/b603https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166e/5e2b/e7c1/fe92I can sure try that. Like I said in the original post, I used ITK-SNAP to reorient the image so that they were both the same. Here's what I fed to antsRegistrationSyN.shAdam RaikesFri, 08 May 2020 03:46:47 -0000https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166e/5e2b/e7c1/fe92https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166e/5e2b/e7c1Are these the inputs to antsRegistrationSyN.sh? If so, that's the first problem. ANTs registration won't correct orientation issues like this. You can try to use antsAI but it might be easier for you to place corresponding landmarks in the two images and use antsLandmarkBasedTransformInitializer to determine an initial transform.Nick TustisonFri, 08 May 2020 03:34:05 -0000https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166e/5e2b/e7c1https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166e/5e2bHere is the original image for the mouse brain without any processing (just in case either the N4 or the reorientation somehow caused the issue I'm seeing). The template/atlas files are here: http://repo.mouseimaging.ca/repo/DSURQE_40micron_nifti/ Please note that the template mask is in a different orientation than the template or labels file (I don't know why they saved it that way). Thanks for help debugging this. I really appreciate it.Adam RaikesThu, 07 May 2020 20:31:41 -0000https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166e/5e2bhttps://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166eYeah, the partial FOV would seem to be incorrect and not consistent with the input images or typical ants registration performance. Can you post the data for us to look at?Nick TustisonThu, 07 May 2020 19:27:52 -0000https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0/166ehttps://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0I'll give that a shot. What about the partial FOV in the warped images? Is that a problem?Adam RaikesThu, 07 May 2020 19:16:41 -0000https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45/dfa0https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45The command calls appear to be correct. My guess is that the headers are different between $template and /templates/DSURQE_40micron_labels.nii. You can try copying the header information from the former to the latter using CopyImageHeaderInformation.Nick TustisonThu, 07 May 2020 00:08:16 -0000https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6/4b45https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6I'm certain that I'm asking a very basic question that I've just somehow missed in the documentation somewhere. I'm attempting to register ex-vivo mouse brains to a template and use the the inverse warp to get the template space atlas into subject space. I'm running this in a singularity container using ANTs v. 2.3.1. The template brain and accompanying mask are 0.04 isotropic while our acquired brains are 0.075 isotropic. My mouse brain has been unbiased as well as reoriented using ITK-SNAP to LPI...Adam RaikesWed, 06 May 2020 23:19:52 -0000https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6I'm certain that I'm asking a very basic question that I've just somehow missed in the documentation somewhere. I'm attempting to register ex-vivo mouse brains to a template and use the the inverse warp to get the template space atlas into subject space. I'm running this in a singularity container using ANTs v. 2.3.1. The template brain and accompanying mask are 0.04 isotropic while our acquired brains are 0.075 isotropic. My mouse brain has been unbiased as well as reoriented using ITK-SNAP to LPI...Adam RaikesWed, 06 May 2020 23:19:26 -0000https://sourceforge.net/p/advants/discussion/840261/thread/17b463f381/?limit=25#bca6https://sourceforge.net/p/advants/discussion/840260/thread/b2256c7b46/?limit=25#2484/e674Instead of trying to run template construction, try to run a single ANTs program, like bias correction. Also, this appears to be a compilation/system issue so you might want to do some google searching in addition to further consultation with your IT support.Nick TustisonWed, 06 May 2020 19:57:27 -0000https://sourceforge.net/p/advants/discussion/840260/thread/b2256c7b46/?limit=25#2484/e674https://sourceforge.net/p/advants/discussion/840260/thread/b2256c7b46/?limit=25#2484Hello, I recently tried to use antsMTC2.sh on the cluster, which is SLURM in our university, to build up a template. After I executed the script on the terminal (please see the attached file named Script_MRI_analysis), I first got an error message in the log file (please see the attached file named testslurm_0505) with a segmentation fault. I found that there was no "Repaired.nii.gz" file, which should be generated from the N4BiasFieldCorrection, so it failed in further steps. I checked the slurm...Hsiang-Yu ChenWed, 06 May 2020 19:37:29 -0000https://sourceforge.net/p/advants/discussion/840260/thread/b2256c7b46/?limit=25#2484https://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#2cd0/4fd5/a831/6c25ExtractRegionFromImageNick TustisonTue, 05 May 2020 23:33:17 -0000https://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#2cd0/4fd5/a831/6c25https://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#2cd0/4fd5/a831Thanks Nick! Is there a command to crop the images, for example I only want to take the 'center' 100x100 voxel of the original 256x256 image?Nam Hoang LeTue, 05 May 2020 22:33:13 -0000https://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#2cd0/4fd5/a831https://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#2cd0/4fd5/f38a/0ce3What is exactly "PaddingSize"? Is it the amount of added voxels on each size of the image, or the final size after the padding? The former. Also, is there a function to get the size of the image? PrintHeaderNick TustisonTue, 05 May 2020 14:29:47 -0000https://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#2cd0/4fd5/f38a/0ce3https://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#2cd0/4fd5/f38aHi, I have a question, maybe trivial. What is exactly "PaddingSize"? Is it the amount of added voxels on each size of the image, or the final size after the padding? Also, is there a function to get the size of the image?Nam Hoang LeTue, 05 May 2020 04:59:03 -0000https://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#2cd0/4fd5/f38ahttps://sourceforge.net/p/advants/discussion/840261/thread/b9d40d4d7c/?limit=25#5923/b36bThere isn't ANTs-specific functionality to handle that data. Although you tried ITK Dicom, you might want to ask over at the ITK discussion forums to see if anybody has a solution.Nick TustisonTue, 05 May 2020 00:02:58 -0000https://sourceforge.net/p/advants/discussion/840261/thread/b9d40d4d7c/?limit=25#5923/b36bhttps://sourceforge.net/p/advants/discussion/840261/thread/b9d40d4d7c/?limit=25#5923Hello ANTs experts, I have a linear transformation file (translation + rotation) in Dicom format (Modality tagged as REG in header) and I want to either convert this to any of mat/tfm/nifti/nrrd/mha etc. format or directly apply it to an image using antsApplyTransforms. I tried the latter but didn't work. I also tried to conver it using ITK Dicom to nifti code but it doesn't seem to be designed for a REG transformation as it only supports GDCMImageIO. Is this possible somehow? Thanks, SethSeth RyanMon, 04 May 2020 22:33:17 -0000https://sourceforge.net/p/advants/discussion/840261/thread/b9d40d4d7c/?limit=25#5923https://sourceforge.net/p/advants/discussion/840261/thread/1b908b9678/?limit=25#f065Hello Nick, thank you very much for the advice, it was really helpful. I had misplaced some landmarks indeed. The result is better now but still needs work. Thank you very much for all your help and quick responses!Alice FermigierMon, 04 May 2020 15:07:40 -0000https://sourceforge.net/p/advants/discussion/840261/thread/1b908b9678/?limit=25#f065https://sourceforge.net/p/advants/discussion/840261/thread/385c248783/?limit=25#df5d/32acCluster system requirements and protocols vary from institution to institution so I really can't provide any direction in that respect. You should ask your cluster administrators who will likely point you to a tutorial or other resources.Nick TustisonSat, 02 May 2020 15:44:12 -0000https://sourceforge.net/p/advants/discussion/840261/thread/385c248783/?limit=25#df5d/32achttps://sourceforge.net/p/advants/discussion/840261/thread/385c248783/?limit=25#df5dThank you Nick , Can i ask you...do you have any advice on how to use antsMotionCorr for a huge amount of volumes and benefit from a PBS cluster? eg how to submit the job? Thanks johanJohan Van AudekerkeSat, 02 May 2020 09:19:44 -0000https://sourceforge.net/p/advants/discussion/840261/thread/385c248783/?limit=25#df5dhttps://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#2cd0/4fd5% ImageMath | grep PadImage PadImage : If Pad-Number is negative, de-Padding occurs Usage : PadImage ImageIn PaddingSize [PaddingVoxelValue=0]Nick TustisonThu, 30 Apr 2020 19:03:36 -0000https://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#2cd0/4fd5https://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#2cd0Thanks. I also want to pad the boundaries of some images with zeros or a background value to make it to a bigger size. Is there a function to do that?Nam Hoang LeThu, 30 Apr 2020 18:13:31 -0000https://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#2cd0https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#56ee/0219Okay, well you need to calculate those transforms. Regarding mixing packages---I already provided the requisite caveat but obviously you're welcome to do whatever you want. As far as I know, there's no universal/general solution that works for every case so just proceed with caution and always look at your results.Nick TustisonThu, 30 Apr 2020 16:09:42 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#56ee/0219https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#56eeNo, I don't think so. By the way, on a side note, it seems that applying afni's 3dcopy can restore the sform matrix that we talked about.MattThu, 30 Apr 2020 16:04:24 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#56eehttps://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#7527/fc83Okay, do you have the transform from each average image to its corresponding T1?Nick TustisonThu, 30 Apr 2020 16:01:56 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#7527/fc83https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#7527Yes, I have the average image from the EPI. ThanksMattThu, 30 Apr 2020 15:59:47 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#7527https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#bf95/2b0fOkay, hvae you made your average motion corrected image? The code is in one of my previous responses.Nick TustisonThu, 30 Apr 2020 15:58:16 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#bf95/2b0fhttps://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#bf95Thanks Nick, I'm afraid I lost you there, would you please elaborate more? or point me to an example? MattMattThu, 30 Apr 2020 15:49:53 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#bf95https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#818b/b823Sure. Now you can register each subject's motion corrected data to the template by concatenating the transforms that go from the the average EPI sequence through the corresponding T1-w image to the template.Nick TustisonThu, 30 Apr 2020 14:45:36 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#818b/b823https://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#e4a3/fe57Try ResampleImage.Nick TustisonThu, 30 Apr 2020 02:19:05 -0000https://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#e4a3/fe57https://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#e4a3Hi, I have used ANTs for registration and intensity normalization of MRI images. Is there a function to resize the x, y dimensions of all the images to the same size, say from 192x192 to 64x64?Nam Hoang LeThu, 30 Apr 2020 01:54:41 -0000https://sourceforge.net/p/advants/discussion/840261/thread/cee83dac74/?limit=25#e4a3https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#818bHi Nick, You are right. I did these two lines of motion correction for one subject and although in fsleyes and ITK-SNAP (it only works on the first volume) the orientations are OK, but sform matrix is not showing. So, there is some effect here. If I skip the motion correction in ANTs, can we proceed to next step using the files pre-processed in FSL? P.S. Interestingly, the template that I created, seems to have not affected and all the matrices are ok. Thanks, MattMattThu, 30 Apr 2020 01:32:41 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#818bhttps://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#818bHi Nick, You are right. I did these two lines of motion correction of one subject and although in fsleyes and ITK-SNAP (it only works on the first volume) the orientations are OK, but sform matrix is not showing. So, there is some effect here. If I skip the motion correction in ANTs, can we proceed to next step using the files pre-processed in FSL? P.S. Interestingly, the template that I created, seems to have not affected and all the matrices are ok. Thanks, MattMattThu, 30 Apr 2020 01:32:12 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#818bhttps://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#818bHi Nick, You are right. I did these two lines of motion correction of one subject and although in fsleyes and ITK-SNAP (it only works on the first volume) the orientations are OK, but sform matrix is not showing. So, there is some effect here. If I skip the motion correction in ANTs, can we proceed to next step using the files preprocessed inFSL? P.S. Interestingly, the template that I created, seems to have not affected and all the matrices are ok. Thanks, MattMattThu, 30 Apr 2020 01:31:47 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#818bhttps://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#818bHi Nick, You are right. I did these two lines of motion correction of one subject and although in fsleyes and ITK-SNAP (it only works on the first volume) the orientations are OK, but sform matrix is not showing. So, there is some effect here. If I skip the motion correction in ANTs, can we proceed to next step using the files FSL? P.S. Interestingly, the template that I created, seems to have not affected and all the matrices are ok. Thanks, MattMattThu, 30 Apr 2020 01:29:12 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#818bhttps://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#74e9/265cYou might first want to see if your data is affected. Try looking at the registered images in both ITK-SNAP and fsleyes.Nick TustisonTue, 28 Apr 2020 19:38:05 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#74e9/265chttps://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#74e9Oh, I see... then this could cause a problem down the line. I want to run group ICA on the final registered EPI files. On the other hand, FSL's registration would not give the best outcome, so I like to use ANTs for registration. Any work around you might think of? Thanks!MattTue, 28 Apr 2020 18:36:28 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#74e9https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#4a7b/1c99You have to be careful about mixing toolkits. There's a well-known difference in how FSL treats the header information vs. ITK/ANTs which dictates the image orientation in physical space. You can read more about it here.Nick TustisonTue, 28 Apr 2020 16:35:00 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#4a7b/1c99https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#4a7bThanks Nick, I have already my EPI data motion corrected using FSL's tools. Since you mentioned these set of parameters might not be optimal on my dataset, I might skip the motion correction for now. In that case, what would be my next step? MattMattTue, 28 Apr 2020 16:15:59 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#4a7bhttps://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#da89/9d2aOkay, so now you want to compute the transformations from your 4-D EPI sequences to your structural data. Typically, we'll do a motion correction of that sequence using antsMotionCorr. $ antsMotionCorr -d 3 -a ${input4dEpi} -o ${averageEpi} $ antsMotionCorr -d 3 -m MI[${averageEpi},${input4dEpi},1,32,0.1] -t Rigid[0.2] -i 500x100x50x0 -s 3x2x1x0 -f 5x4x2x1 -o [${outputPrefix},${outputPrefix}Warped.nii.gz] -v 1 Note that these is simply one set of parameters which might not be optimal for your sequence...Nick TustisonTue, 28 Apr 2020 14:01:27 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#da89/9d2ahttps://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#da89Hello, I have followed the script you mentioned, now I have all these files for each subject. Ready for next step. Thanks!MattTue, 28 Apr 2020 12:16:17 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#da89https://sourceforge.net/p/advants/discussion/840261/thread/1b908b9678/?limit=25#872e/3e61Okay, those landmarks look better but you also need to check your bspline landmarks. Run this antsLandmarkBasedTransformInitializer 3 \ $landmarks_human \ $landmarks_macaque \ bspline \ $bspline_init and take a look at the resulting displacement field. An easy way to do this is in ITK-SNAP: Layer inspector --> General --> Display mode: Deformation Grid Display. You definitely have some mismatched landmarks. Also, instead of antsRegistrationSyN.sh use antsRegistrationSyNQuick.sh. You'll get much quicker...Nick TustisonMon, 27 Apr 2020 18:40:57 -0000https://sourceforge.net/p/advants/discussion/840261/thread/1b908b9678/?limit=25#872e/3e61https://sourceforge.net/p/advants/discussion/840261/thread/1b908b9678/?limit=25#872eHi Nick, thank you for your answer. The error in the affine transform was due to a lack of landmarks in the posterior part of the brain, this is what I obtained with antsApplyTransforms -d 3 -v 1 \ -i $macaque_template \ -r $human_template \ -o test.nii.gz \ -n linear \ -t $affine_init after adding two landmarks at the surface of the marginal and the parieto-occipital sulci : https://we.tl/t-9ftEwzAgR5Alice FermigierMon, 27 Apr 2020 16:27:37 -0000https://sourceforge.net/p/advants/discussion/840261/thread/1b908b9678/?limit=25#872ehttps://sourceforge.net/p/advants/discussion/840261/thread/1b908b9678/?limit=25#a765/e177Okay, when I debug normalization issues, I think it's best to look at the results after each step. If we take a look at the results after the first landmark initialization, it's clear that something is off with one or more of your landmark pairs. Take a look at the attached screenshot which shows the registered $macaque_template in the space of the $human_template. Specifically, you can do antsApplyTransforms -d 3 -v 1 \ -i $macaque_template \ -r $human_template \ -o test.nii.gz \ -n linear \ -t...Nick TustisonMon, 27 Apr 2020 15:12:10 -0000https://sourceforge.net/p/advants/discussion/840261/thread/1b908b9678/?limit=25#a765/e177https://sourceforge.net/p/advants/discussion/840261/thread/1b908b9678/?limit=25#a765Hi Nick! Sorry, about that. Here is the full script and the whole data and outputs via a wetransfer link : https://we.tl/t-qZNicTMGQ4 datadir= human_template=${datadir}/Human.nii.gz macaque_template=${datadir}/Macaque.nii.gz landmarks_human_few=${datadir}/Affine_landmarks_human.nii.gz landmarks_macaque_few=${datadir}/Affine_landmarks_macaque.nii.gz affine_init=${datadir}/macaque2human_affine.txt landmarks_human=${datadir}/Bspline_landmarks_human.nii.gz landmarks_macaque=${datadir}/Bspline_landmarks_macaque.nii.gz...Alice FermigierMon, 27 Apr 2020 10:42:05 -0000https://sourceforge.net/p/advants/discussion/840261/thread/1b908b9678/?limit=25#a765https://sourceforge.net/p/advants/discussion/840260/thread/7a7853ed13/?limit=25#ebb4/5909/02a5/dc20/452a/3a55It can handle 3-D images. It's just that your images are atypical, probably incorrect, and that is probably why the program segfaults.Nick TustisonMon, 27 Apr 2020 04:28:27 -0000https://sourceforge.net/p/advants/discussion/840260/thread/7a7853ed13/?limit=25#ebb4/5909/02a5/dc20/452a/3a55https://sourceforge.net/p/advants/discussion/840260/thread/7a7853ed13/?limit=25#ebb4/5909/02a5/dc20/452aThanks for your suggestion. I'm wondering if this package can only process 2D images instead of 3D volume? If not, is there any thickness-analysis relavent package from ANTs that can process 3D volumes?Shuo ChenMon, 27 Apr 2020 03:44:02 -0000https://sourceforge.net/p/advants/discussion/840260/thread/7a7853ed13/?limit=25#ebb4/5909/02a5/dc20/452ahttps://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#ae03OK Nick, now I have this for all subjects.MattMon, 27 Apr 2020 03:10:04 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#ae03https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#ae03No, just for one. for all, it is in progress...MattMon, 27 Apr 2020 02:07:59 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#ae03https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#7753/b1ffGreat. Did you do that for all your subjects?Nick TustisonMon, 27 Apr 2020 02:05:36 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#7753/b1ffhttps://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#7753Hi Nick, Thanks! this is how I ran this: antsRegistrationSyNQuick.sh -d 3 -f template0.nii.gz -m sbj_MPRAGE_brain.nii.gz -o sub_reg -n 1 it took ~5 mins to finish and it created these files: sub_reg0GenericAffine.mat sub_reg1InverseWarp.nii.gz sub_reg1Warp.nii.gz sub_regInverseWarped.nii.gz sub_regWarped.nii.gz MattMattMon, 27 Apr 2020 01:40:50 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#7753https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#83fc/6d31Okay, the first thing to do is delete all those files except for template0.nii.gz. The subject-specific files are not optimal (outdated) and the other template* files are not useful. Once you do that you can continue with your processing: Let's start with registering each subject to the template. First try: $ antsRegistrationSyNQuick.sh -d 3 -f $template -m $subjectT1 -o $outputPrefix -n ${numberOfThreads} Once you get that done, let me know and we'll move on to the second step.Nick TustisonSun, 26 Apr 2020 23:44:54 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#83fc/6d31https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#83fcHello, Thanks for your help. I managed to create my template using antsMultivariateTemplateConstruction.sh from each subjects MPRAGE images! Since I am very new to ANTs, I appreciate your help again: my goal is to use these to do nonlinear registration of each subject 4D data (EPI image) to this newly created template. So, antsMultivariateTemplateConstruction.sh creates 4 files as the output template: template0.nii.gz (the output template) template0Affine.txt template0warp.nii.gz templatewarplog.txt...MattSun, 26 Apr 2020 21:58:55 -0000https://sourceforge.net/p/advants/discussion/840260/thread/23bc83c087/?limit=25#83fchttps://sourceforge.net/p/advants/discussion/840260/thread/7a7853ed13/?limit=25#ebb4/5909/02a5/dc20These aren't typical input to the LaplacianThickness program for which we don't really provide support. The program was designed for gray and white matter probability images. Although you could probably adapt the program, it would be on you to actually made the changes for accommodation in the code.Nick TustisonSun, 26 Apr 2020 21:06:44 -0000https://sourceforge.net/p/advants/discussion/840260/thread/7a7853ed13/?limit=25#ebb4/5909/02a5/dc20https://sourceforge.net/p/advants/discussion/840260/thread/7a7853ed13/?limit=25#ebb4/5909/02a5Hi, attached are two 3D volume segmentation labels. I obtain that error by using these two volumes as inputsShuo ChenSun, 26 Apr 2020 19:52:24 -0000https://sourceforge.net/p/advants/discussion/840260/thread/7a7853ed13/?limit=25#ebb4/5909/02a5https://sourceforge.net/p/advants/discussion/840260/thread/7a7853ed13/?limit=25#ebb4/5909Can you post your images?Nick TustisonSun, 26 Apr 2020 14:34:26 -0000https://sourceforge.net/p/advants/discussion/840260/thread/7a7853ed13/?limit=25#ebb4/5909https://sourceforge.net/p/advants/discussion/840260/thread/7a7853ed13/?limit=25#ebb4I'm trying to use LaplcianThickness function for calculating 3D retinal thickness using Nipype module in python. However, I can successfully pass in 3D Nifti volumes, but Segmentation fault (core dumped) error will pop after all calculation is done. Does anyone know what may be the issue? I have tried ANTs package on Anaconda and Linux, neither of them works.Shuo ChenSun, 26 Apr 2020 06:08:44 -0000https://sourceforge.net/p/advants/discussion/840260/thread/7a7853ed13/?limit=25#ebb4