Freesurfer September 2022

freesurfer@nmr.mgh.harvard.edu

92 participants
129 discussions

Re: [Freesurfer] problem with autorecon2-cp
by Mostafa Fakhri 07 Sep '22

07 Sep '22

External Email - Use Caution Hi Bruce, It works.Thank you so much. Actually I need just rawavrg.mgz and wm.seg.mgz, I think using autorecon2 is quick way to to produce these images. Is this correct? Mostafa

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Re: [Freesurfer] segment_subregions failed
by Nolan, Jackson 06 Sep '22

06 Sep '22

Thanks for the info about the build, Yes, I think the issue is coming from some old information on your system, as that build stamp is from 2009. You may have both versions of FreeSurfer installed on your system, but the old version is taking priority. If both are installed on your system, you can start with a fresh terminal, without sourcing FreeSurfer, then run the setup script for 7.3.2. Sourcing multiple versions in the same terminal session can cause issues finding the correct version of the utilities. Otherwise, I would recommend removing the FreeSurfer files you currently have on your system and then doing a clean install of 7.3.2. Best, Jackson ________________________________ From: Md. Mamun Al-Amin <mdalaminbadal(a)gmail.com> Sent: Wednesday, August 31, 2022 6:02 AM To: Nolan, Jackson <JNOLAN5(a)mgh.harvard.edu> Subject: Re: [Freesurfer] segment_subregions failed External Email - Use Caution Hi Jackson, I do not know how freesurfer was built (from the git repo or somewhere else). I requested our HPC department at Indiana university to install an updated version of freesurfer. Interestingly, I see the 'build-stamp.txt' file contains only the text "freesurfer-x86_64-redhat-linux-gnu-dev4-20090216". Do you think this old information is responsible for this failure? Kind regards Md. Mamun Al-Amin, PhD --------------------------- Postdoctoral Fellow Stark Neuroscience Research Institute Indiana University School of Medicine 320 W. 15th Street, NB Bldg Rm 103 Indianapolis, IN 46202 On Tue, Aug 30, 2022 at 12:53 PM Nolan, Jackson <JNOLAN5(a)mgh.harvard.edu<mailto:JNOLAN5@mgh.harvard.edu>> wrote: If you did not build FreeSurfer from the git repo, could you send the build stamp? It is located in a file called 'build-stamp.txt' in the FREESURFER_HOME directory. Best, Jackson ________________________________ From: Nolan, Jackson <JNOLAN5(a)mgh.harvard.edu<mailto:JNOLAN5@mgh.harvard.edu>> Sent: Monday, August 29, 2022 4:25 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>; mdalaminbadal(a)gmail.com<mailto:mdalaminbadal@gmail.com> <mdalaminbadal(a)gmail.com<mailto:mdalaminbadal@gmail.com>> Subject: Re: [Freesurfer] segment_subregions failed Greetings, I am having some trouble reproducing that error. Could you send me the commit number of the git reop you cloned? Jackson Nolan, BSc - Programmer Laboratory for Computational Neuroimaging (LCN<https://secure-web.cisco.com/1MlxQMEDBghD0Z_Lu-oEVCntF2aEel3BSjl7JHkL3B0wmx…>) Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, Mass General Hospital (413) 244-8583 | jnolan5(a)mgh.harvard.edu<mailto:jnolan5@mgh.harvard.edu> ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Md. Mamun Al-Amin <mdalaminbadal(a)gmail.com<mailto:mdalaminbadal@gmail.com>> Sent: Monday, August 15, 2022 12:12 PM To: Freesurfer support list <Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] segment_subregions failed External Email - Use Caution Hi Freesurfer experts, I have been trying to segment thalamus using segment_subregions command available in freesurfer 7.3.2. Unfortunately, I have been encountering the following error. IN-NSCC-050385:~ mdalamin$ segment_subregions thalamus --cross sub-0023 Step 1: preprocessing inputs for thalamus segmentation Running command: mri_convert /var/folders/3b/zd9p0z7s6nx_m1_xyg0tqqj0dgxn6r/T/tmpzh3k0uay/tempImage.mgz /var/folders/3b/zd9p0z7s6nx_m1_xyg0tqqj0dgxn6r/T/tmpzh3k0uay/tempImage.mgz -odt float -rt cubic -vs 0.5 0.5 0.5 Preprocessing took 6 seconds Step 2: aligning atlas to reference segmentation Traceback (most recent call last): File "/Applications/freesurfer/7.3.2//python/scripts/segment_subregions", line 99, in <module> subregions.run_cross_sectional(args.structure, parameters) File "/Applications/freesurfer/7.3.2/python/packages/freesurfer/subregions/process.py", line 52, in run_cross_sectional model.align_atlas_to_seg() File "/Applications/freesurfer/7.3.2/python/packages/freesurfer/subregions/core.py", line 240, in align_atlas_to_seg mask = mask.resize(1, interp='nearest') TypeError: resize() got an unexpected keyword argument 'interp' Any suggestions to troubleshoot this problem? Kind regards Md. Mamun Al-Amin, PhD --------------------------- Postdoctoral Fellow Stark Neuroscience Research Institute Indiana University School of Medicine 320 W. 15th Street, NB Bldg Rm 103 Indianapolis, IN 46202 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline<https://secure-web.cisco.com/1V5L0UjKqtIUQvLo6ogKgtWb9BwsO4ECeh_yWdEE960ZTG…> .

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Recon-all issue with decompressing in mri_convert step
by Beatrice Everall 06 Sep '22

06 Sep '22

External Email - Use Caution - Hi there :) - I am trying to run recon-all on MRI data; I have multiple sequences including T1 maps and MAGiC. I have tried to run recon-all on these sequences but get the same error each time: - - ERROR: 512, see /tmp/tmp.H88WWu.dcmdjpeg.out for more details - - However when looking in that location I only see a H88WWu file, not H88WWu.dcmdjpeg.out. - I am using the Ubuntu 18.04 VM with the 7.2.0 release. - - Attached is the recon-all.log. - - Any suggestions would be very appreciated! - Thanks - Beatrice

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Group Analysis - glmfit results
by rstein03＠student.ubc.ca 06 Sep '22

06 Sep '22

External Email - Use Caution Hello Freesurfer Team, I recently ran analysis to compare change in cortical thickness between an Intervention and Control group longitudinally. The contrast is set up as INT-CON, and therefore I would interpret a positive change as the intervention having a greater increase in cortical thickness or less atrophy than the control group. The cluster that survived the Monte-Carlo simulation showed a positive difference in the LH superior parietal region when running both an ‘abs’ and ‘pos’ simulation (these showed the same cluster.summary outputs). There was not a significant cluster when running the ‘neg’ simulation. When I compared the mean change in thickness between groups (cache.th13.abs.y.ocn.dat file), it showed that the control group experienced less atrophy than the intervention despite having a positive cluster output. One possible solution I considered is accounting for baseline differences between groups when looking at mean change. Does glmfit control for baseline cortical thickness in the cluster analysis that is not accounted for in the mean change values from the cache.th13.abs.y.ocn.dat file? Is there another possible explanation for this discrepancy? Thank you in advance, Ryan S Ryan G. Stein MSc Student, Rehabilitation Sciences Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health University of British Columbia | Vancouver Campus | Musqueam Traditional Territory

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Question about reconall pipeline
by zhoudongyue＠mail.dlut.edu.cn 06 Sep '22

06 Sep '22

External Email - Use Caution Dear FreeSurfer experts: I updated Freesurfer 7.0.0 on my ubantu system, but there is something wrong so that I can't finish running recon-all pipieline. It stopped at mris_fill in auto-recon2.And I don't know why. It didn't happen when I use Freesurfer 6.0. What should I do to fix this problem? Bests, Dongyue

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TRACULA pathways to MNI space
by Woo-Suk Tae 06 Sep '22

06 Sep '22

External Email - Use Caution Dear Freesurfer experts I finished TRACULA's trac-all steps. Then I'd like to transform all DTI pathways to MNI space. Are there any commands in freesurfer or any external neuroimaging softwares. My scripts did not provided no transformation to MNI space. #bet /Users/anal/RH_nml/FS/01/mri/orig/001.nii.gz /Users/anal/RH_nml/FS/01/mri/orig/001_betted.nii.gz #flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in /Users/anal/RH_nml/FS/01/mri/orig/001_betted.nii.gz -omat /Users/anal/RH_nml/FS/01/mri/orig/affine_transf.mat fnirt --in=/Users/anal/RH_nml/FS/01/mri/orig/001.nii.gz --aff=/Users/anal/RH_nml/FS/01/mri/orig/affine_transf.mat --cout=/Users/anal/RH_nml/FS/01/mri/orig/nonlinear_transf --config=T1_2_MNI152_2mm applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_1mm --in=/Users/anal/RH_nml/FS/01/mri/orig/001.nii.gz --warp=/Users/anal/RH_nml/FS/01/mri/orig/nonlinear_transf --out=/Users/anal/RH_nml/FS/01/mri/orig/warped_001.nii.gz applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_1mm --in=/Users/anal/RH_nml/TRA/01/dpath/fmajor_PP_avg33_mni_bbr/path.pd.nii.gz --warp=/Users/anal/RH_nml/FS/01/mri/orig/nonlinear_transf --premat=func2struct.mat --out=/Users/anal/RH_nml/TRA/01/dpath/fmajor_PP_avg33_mni_bbr/warped_fmajor.nii.gz Sincerely Woo-Suk, Tae Seoul, Korea -- ---------------------------------------------------------------------------------------- Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Medical Research Center Anam Hospital, Korea University Medical Center, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6831 email: wstae(a)korea.ac.kr, woosuk.tae(a)gmail.com, wo <woostae(a)naver.com>ostae(a)gmail.com ----------------------------------------------------------------------------------------

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Using Schaefer Atlas with freesurfer - looking for updates
by Riccardo Iandolo 06 Sep '22

06 Sep '22

External Email - Use Caution Dear Freesurfer users, I'm looking for a follow-up to the following thread: https://secure-web.cisco.com/1CwBvdV81hlu3V-nr4FFAU9BtvPdQA7xOATLE9DZ90A1TR… It seems that some developments were going one at that time in order to make this additional feature. If not, are there any suggestions on how I can proceed? My goal is to evaluate thickness in the areas of the Shaefer atlas (e.g. 200 Parcels, 17 networks). I would like to use freesurer instead of other methods, because I've already run recon-all on my subjects I also found these two threads and I followed them: https://secure-web.cisco.com/18ThCQthzRDLUIFuFhE3YIwmFpsZmPh1YYNCGMJ2pk946Q… https://secure-web.cisco.com/1LlRbEwO6izBxoa40Ec6gp9DEucysGSq1sGJtDzjPgkGsQ… https://secure-web.cisco.com/1asVqnAkeW3NaKs3L475aFajf436YyeOdGEa_14PcTHgCR… However, these informations have not been very helpful because the .annot file (derived from gcs files) doesn't contain any surface information. Thank you in advance for any help. Best, Riccardo

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Re: [Freesurfer] samseg longitudinal processing - process killed
by Cerri, Stefano 05 Sep '22

05 Sep '22

Hi yvg, It is most likely a memory error problem. You will need to allocate more RAM to your calls. You probably need at least 32GB or RAM for such big images (might be even more). You can process the FLAIR images with mri_robust_template since they are slighly smaller than your T1 images. Stefano Dear Samseg developers, I have very high resolution T1 (512 x 512 x 240; voxel size: 0.469 x 0.469 x 1) and FLAIR images ( 384 x 384 x 128; voxel size: 0.495 x 0.495 x 1) and I would like to process them with the longitudinal processing of samseg but I have encountered different issues: 1.- mri_robust_template with T1 images: the process is killed after the following steps: Registration::findSaturation - computing centroids - computing initial transform -- using translation info - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 4 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 4 ) ./samseg_mutua.sh: line 20: 1511261 Killed mri_robust_template ... 2.- mri_robust_template with FLAIR images can be processed without errors, but when I execute run_samseg_long to the FLAIR images, the process is killed without further explanations after the following command: "Transforming points[0.49479165 0.49479164 0.49479165]". Could you please please help me? Best, yvg

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samseg longitudinal processing - process killed
by Yolanda Vives-Gilabert 05 Sep '22

05 Sep '22

External Email - Use Caution Dear Samseg developers, I have very high resolution T1 (512 x 512 x 240; voxel size: 0.469 x 0.469 x 1) and FLAIR images ( 384 x 384 x 128; voxel size: 0.495 x 0.495 x 1) and I would like to process them with the longitudinal processing of samseg but I have encountered different issues: 1.- mri_robust_template with T1 images: the process is killed after the following steps: Registration::findSaturation - computing centroids - computing initial transform -- using translation info - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 4 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 4 ) ./samseg_mutua.sh: line 20: 1511261 Killed mri_robust_template ... 2.- mri_robust_template with FLAIR images can be processed without errors, but when I execute run_samseg_long to the FLAIR images, the process is killed without further explanations after the following command: "Transforming points[0.49479165 0.49479164 0.49479165]". Could you please please help me? Best, yvg

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Re: [Freesurfer] Samseg dice is low
by Cerri, Stefano 04 Sep '22

04 Sep '22

Hi Dilek, 0.2 Dice seems extremely low. Also, in my experience, a threshold of 0.05 on T1w-FLAIR scans will show up many FP lesions. We usually reported a Dice in the range of 0.50-0.65 on various datasets (MS and WMH, default threshold, T1w-FLAIR), so I'm surprised by a such low value. Can you share with us your run_samseg command? Stefano Date: Sun, 4 Sep 2022 15:53:17 +0300 From: Dilek ?zkan <dozkan521(a)gmail.com> Subject: To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAPQSyvLqkvjk7JFxFoAG8RcX7ff40TS70vzvF6uWWHwC6CgqEg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello all, I use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I use the T1 and Flair for this. (just these are inputs) I registered *flair and t1 to DIR *for every patient. (My manual lesion masks are on DIR imaging.) I controlled the registrations, these are true. I created a binary lesion mask using *threshold 0.05. *(mri_binarize --i /data/projects/MS_MRI/posteriors/Lesions.mgz --o /data/projects/MS_MR/binarize/lesion_binary.mgz --min 0.05) I checked the dice score with ground truth values with python. *threshold *0.05= *dice* 0,2 of the dataset Do you have any recommendations to increase the dice? # cvs_version 7.2.0 # sysname Linux # machine x86_64 Best regards

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Freesurfer September 2022