Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Shortening recon-all process time and longitudinal process
by Yoonho Hwang 08 Sep '22

08 Sep '22

External Email - Use Caution Dear Bruce Fischl, Hi, I'm Yoonho. In the previous post, "Re:[Freesurfer] Inquiry about process time by use "recon-all" (Fri, 12 Jan 2018 12:29:19-0800)", I found that the process time for recon-all depend on both how abnormal the anatomy is and how high the CNR of your scan is. 1. *Does "how abnormal the anatomy" mean that there is an anatomical abnormality due to a disease based on MR image and "how high the CNR of your scan is" mean that there is a CNR, [x_mean (gray matter) - y_mean (white matter)] / standard deviation_air (background)?* 2. *Related to process time for recon-all based on the FS ver.7.2.0, is open-mp effect stronger than acquisition parameter optimization effect? Which one is more helpful in reducing the process time?* In the longitudinal analysis for freesurfer, 1. *Is it possible to use longitudinal analysis of MR images obtained from equipment with different magnetic field strengths (1.5T vs 3T) in time series for the same subjects?* Looking forward to your feedback. Thank you very much. Sincerely, Yoonho

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ERROR! FOV=288.000 > 256
by Ellie Shaw 07 Sep '22

07 Sep '22

External Email - Use Caution Hi there, I am attempting to perform the recon-all command for my T1 nii file. When I run the recon-all command I get the following error message: ERROR! FOV=288.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. I am seeking some support to overcome this issue - I understand this would include the flag -cw256. Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b Platform: OSX 7.2.0 Recon-all.log file attached below Thank you in advance! Kind regards, Ellie

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mri_glmfit error: MatrixResidualForming(): X is not invertable
by Piot, Alex 07 Sep '22

07 Sep '22

External Email - Use Caution Hello Freesurfer experts, I am trying to perform a GLM, using the volume of a brain region as a covariate. I am doing a two-group, one covariate design. I originally tried to use QDEC to facilitate the process and received an error message that the mri_glmfit command had failed. I then saw that QDEC was deprecated and followed the instructions set out on the freesurfer wiki for doing it manually (https://secure-web.cisco.com/1W0gEAYXZeH6XMYzikihrf4Ct-vcV_3e-WmTr1eqTVlVGW…) I received the same error message as I had with QDEC on the command line: ERROR: MatrixResidualForming(): X is not invertable RD is not invertable n = 1 This only occurs for certain of the brain regions used as covariates; for others, the QDEC and command-line streams work perfectly. Additionally, I've noticed that if I input different numbers for the covariate values in the fsgd file, the command runs smoothly. I haven't been able to find a similar error on the mailing list, does anyone have an idea of how to work around this? I would greatly appreciate it. Please find attached my fsgd file, and the full log of what happens after I run the mri_glmfit command (when it works and when it doesn't) The hands.fsgd file doesn't work, whereas the hands_works.fsgd file does. Freesurfer version: 7.2.0, Ubuntu 20.04, Windows WSL Best wishes, Alex -- Alexandre Piot, MSc. Queen Square Institute of Neurology President of the Application of Psychedelics Society <https://secure-web.cisco.com/1txv4iCOx4-mObxXkQBwlHnKAPMdNbmkUOMySvRIxTq9ls…> -- UCL UNITy Project<https://secure-web.cisco.com/11-VCBFrldtskQk64mTlGciM29YjbhiPBFq0qJNEn4t16f…>

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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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