Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

Help with FreeSurfer Tutorial FsFast Group Level
by Tchir, Sophia Mae 17 Jul '22

17 Jul '22

Hello, I've been trying to go through the FreeSurfer tutorials from the FreeSurfer wiki website (FsFastTutorialV6.0/FsFastGroupLevelPerm - Free Surfer Wiki (harvard.edu)<https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLev…>, but I've run into a roadblock with the FsFast Group Level tutorial. I have this version of FreeSurfer: /FreeSurfer/6.0.1-centos6_x86_64 and I'm trying to run it remotely through NoMachine on this system: My issue is with step 3.2: Correcting for Multiple Comparisons. [cid:8a8a9d8a-afaf-420d-8092-2525282e7e16] When I try to run "mri_glmfit-sim" I keep getting told that the included tag "--perm" is unrecognized. [cid:e82f076f-dc27-4767-90c9-8c4fc2603831] Running the help flag for "mri_glmfit" has not been helpful, as I do not see the flag in the information provided. Perm is mentioned here, but i'm not sure how to use this information. Do you have any recommendations for what to do? Is it an issue with my version of freesurfer? Thank you, Sophia Sophia Tchir Clinical Research Coordinator | MGH IASLab | Northeastern University

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Ubuntu 18.04.06 archive pass code
by Bevan Roberts 17 Jul '22

17 Jul '22

External Email - Use Caution Request for the pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z

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Expand Zip file
by David Bjanes 17 Jul '22

17 Jul '22

External Email - Use Caution Hi all, Trying to get open the *.zip file to install a Windows VM to run FreeSurfer. I need a passcode to extract the contents of the Ubuntu VM. Anyone know what that is? Thanks! David ****************************** David Bjånes, Ph.D. Neilsen Foundation Fellow Andersen Lab Caltech

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mri_robust_template - MyMatrix::RotationMean Error
by Andrew Beaudin 16 Jul '22

16 Jul '22

External Email - Use Caution Hello Freesurfer Experts, I am trying to use mri_robust_template (with its default 6 DOF registration) outside of the Freesurfer longitudinal pipeline to generate within-participant T1 templates from 2 time points. Unfortunately, I am coming up against a 'MyMatrix::RotationMean input(s) not rotation' error on images acquired on our GE 3T Discovery 750 system, but not our colleagues' Seimens 3T Prisma images. I have pasted the output from the --debug flag below (3rd row from bottom is the MyMatrix::RotationMean message). Briefly: - the images I am using are skull-stripped niftis. - I am running Freesurfer 6.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) on a WSL2 Ubuntu 18.04 installation. - the call is: mri_robust_template --mov 2001A_T1o_brain.nii.gz 2001B_T1o_brain.nii.mgz --lta 2001A2template.lta 2001B2template.lta --average 1 --template 2001_template.nii.gz --satit - I have tried the following with no success: 1) using the --iscale flag - same result as shown below. 2) using --inittp 0 - results in a 'Segmentation fault' 3) using --average 0 - same result as shown below 4) using Freesurfer v7.2 - same result as below 5) running mri_robust_template call on Catalina and Big Sur systems with FS v6.0 - same result as below. Currently, the only way to get mri_robust_template to work with our GE images is to run it with the --affine flag. I would prefer to use the rigid body registration but am at a loss for why these images are failing using the rigid body registration is failing. Any help/insights/recommendations are greatly appreciated. Thank you very much. Andrew ---- Andrew Beaudin, PhD | Postdoctoral Scholar University of Calgary | Cumming School of Medicine Department of Clinical Neurosciences HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1 Phone: (403) 210-6273 DEBUG REPORT: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ --mov: Using 2001A_T1o_brain.nii.gz as movable/source volume. --mov: Using 2001B_T1o_brain.nii.gz as movable/source volume. Total: 2 input volumes --lta: Will output LTA transforms --average: Using method 1 for template computation. --template: Using 2001_template.nii.gz as template output volume. --satit: Will estimate SAT iteratively! --debug: Will output debug info and files! reading source '2001A_T1o_brain.nii.gz'... converting source '2001A_T1o_brain.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '2001B_T1o_brain.nii.gz'... converting source '2001B_T1o_brain.nii.gz' to bspline ... MRItoBSpline degree 3 Will use TP 2 as random initial target (seed 108242 ). MultiRegistration::initializing Xforms (init 2 , maxres 0 , iterate 5 , epsit 0.01 ) : MultiRegistration Parameters Outdir: ./ TransOnly: false Rigid: true Robust: true Satit: true Iscale: false IscaleOnly: false NoMulti: false SubsampleSize: -1 HighIt: -1 FixVoxel: false KeepType: true Average: 1 DoublePrec: false BackupWeights: false SampleType: 5 CRASCenter: false Debug: 1 [init] ========================= TP 1 to TP 2 ============================== Register TP 1 ( 2001A_T1o_brain.nii.gz ) to TP 2 ( 2001B_T1o_brain.nii.gz ) Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE ) Type Source : 3 Type Target : 3 keeping type Mov: (1, 1, 1)mm and dim (176, 256, 256) Dst: (1, 1, 1)mm and dim (176, 256, 256) Asserting both images: 1mm isotropic - no Mov reslice necessary - no Dst reslice necessary 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: 3 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 3 ) - Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter: -- Iteration: 1 trying sat: 16 min sat: 16 ( 0.729941 ), max sat: 0 ( -1 ), sat diff: -16, (wlimit=0.16) -- Iteration: 2 trying sat: 32 min sat: 32 ( 0.713406 ), max sat: 0 ( -1 ), sat diff: -32, (wlimit=0.16) -- Iteration: 3 trying sat: 64 min sat: 64 ( 0.692689 ), max sat: 0 ( -1 ), sat diff: -64, (wlimit=0.16) -- Iteration: 4 trying sat: 128 min sat: 128 ( 0.666858 ), max sat: 0 ( -1 ), sat diff: -128, (wlimit=0.16) -- Iteration: 5 trying sat: 256 min sat: 256 ( 0.637119 ), max sat: 0 ( -1 ), sat diff: -256, (wlimit=0.16) -- Iteration: 6 trying sat: 512 min sat: 512 ( 0.591624 ), max sat: 0 ( -1 ), sat diff: -512, (wlimit=0.16) -- Iteration: 7 trying sat: 1024 min sat: 1024 ( 0.550606 ), max sat: 0 ( -1 ), sat diff: -1024, (wlimit=0.16) -- Iteration: 8 trying sat: 2048 min sat: 2048 ( 0.485668 ), max sat: 0 ( -1 ), sat diff: -2048, (wlimit=0.16) -- Iteration: 9 trying sat: 4096 min sat: 4096 ( 0.370434 ), max sat: 0 ( -1 ), sat diff: -4096, (wlimit=0.16) -- Iteration: 10 trying sat: 8192 min sat: 8192 ( 0.19981 ), max sat: 0 ( -1 ), sat diff: -8192, (wlimit=0.16) -- Iteration: 11 trying sat: 16384 min sat: 8192 ( 0.19981 ), max sat: 16384 ( 0.0606314 ), sat diff: 8192, (wlimit=0.16) -- Iteration: 12 trying sat: 12288 min sat: 8192 ( 0.19981 ), max sat: 12288 ( 0.103499 ), sat diff: 4096, (wlimit=0.16) -- Iteration: 13 trying sat: 10240 min sat: 8192 ( 0.19981 ), max sat: 10240 ( 0.142423 ), sat diff: 2048, (wlimit=0.16) -- Iteration: 14 trying sat: 9216 min sat: 9216 ( 0.16727 ), max sat: 10240 ( 0.142423 ), sat diff: 1024, (wlimit=0.16) -- Iteration: 15 trying sat: 9728 min sat: 9216 ( 0.16727 ), max sat: 9728 ( 0.155264 ), sat diff: 512, (wlimit=0.16) -- Iteration: 16 trying sat: 9472 min sat: 9472 ( 0.160488 ), max sat: 9728 ( 0.155264 ), sat diff: 256, (wlimit=0.16) -- Iteration: 17 trying sat: 9600 min sat: 9472 ( 0.160488 ), max sat: 9600 ( 0.157199 ), sat diff: 128, (wlimit=0.16) -- Iteration: 18 trying sat: 9536 min sat: 9472 ( 0.160488 ), max sat: 9536 ( 0.159131 ), sat diff: 64, (wlimit=0.16) -- Iteration: 19 trying sat: 9504 min sat: 9472 ( 0.160488 ), max sat: 9504 ( 0.159604 ), sat diff: 32, (wlimit=0.16) -- Iteration: 20 trying sat: 9488 min sat: 9472 ( 0.160488 ), max sat: 9488 ( 0.159903 ), sat diff: 16, (wlimit=0.16) -- Iteration: 21 trying sat: 9480 min sat: 9480 ( 0.160034 ), max sat: 9488 ( 0.159903 ), sat diff: 8, (wlimit=0.16) -- Iteration: 22 trying sat: 9484 min sat: 9484 ( 0.160123 ), max sat: 9488 ( 0.159903 ), sat diff: 4, (wlimit=0.16) -- Iteration: 23 trying sat: 9486 min sat: 9484 ( 0.160123 ), max sat: 9486 ( 0.159831 ), sat diff: 2, (wlimit=0.16) -- Iteration: 24 trying sat: 9485 min sat: 9484 ( 0.160123 ), max sat: 9485 ( 0.159908 ), sat diff: 1, (wlimit=0.16) -- Iteration: 25 trying sat: 9484.5 - final SAT: 9485 ( it: 25 , weight check 0.159908 <= 0.16 ) Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 ) - initial transform: Ti = [ ... 1.0000000000000 0 0 -2.0251428914711 0 1.0000000000000 0 6.0311902437196 0 0 1.0000000000000 2.8105113695639 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 3 S( 22 32 32 ) T( 22 32 32 ) Iteration(f): 1 -- diff. to prev. transform: 2.97694 Iteration(f): 2 -- diff. to prev. transform: 0.0903233 Iteration(f): 3 -- diff. to prev. transform: 0.0191757 Iteration(f): 4 -- diff. to prev. transform: 0.0116139 Iteration(f): 5 -- diff. to prev. transform: 0.00140989 <= 0.01 :-) Resolution: 2 S( 44 64 64 ) T( 44 64 64 ) Iteration(f): 1 -- diff. to prev. transform: 1.81202 Iteration(f): 2 -- diff. to prev. transform: 0.199033 Iteration(f): 3 -- diff. to prev. transform: 0.00925469 <= 0.01 :-) Resolution: 1 S( 88 128 128 ) T( 88 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 1.02247 Iteration(f): 2 -- diff. to prev. transform: 0.0229168 Iteration(f): 3 -- diff. to prev. transform: 0.000719712 <= 0.01 :-) Resolution: 0 S( 176 256 256 ) T( 176 256 256 ) Iteration(f): 1 -- diff. to prev. transform: 0.664624 Iteration(f): 2 -- diff. to prev. transform: 0.0108463 Iteration(f): 3 -- diff. to prev. transform: 0.000585613 <= 0.01 :-) - final transform: Tf = [ ... 0.9994709868827 -0.0113151175724 -0.0304912199489 4.8530791096303 0.0126622658755 0.9989355014916 0.0443568583483 2.1370162587100 0.0299568590234 -0.0447194809223 0.9985503265352 5.4716006804225 0 0 0 1.0000000000000 ] - final iscale: If = 1 CentroidT = [ 86.5860705940972 104.6067830299094 138.6676688710562 1.0000000000000 ] CentroidSinT = [ 88.1595712077722 107.7558909090270 139.3780739549505 1.0000000000000 ] Centroid = [ 87.3728209009347 106.1813369694682 139.0228714130033 1.0000000000000 ] MyMatrix::RotationMean input(s) not rotation meant = [ -1.2248131651588 1.2892456671960 3.1420193014715 ] Input rotation's max deviation from rotation is: 0.000393411 Andrew ---- Andrew Beaudin, PhD | Postdoctoral Scholar University of Calgary | Cumming School of Medicine Department of Clinical Neurosciences HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1 Phone: (403) 210-6273

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Freesurfer MC simulations with fsaverage5
by Zhukovsky, Peter 16 Jul '22

16 Jul '22

Dear Freesurfer team, I have a more general question about how best to approach multiple comparison correction for a large dataset where permutations are not viable and where fsaverage resolution is too high. I've fitted a GLM with mri_fitglm in the fsaverage5 space, which results in smaller files and quicker compute times. Next, I've attempted to create MC simulations for fsaverage5 (following https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo) but am running into errors from mri_mcsim: Segmentation Fault (core dumped) mri_mcsim works fine on subject bert, however. I am aware that others also had this problem with fsaverage5: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg70327.html Could you please advise on the best way to run MC correction with large-scale data (30k+ subjects)? Thank you for your help, Best wishes, Peter PS Please find the full mri_mcsim output here: mri_mcsim --o ./mult-comp-cor/fsaverage5/lh/cortex --base mc-z --surface fsaverage5 lh --nreps 5000 --fwhm 10 7.1.1 cwd /<path>/fsaverage5/surf cmdline mri_mcsim --o ./mult-comp-cor/fsaverage5/lh/cortex --base mc-z --surface fsaverage5 lh --nreps 5000 --fwhm 10 sysname Linux hostname dev01.camhres.ca machine x86_64 user pzhukovsky OutTop ./mult-comp-cor/fsaverage5/lh/cortex CSDBase mc-z nreps 5000 fwhmmax 30 subject fsaverage5 hemi lh surfname white FixVertexAreaFlag 1 UseAvgVtxArea 0 SaveFile ./mult-comp-cor/fsaverage5/lh/cortex/mri_mcsim.save StopFile ./mult-comp-cor/fsaverage5/lh/cortex/mri_mcsim.stop UFSS (null) Creating ./mult-comp-cor/fsaverage5/lh/cortex Loading /<path>/data/fsaverage5/surf/lh.white group_avg_surface_area 84969.3 group_avg_vtxarea_loaded 1 Loading label file cortex Loading /<path>/data/fsaverage5/label/lh.cortex.label Segmentation fault (core dumped)

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Re: [Freesurfer] recon-all finished without error but no results
by Boa Sorte Silva, Narlon 16 Jul '22

16 Jul '22

External Email - Use Caution Hi Zixuan, I would try keeping the input and output folders separate (i.e., use a different output folder). Also, usually we don’t need to specific the subject’s directory in the command line if it’s already set up in the environment. Nárlon Cássio From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Zixuan Lin <zlin14(a)outlook.com> Reply-To: Freesurfer support list <Freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, July 13, 2022 at 8:53 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] recon-all finished without error but no results [CAUTION: Non-UBC Email] External Email - Use Caution Hello! I am trying to run recon-all but it only converted the original image to .mgz and finished without error. I checked all other folders and it's empty. Attached please find the recon-all.log. The command line I used is recon-all -i hc01.nii -s hc01 -sd /home/zlin/Documents/MDD_CVR/control Could you please help me check what happens here? Thanks a lot, Zixuan.

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Image Edits
by Rachel Wagner 15 Jul '22

15 Jul '22

External Email - Use Caution Hello all! I hope you are all keeping well. I was wondering if there was a way to save images from freeview that are higher quality than png? In addition, is there a way to set the color bar scale from 0 to 1 and hopefully at 10 internals 0, 0.1, 0.2, 0.3...1? Even when selecting the ‘fixed axis’ option, it seems to automatically adjust. Thanks! Rachel Wagner

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Re: [Freesurfer] FSLOUTPUTTYPE=NIFTI_PAIR: Command not found
by fsbuild 15 Jul '22

15 Jul '22

External Email - Use Caution Hello Deanna, Something is executing the “export” command which is fine in bash or sh, but not in csh or tcsh (which needs “setenv”). export: Command not found.You could try manually running the scripts that get sourced with “tcsh -xf” to better see if they return that error, e.g., % tcsh -xf  $HOME/.afni/help/all_progs.COMP% tcsh -xf  ${FSLDIR}/etc/fslconf/fsl.csh You may want to temporarily rename your .cshrc or comment out the contents before running what’s in $HOME/.cshrc manually.  But if something gets run that does an export command, then it won’t matter what is currently set in your environment. - R. On Jul 15, 2022, at 12:48, Deanna Aghbashian <daghbashian07(a)gmail.com> wrote:        External Email - Use Caution        Hello FreeSurfer Developers, I have set up with terminal in tcsh, and it was working without error. However, when I logged on late last week I got an error in setting up environment for FreeSurfer on Mac OS Monterey Version 12.4 -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSLOUTPUTTYPE=NIFTI_PAIR: Command not found. export: Command not found.. FSL_DIR /usr/local/fsl [MacBook-Pro:~] deanna% nano ~/.cshrc Within my tcsh profile, I do not have anything to indicate to have FSLOUTPUTTYPE to be NIFTI_PAIR, nor do I have a line to export. I have also checked the SetUpFreeSurfer.csh, FreeSurferEnv.csh. I have tried clearing out my profile and recreating it, deleting and reinstalling FSL and FreeSurfer. When I use echo $FSLOUTPUTTYPE it comes back as NIFTI_GZ. My profile is below: # auto-inserted by @update..afni.binaries : setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace # set up tab completion for AFNI programs if ( -f $HOME/..afni/help/all_progs.COMP ) then    source $HOME/.afni/help/all_progs.COMP endif if ( $?DYLD_LIBRARY_PATH ) then   setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace else   setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace endif set path = ( $path $HOME/abin ) # include directories for FSL setenv FSLDIR /usr/local/fsl source ${FSLDIR}/etc/fslconf/fsl.csh setenv PATH ${FSLDIR}/bin:${PATH} setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh Does anyone have any suggestions? Thanks, Deanna _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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ATTACHMENT REMOVED--asegstats2table
by John Absher 15 Jul '22

15 Jul '22

Please be advised, This message contained one or more of the following prohibited file types: (.zip,.bat,.exe,.pif,.scr). The file(s) have been automatically removed from the message, in order to protect the privacy of our patients and employees, and to protect the integrity of our systems and data. As a security measure to prevent potential viruses and malware, Partners prohibits the receipt of attached files that have the potential to execute malicious code. You should contact the sender, and if you are sure that the original attached file(s) are safe, please use the Partners Secure File Transfer system, https://transfer.partners.org <https://transfer.partners.org> to work with the sender to securely transfer the removed attachment(s). If you do not have an account on the Partners Secure File Transfer System, please register for an account by using the following steps: 1. Go to https://transfer.partners.org <https://transfer.partners.org> 2. Click on "I don't have an account yet" 3. Enter your email address and click Register 4. You will receive an email with final instructions More information can be found at http://rc.partners.org/sFTP <http://rc.partners.org/sFTP> (Partners login required) If you have any questions or issues please enter a ticket in ServiceNow or call your Service Desk. **** Original message follows **** External Email - Use Caution Hi, We run freesurfer 6 on an HPC environment. We received this error when trying to run an asegstats2table script: [jabsher@node0130 results]$ ./asegstats2table_scr File "/zfs/hpcnirc/usr/bin/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax File "/zfs/hpcnirc/usr/bin/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax [jabsher@node0130 results]$ We are running this version: You are running this version of FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Here are the loaded modules: Currently Loaded Modules: 1) libxml2/2.9.10-gcc/8.3.1 2) openblas/0.3.10-gcc/8.3.1 3) matlab/2021b 4) anaconda3/5.1.0-gcc/8.3.1 5) openmpi/3.1.6-gcc/8.3.1-cuda10_2-ucx 6) cuda/10.2.89-gcc/8.4.1 The script is attached. We've gone to the wiki page (asegstats2table - Free Surfer Wiki (harvard.edu)<https://secure-web.cisco.com/1eU_J79ltbqe0p9Duk2YmurJuRaHFOpDSqizGlzIClXlSH…> and tried essentially all permutations, including specifying the aseg.stats files by name for each subject. The "use -subjects" error comes up every time, and we tried this as specified, with -subjects followed by all the directory/subject names, with a \ at the end of each line for readability. I know this must be something very straightforward, but hoping you can help. Thanks, Warm Regards, John R. Absher, MD, FAAN Associate Professor, University of South Carolina School of Medicine Greenville Department of Internal Medicine, Division of Neurology Clinical Assistant Professor, Clemson University School of Health Research (CUSHR) Graduate Faculty, Clemson University School of Public Health Sciences Prisma Health-Upstate 200 Patewood Drive, Suite 350B Greenville, SC 29615 John.Absher(a)prismahealth.org<mailto:John.Absher@prismahealth.org> or absher(a)mailbox.sc.edu<mailto:absher@mailbox.sc.edu> or jabsher(a)clemson.edu<mailto:jabsher@clemson.edu> 864-454-4500 (office) 864-350-6655 (mobile) 864-454-4505 (fax) [cid:image001.jpg@01D89871.8F9C2110] Inspire health. Serve with compassion. Be the difference. ---------------------------------------------------------------------- CONFIDENTIALITY NOTICE This message is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is strictly prohibited by law. If you have received this communication in error, please notify me immediately. A MIME attachment of type <application/octet-stream> was removed here by a drop-attachments-by-name filter rule on the host <esa8.hc4087-85.iphmx.com>.

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FSLOUTPUTTYPE=NIFTI_PAIR: Command not found
by Deanna Aghbashian 15 Jul '22

15 Jul '22

External Email - Use Caution Hello FreeSurfer Developers, I have set up with terminal in tcsh, and it was working without error. However, when I logged on late last week I got an error in setting up environment for FreeSurfer on Mac OS Monterey Version 12.4 -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSLOUTPUTTYPE=NIFTI_PAIR: Command not found. export: Command not found. FSL_DIR /usr/local/fsl [MacBook-Pro:~] deanna% nano ~/.cshrc Within my tcsh profile, I do not have anything to indicate to have FSLOUTPUTTYPE to be NIFTI_PAIR, nor do I have a line to export. I have also checked the SetUpFreeSurfer.csh, FreeSurferEnv.csh. I have tried clearing out my profile and recreating it, deleting and reinstalling FSL and FreeSurfer. When I use echo $FSLOUTPUTTYPE it comes back as NIFTI_GZ. My profile is below: # auto-inserted by @update.afni.binaries : setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace # set up tab completion for AFNI programs if ( -f $HOME/.afni/help/all_progs.COMP ) then source $HOME/.afni/help/all_progs.COMP endif if ( $?DYLD_LIBRARY_PATH ) then setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace else setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace endif set path = ( $path $HOME/abin ) # include directories for FSL setenv FSLDIR /usr/local/fsl source ${FSLDIR}/etc/fslconf/fsl.csh setenv PATH ${FSLDIR}/bin:${PATH} setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh Does anyone have any suggestions? Thanks, Deanna

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