Freesurfer April 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
170 discussions

Hippocampal Subfield Segmentation Error
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 14 Apr '20

14 Apr '20

External Email - Use Caution Dear Freesurfer experts, I am having a problem with hippocampal subfield segmentation. The issue appears to be related to JavaVM - after I run the code: recon-all -s (subject ID) -hippocampal-subfields-T1 This is the error: JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. Fatal Error on startup: Unable to start the JVM because of a bad Java option or unknown error. Please check your java.opts file. Any suggestions? Thank you, Alex

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Re: [Freesurfer] Overlap of vertices in downsampled data
by Ersin Ersözlü 14 Apr '20

14 Apr '20

External Email - Use Caution We calculated p-value/tstat overlays using FSL PALM comparing the cortical thickness of different groups. We aim for a measure of similarity in cortical thickness between some of the groups. Our idea was to use dice overlap between groups to test similarity in atrophy patterns. We tried to use ‚mri_compute_overlap‘ to obtain these measures but when we used the p-value overlays we found that mrs_compute_overlap returned us the dice overlap for cortical regions and also white matter and unknown labeled regions what is not expected in a cortical thickness stats map I guess. So we doubt that is the correct way to use these overlays. Do you have any idea how to calculate the dice overlap of statistical overlays (vertex wise)? Thanks, Ersin Ersözlü <freesurfer-request(a)nmr.mgh.harvard.edu> adresine sahip kullanıcı 9 Nis 2020 Per, 18:01 tarihinde şunu yazdı: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Error in Tracula-all -prep (Yendiki, Anastasia) > 2. Re: Tracula: tract length meaning (Yendiki, Anastasia) > 3. Re: Hippocampal Subfield Segmentation Error > (Lab of Autism and Developmental Neuroscience, Lab of Autism and > Developmental Neuroscience) > 4. Re: mri_convert input files (Douglas N. Greve) > 5. Re: mri_glmfit-sim FWHM error (Douglas N. Greve) > 6. Re: Aseg file issue (Douglas N. Greve) > 7. Overlap of vertices in downsampled data (Ersin Ers?zl?) > 8. Re: Overlap of vertices in downsampled data (Douglas N. Greve) > 9. Re: Fwd: Is it possible to load flatmaps in freeview and draw > ROI's on them? (Ruopeng Wang) > 10. Re: Aseg file issue > (Lab of Autism and Developmental Neuroscience, Lab of Autism and > Developmental Neuroscience) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 9 Apr 2020 02:34:53 +0000 > From: "Yendiki, Anastasia" <AYENDIKI(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Error in Tracula-all -prep > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > MN2PR04MB575785A35596BD0BB37BF85A8AC10(a)MN2PR04MB5757.namprd04.prod.outlook.com > > > > Content-Type: text/plain; charset="us-ascii" > > Hi Salah - It looks like it didn't find your subject's freesurfer recon > when it was doing the pre-processing, so it skipped some steps that you > need to go beyond that point. Based on your SUBJECTS_DIR and your subject > name, it looked for this file: > /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/mri/brain.mgz > > Any chance this was missing or unreadable? > > a.y > ________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu < > freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Salah Showiheen < > sshowiheen(a)gmail.com> > Sent: Monday, April 6, 2020 11:49 PM > To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] Error in Tracula-all -prep > > > External Email - Use Caution > > Hi Freesurfer community, > > I have an issue that I spent ages trying to figure out and this error has > been asked about back in (17/12/2016) and the title is ([Freesurfer] > Tracula trac -all preprocessing error. > > my error is: > > ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni > > There is an issue that the mini folder is empty. > > Attached is the log file and the configuration file (tracula_conf.txt) > > > > Regards, > Salah >

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Can I rename subject id safely?
by Xiaojiang Yang 14 Apr '20

14 Apr '20

External Email - Use Caution Dear FS developers, I have done some recon-all computing for a group of subjects, subject1, subject2, . , subjectn, and the results are in the $SUBJECTS_DIR directory: $SUBJECTS_DIR |_ subject1 |_ subject2 .. |_ subjectn Now I decide to change the format of the subject IDs. Can I just rename the sub-directories subject1, subject2, . subject to other names, without worrying about any inconsistencies? Thank you! Xiaojiang

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Re: [Freesurfer] PETSurfer / Questions
by Ferraro, Pilar 14 Apr '20

14 Apr '20

External Email - Use Caution Dear Freesurfer experts, We are conducting a PETSurfer analysis, and have some questions on the best way to proceed. Briefly, this is what we have done: After running the standard Freesurfer analysis an all the T1 images, we have generated the segmentation for the GTM. Afterwards, we have registered the PET images with the anatomicals, obtaining the template.reg.lta. To check the preliminary results without any PVC, we have used the template.reg.lta to sample the PET volume onto the surface, with the following command: mri_vol2surf --mov subject_PET.nii \ --reg subject_template.reg.lta \ --projfrac 0.5 --interp nearest \ --hemi lh --o lh.sig.mgh We therefore obtained the lh.sig.mgh First question. Is this procedure correct? Second question. Is the format of the of the output (.mgh) correct? In the wiki it is reported that: “If you are not using PVC, you can use the template.reg.lta to sample the PET volume onto the surface using mri_vol2surf, then apply standard surface-based analysis”. Third question. At this point should we directly run the mri_glmfit with the previously obtained lh.sig.mgh? Like in this way: mri_glmfit \ --y lh.sig.mgh \ --fsgd fsgd file dods\ --C cor.mtx file \ --surf fsaverage lh \ --cortex \ --glmdir glmdir Many thanks for any information you’ll be able to provide, Best, Pilar Maria Ferraro Il giorno 7 apr 2020, alle ore 6:00 PM, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> ha scritto: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. vertex number to MNI coordinates (Marina Fern?ndez) 2. Install Freesurfer on Ubuntu (Stephan) 3. Re: vertex number to MNI coordinates (Douglas N. Greve) 4. Re: Install Freesurfer on Ubuntu (Peer Herholz) 5. Re: Install Freesurfer on Ubuntu (fsbuild) 6. Permutation with Non-Orthogonal Matrices (Hua, Jessica) 7. Re: Permutation with Non-Orthogonal Matrices (Douglas N. Greve) 8. Error in Tracula-all -prep (Salah Showiheen) 9. hippocampus subfield segmentation using Siemen and GE scans (Kate Marvel) 10. Chorid-plexus in Freesurfer reconall (Lijun An) 11. Re: Chorid-plexus in Freesurfer reconall (Bruce Fischl) 12. whether freesurfer version 7 still support GPU (Frank Robert) 13. Re: hippocampus subfield segmentation using Siemen and GE scans (Iglesias Gonzalez, Juan E.) 14. Re: whether freesurfer version 7 still support GPU (Hoopes, Andrew) 15. Re: hippocampus subfield segmentation using Siemen and GE scans (Kate Marvel) 16. Re: whether freesurfer version 7 still support GPU (Frank Robert) 17. Re: whether freesurfer version 7 still support GPU (Hoopes, Andrew) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Apr 2020 22:06:24 +0200 From: Marina Fern?ndez <marina.fdez.alvarez(a)gmail.com> Subject: [Freesurfer] vertex number to MNI coordinates To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAALjZmd_9caMAE8uHbn_vu4o_4Lkc8mWyXTatSUr4AAQpznq0w(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear Freesurfer experts, I hope you can help me with the following questions: 1. What is the best way to know the MNI coordinates to which a vertex of a surface corresponds? 2. I have projected the surfaces of the subjects onto the average subject from this dataset. Can I know the MNI coordinates corresponding to a vertex of the average subject of my dataset? Or do I need to project it onto the fsaverage to know the correspondence to de MNI space? 3. I know that the average surface is constructed by computing the MNI305 coordinate at each vertex, But how can I obtain the MNI152 coordinates (instead of MNI305) to which a vertex corresponds? (if it is possible). Thank you very much in advance. Best regards, Marina -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200406/4… ------------------------------ Message: 2 Date: Mon, 6 Apr 2020 22:50:15 +0200 From: Stephan <stephan.wunderlich22(a)gmail.com> Subject: [Freesurfer] Install Freesurfer on Ubuntu To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAJzKAwch6QOUHhd1sSe+exK4EiU-gw-6uos=URxbgO-tm_Kixw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi, ist there an official guideline how to install Freesurfer on Ubuntu? Best, Stephan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200406/1… ------------------------------ Message: 3 Date: Mon, 6 Apr 2020 16:51:09 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] vertex number to MNI coordinates To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <fb5fba0f-6aa5-a21b-fac9-5e4f54b282d4(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" answers below, but overall, take a look at https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 4/6/2020 4:06 PM, Marina Fern?ndez wrote: ????????External Email - Use Caution Dear Freesurfer experts, I hope you can help me with the following questions: 1. What is the best way to know the MNI coordinates to which a vertex of a surface corresponds? I think freeview will display the mni305 coords 2. I have projected the surfaces of the subjects onto the average subject from this dataset. Can I know the MNI coordinates corresponding to a vertex of the average subject of my dataset? Or do I need to project it onto the fsaverage to know the correspondence to de MNI space? An average subject is always in mni305 3. I know that the average surface is constructed by computing the MNI305 coordinate at each vertex, But how can I obtain the MNI152 coordinates (instead of MNI305) to which a vertex corresponds? (if it is possible). See case 8 in website above Thank you very much in advance. Best regards, Marina _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200406/8… ------------------------------ Message: 4 Date: Mon, 6 Apr 2020 17:17:09 -0400 From: Peer Herholz <herholz.peer(a)gmail.com> Subject: Re: [Freesurfer] Install Freesurfer on Ubuntu To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <D6B4D694-5DE6-414F-B723-6B8AB66A7C8E(a)gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi Stephan, please have a look at the "FreeSurfer Download and Install? page within the FreeSurfer documentation: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall <https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall> HTH, cheers, Peer On Apr 6, 2020, at 4:50 PM, Stephan <stephan.wunderlich22(a)gmail.com> wrote: External Email - Use Caution Hi, ist there an official guideline how to install Freesurfer on Ubuntu? Best, Stephan _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200406/5… ------------------------------ Message: 5 Date: Mon, 06 Apr 2020 23:25:11 +0200 From: fsbuild <fsbuild(a)contbay.com> Subject: Re: [Freesurfer] Install Freesurfer on Ubuntu To: freesurfer(a)nmr.mgh.harvard.edu Cc: stephan.wunderlich22(a)gmail.com Message-ID: <1586208311.5e8b9e3757315(a)trashmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Stephan, There is some information here about packages to install in order to run freesurfer - see highlighted "apt-get install" commands. https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements I think you will also need to install these packages, libjpeg62_6b2-3_amd64.deb https://drive.google.com/file/d/1Zdd-C3EQEEww180OzxEk1WV0h9obZYkD/view?usp=… libpng12-0_1.2.54-1ubuntu1_amd64.deb https://drive.google.com/file/d/1OWQSWL8a3Y8f1Weiauj9Lr2d3mtvZOm5/view?usp=… We also have an Ubuntu VM you can download.  While you may prefer to run on your own Ubuntu machine, it could also serve as a reference for you to see what we installed on Ubuntu 18.04 (including those extra packages). https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 - R. On Apr 6, 2020, at 16:50, Stephan <stephan.wunderlich22(a)gmail.com> wrote:        External Email - Use Caution        Hi,ist there an official guideline how to install Freesurfer on Ubuntu?Best,Stephan_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200406/c… ------------------------------ Message: 6 Date: Mon, 6 Apr 2020 22:45:44 +0000 From: "Hua, Jessica" <jphc55(a)mail.missouri.edu> Subject: [Freesurfer] Permutation with Non-Orthogonal Matrices To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BY5PR01MB565249DA0CF1967FD1ACF16E93C20(a)BY5PR01MB5652.prod.exchangelabs.com> Content-Type: text/plain; charset="iso-8859-1" External Email - Use Caution Hi FreeSurfer Experts, As recommended I ran the following command: mri_glmfit-sim --glmdir rh.volume.AgeSex.10.glmdir --perm 1000 3.0 abs --perm-resid --cwp 0.05 --2spaces And I got the following error message: ERROR: Flag --perm-resid unrecognized. Best, Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200406/f… ------------------------------ Message: 7 Date: Mon, 6 Apr 2020 22:59:09 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Permutation with Non-Orthogonal Matrices To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <9f714ae7-979c-ff50-7514-5f7a7212de59(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" did you download the patch as described here ("If You're Not at an Organized Course")? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.… On 4/6/2020 6:45 PM, Hua, Jessica wrote: ????????External Email - Use Caution Hi FreeSurfer Experts, As recommended I ran the following command: mri_glmfit-sim --glmdir rh.volume.AgeSex.10.glmdir --perm 1000 3.0 abs --perm-resid --cwp 0.05 --2spaces And I got the following error message: ERROR: Flag --perm-resid unrecognized. Best, Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate?Clinical Psychology University of Missouri _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200406/8… ------------------------------ Message: 8 Date: Tue, 7 Apr 2020 13:49:43 +1000 From: Salah Showiheen <sshowiheen(a)gmail.com> Subject: [Freesurfer] Error in Tracula-all -prep To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAFc5Rtf0kovaRpurYSsexxyeCiS8qa=tGdSYX=GMbMxy8s4YxA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi Freesurfer community, I have an issue that I spent ages trying to figure out and this error has been asked about back in (17/12/2016) and the title is ([Freesurfer] Tracula trac -all preprocessing error. my error is: ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni There is an issue that the mini folder is empty. Attached is the log file and the configuration file (tracula_conf.txt) Regards, Salah -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200407/2… -------------- next part -------------- # FreeSurfer SUBJECTS_DIR # I added this command: export SUBJECTS_DIR=/Volumes/HD/Post_HARDI/PAH_Clinical_110/07 # to allow setting the environment to this: setenv SUBJECTS_DIR /Volumes/../.. # To run the tracula: trac-all -prep -c /Volumes/G_RAID/Backup_Salah/Post_HARDI/PAH_Clinical_110/tracula_conf.txt # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /Volumes/HD/Post_HARDI/PAH_Clinical_110/07 # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07 # Subject IDs # set subjlist = C07 # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then the gradient table and b-value table must be specified (see below) # set dcmroot = /Volumes/HD/Post_HARDI/PAH_Clinical_110 set dcmlist = 07/C_64_b3000/0001.dcm # Diffusion gradient tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # The tables must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # set bveclist = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/DTI/bvecs_C07.txt # Diffusion gradient table (if using the same one for all scans) # Must be specified if it cannot be read from the DICOM headers # The table must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # set bvecfile = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/DTI/bvecs_C07.txt # Diffusion b-value tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # set bvallist = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/DTI/bvals_C07.txt # Diffusion b-value table (if using the same one for all scans) # Must be specified if it cannot be read from the DICOM headers # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # set bvalfile = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/DTI/bvals_C07.txt # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = 07/C_64_b3000/0001.dcm # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = 07/C_64_b3000/0001.dcm # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # # set echospacing = 0.7 # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.5 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # set mnitemp = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/mni_template.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # # set cvstemp = donald # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: $FREESURFER_HOME/subjects # # set cvstempdir = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07 # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # set pathlist = ( lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist # Default: 7 for the forceps major, 6 for the corticospinal tract, # 4 for the angular bundle, and 5 for all other paths # set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # # set trainfile = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07 # Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # set nburnin = 200 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 7500 # set nsample = 7500 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 # Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a single curve. This is a sign that the # initial guess for the pathway was problematic, perhaps due to poor alignment # between the individual and the atlas. Setting the reinit parameter to 1 and # rerunning "trac-all -prior" and "trac-all -path", only for the specific # subjects and pathways that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # set reinit = 0 -------------- next part -------------- A non-text attachment was scrubbed... Name: trac-all.log Type: application/octet-stream Size: 142834 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200407/2… ------------------------------ Message: 9 Date: Tue, 7 Apr 2020 05:25:32 -0500 From: Kate Marvel <kmarvel54(a)gmail.com> Subject: [Freesurfer] hippocampus subfield segmentation using Siemen and GE scans To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAG9yhu7psfpBdomKPF2Xtu5E+SvGsWKBA20Dy40f7ZrMcawFwA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi Freesurfer Community, I have run Hippocampus subfield segmentation using scans from GE and Siemens. The field of view (FOV) for GE and Siemens are different, with FOV of 8 and 9 respectively. Will this affect the analysis since they have different FOV? Thanks, Kate -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200407/2… ------------------------------ Message: 10 Date: Tue, 7 Apr 2020 19:04:37 +0800 From: Lijun An <lijun.an(a)hotmail.com> Subject: [Freesurfer] Chorid-plexus in Freesurfer reconall To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CWLP123MB2180B25276FBC0E5467F0D349AC30(a)CWLP123MB2180.GBRP123.PROD.OUTLOOK.COM> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear Freesurfer experts, I have a little question about the structure 'chorid-plexus', I am not very deep in brain anatomy and function. Could anyone have a sense of what is the normal range of this structure volume from Freesurfer reconall? I found that mean of 'chorid-plexus' in ADNI is around 1500 mm^3, when I ran reconall for my local subejcts (a local dataset), I found the mean of 'chorid-plexus' is around 800 mm^3. Could anyone give an explanation or a paper I could refer to for this 'chorid-plexus' structure? Thanks so much! Best Regards, An Lijun -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200407/9… ------------------------------ Message: 11 Date: Tue, 7 Apr 2020 09:59:49 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Chorid-plexus in Freesurfer reconall To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.21.2004070957190.13248(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi An Lijun The choroid is a plexus of ependymal cells that produce CSF. it is pretty tough to segment and mostly we include it to get more accurate segmenations of the hippocampus where it is adjacent to ventricle and the ventricles themselves. I'm not sure I've ever seen any normative stats on it though. You can read more here: https://en.wikipedia.org/wiki/Choroid_plexus cheers Bruce On Tue, 7 Apr 2020, Lijun An wrote: ????????External Email - Use Caution???????? Dear Freesurfer experts,? I have a little question about the structure 'chorid-plexus', I am not very deep in brain anatomy and function. Could anyone have a sense of what is the normal range of this structure volume from Freesurfer reconall? I found that mean of 'chorid-plexus' in ADNI is around 1500 mm^3, when I ran reconall for my local subejcts (a local dataset), I found the mean of 'chorid-plexus' is around 800 mm^3. Could anyone give an explanation or a paper I could refer to for this 'chorid-plexus' structure? Thanks? so much!? ? Best Regards,An Lijun ------------------------------ Message: 12 Date: Tue, 7 Apr 2020 09:13:33 -0500 From: Frank Robert <frabob2015(a)gmail.com> Subject: [Freesurfer] whether freesurfer version 7 still support GPU To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Cc: frabob2015(a)gmail.com Message-ID: <CANfWN_Y-J8uQ+UaqODBVOHLWpNHGGr0hTUKMSSiv-Cw+7HoQEg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Freesurfer team I checked the freesurfer version 7.0. It says that " but for now you should know that some features are not present in v7 (QDEC, GPU-capability, and recon-all -make)." https://surfer.nmr.mgh.harvard.edu/fswiki/dev7beta1 But from the hardware setup, it still needs Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers. This makes me confused. Since version 7 does not support GPU anymore, why does it still need the Graphic card? I found GPU may be helpful for some abnormal brain such as large ventricles. It may speed the calculation time. I do not know my observation is correct or not. Thanks Frank -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200407/3… ------------------------------ Message: 13 Date: Tue, 7 Apr 2020 14:48:05 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Subject: Re: [Freesurfer] hippocampus subfield segmentation using Siemen and GE scans To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <EA967479-5618-4412-9A99-4158F261E2F2(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" It should be fine but please make sure you correct by scanner in subsequent analyses. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Kate Marvel <kmarvel54(a)gmail.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, April 7, 2020 at 06:26 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] hippocampus subfield segmentation using Siemen and GE scans External Email - Use Caution Hi Freesurfer Community, I have run Hippocampus subfield segmentation using scans from GE and Siemens. The field of view (FOV) for GE and Siemens are different, with FOV of 8 and 9 respectively. Will this affect the analysis since they have different FOV? Thanks, Kate -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200407/8… ------------------------------ Message: 14 Date: Tue, 7 Apr 2020 15:06:28 +0000 From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> Subject: Re: [Freesurfer] whether freesurfer version 7 still support GPU To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Cc: "frabob2015(a)gmail.com" <frabob2015(a)gmail.com> Message-ID: <737D7BF9-02F7-4498-B9E0-1F37577B7DF6(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Frank, We still recommend this since freeview benefits from having a fast GPU. best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Frank Robert <frabob2015(a)gmail.com> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, April 7, 2020 at 10:15 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Cc: "frabob2015(a)gmail.com" <frabob2015(a)gmail.com> Subject: [Freesurfer] whether freesurfer version 7 still support GPU External Email - Use Caution Hello Freesurfer team I checked the freesurfer version 7.0. It says that " but for now you should know that some features are not present in v7 (QDEC, GPU-capability, and recon-all -make)." https://surfer.nmr.mgh.harvard.edu/fswiki/dev7beta1 But from the hardware setup, it still needs Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers. This makes me confused. Since version 7 does not support GPU anymore, why does it still need the Graphic card? I found GPU may be helpful for some abnormal brain such as large ventricles. It may speed the calculation time. I do not know my observation is correct or not. Thanks Frank -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200407/f… ------------------------------ Message: 15 Date: Tue, 7 Apr 2020 10:12:06 -0500 From: Kate Marvel <kmarvel54(a)gmail.com> Subject: Re: [Freesurfer] hippocampus subfield segmentation using Siemen and GE scans To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAG9yhu6g6F_wdBgZ+cGJ=pVUTym9A2iAj=3-RPg=swVfaC859g(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Thank you so much Iglesias. kate On Tue, Apr 7, 2020, 9:48 AM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote: It should be fine but please make sure you correct by scanner in subsequent analyses. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Kate Marvel <kmarvel54(a)gmail.com> *Reply-To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> *Date: *Tuesday, April 7, 2020 at 06:26 *To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> *Subject: *[Freesurfer] hippocampus subfield segmentation using Siemen and GE scans * External Email - Use Caution * Hi Freesurfer Community, I have run Hippocampus subfield segmentation using scans from GE and Siemens. The field of view (FOV) for GE and Siemens are different, with FOV of 8 and 9 respectively. Will this affect the analysis since they have different FOV? Thanks, Kate _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200407/f… ------------------------------ Message: 16 Date: Tue, 7 Apr 2020 10:23:42 -0500 From: Frank Robert <frabob2015(a)gmail.com> Subject: Re: [Freesurfer] whether freesurfer version 7 still support GPU To: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> Cc: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CANfWN_YPoEBKDNK6evpr9HWvMj5b_xagWDDEbn1dO_HLEiJT0w(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Dr. Hoopes Does it mean that in Beta version 7, there is no GPU capability. But stable version 7 still support the existing GPU capacity.. Is it correct? BR Frank On Tue, Apr 7, 2020 at 10:06 AM Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu> wrote: Hi Frank, We still recommend this since freeview benefits from having a fast GPU. best Andrew *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Frank Robert <frabob2015(a)gmail.com> *Reply-To: *FS Help <freesurfer(a)nmr.mgh.harvard.edu> *Date: *Tuesday, April 7, 2020 at 10:15 AM *To: *FS Help <freesurfer(a)nmr.mgh.harvard.edu> *Cc: *"frabob2015(a)gmail.com" <frabob2015(a)gmail.com> *Subject: *[Freesurfer] whether freesurfer version 7 still support GPU * External Email - Use Caution * Hello Freesurfer team I checked the freesurfer version 7.0. It says that " but for now you should know that some features are not present in v7 (QDEC, GPU-capability, and recon-all -make)." https://surfer.nmr.mgh.harvard.edu/fswiki/dev7beta1 But from the hardware setup, it still needs Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers. This makes me confused. Since version 7 does not support GPU anymore, why does it still need the Graphic card? I found GPU may be helpful for some abnormal brain such as large ventricles. It may speed the calculation time. I do not know my observation is correct or not. Thanks Frank 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200407/9… ------------------------------ Message: 17 Date: Tue, 7 Apr 2020 15:27:40 +0000 From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> Subject: Re: [Freesurfer] whether freesurfer version 7 still support GPU To: Frank Robert <frabob2015(a)gmail.com> Cc: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <FBF997D9-29E3-4698-AD28-FA72846B81D0(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" It means CUDA-accelerated binaries/recons on the GPU are no longer supported after freesurfer 6.0. I will make that clarification in the wiki page. Sorry for the confusion. Andrew From: Frank Robert <frabob2015(a)gmail.com> Date: Tuesday, April 7, 2020 at 11:24 AM To: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> Cc: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] whether freesurfer version 7 still support GPU External Email - Use Caution Hello Dr. Hoopes Does it mean that in Beta version 7, there is no GPU capability. But stable version 7 still support the existing GPU capacity.. Is it correct? BR Frank On Tue, Apr 7, 2020 at 10:06 AM Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu<mailto:AHOOPES@mgh.harvard.edu>> wrote: Hi Frank, We still recommend this since freeview benefits from having a fast GPU. best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Frank Robert <frabob2015(a)gmail.com<mailto:frabob2015@gmail.com>> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday, April 7, 2020 at 10:15 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Cc: "frabob2015(a)gmail.com<mailto:frabob2015@gmail.com>" <frabob2015(a)gmail.com<mailto:frabob2015@gmail.com>> Subject: [Freesurfer] whether freesurfer version 7 still support GPU External Email - Use Caution Hello Freesurfer team I checked the freesurfer version 7.0. It says that " but for now you should know that some features are not present in v7 (QDEC, GPU-capability, and recon-all -make)." https://surfer.nmr.mgh.harvard.edu/fswiki/dev7beta1 But from the hardware setup, it still needs Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers. This makes me confused. Since version 7 does not support GPU anymore, why does it still need the Graphic card? I found GPU may be helpful for some abnormal brain such as large ventricles. It may speed the calculation time. I do not know my observation is correct or not. Thanks Frank 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200407/8… ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 194, Issue 8 ******************************************

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Re: [Freesurfer] Overlap of vertices in downsampled data
by Ersin Ersözlü 14 Apr '20

14 Apr '20

External Email - Use Caution Hi Douglas, I was wondering if I could explain our problem clearly. thanks again, Ersin

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Re: [Freesurfer] Trac-All Error
by Hua, Jessica 13 Apr '20

13 Apr '20

External Email - Use Caution Hi Dr. Yendiki, I wasn't sure if I could attach files to the FreeSurfer, so I have also emailed your work email. Attached is my full configuration file as well as my error log. Best, Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Queries on the Function of Freesurfer
by Koustav Chatterjee 13 Apr '20

13 Apr '20

External Email - Use Caution Dear all, I am a beginner in FreeSurfer world. I have 4 questions. It would be kind enough if you could clarify my confusions. - I have came across that 'Freesurfer can reconstruct 2D cortical surface from 3D T1 MRI brain image'. However, I know that T1 2D brain images are being fed to freesurfer for 'Recon-all...-all' to function all its pre-processing steps. Whether ".......reconstruct 2D cortical surface from 3D T1 MRI image" this *statement is true*? Is there any step where FreeSurfer make a 3D image from 2D T1 images and again reconstruct them into 2D cortical surface through preprocessing steps? - Can FreeSurfer only recognize 'T1 weighted images' for processing? Why only T1, why not T2 or Flair etc? - Can we estimate the volume of substantia nigra, pedunculopontine nucleus and locus cereleus using FreeSurfer? If so any specific version of Freesurfer is required? - If I have Freesurfer installed in my PC; I also have T1 and diffusion weighted image sequence of a subject. Can I use 'Tracula' to analyse tracts of that subject's brain directly? How could I analyse tracts in Freesurfer? Thank you for your time and effort. Regards, Koustav

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Optimized T1 and T2 sequences at Martinos for Freesurfer 6 Reconstructions
by Chinappen, Dhinakaran Maheswaran 13 Apr '20

13 Apr '20

Dear Freesurfer Experts, We would like to confirm the best T1 and T2 sequences at Martinos for Freesurfer 6 reconstruction. There is a document on the FS Wiki (https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&…) and we just want to make sure it is the correct one for future scans at Martinos. Thank you for your help, Dhina -- Dhinakaran M. Chinappen, Incoming PhD Candidate, M.Eng, MBA Clinical Research Coordinator, Chu Lab: http://chulab.mgh.harvard.edu/ Neurology Department, Massachusetts General Hospital e: dchinappen(a)mgh.harvard.edu m: 1-267-257-1224

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training set
by javier quilis 13 Apr '20

13 Apr '20

External Email - Use Caution Hello everyone, I'm trying to do a study of a comparison between the automated methods to analyze structural MRI from FSL and Freesurfer. I am interested in the training set used by Freesurfer to do the brain segmentation and I can not find a detailed description of it. Is there any source where this set is described? Thanks in advance. Bests, Javier Quilis

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Trac-all Error
by Hua, Jessica 13 Apr '20

13 Apr '20

External Email - Use Caution Hi FreeSurfer, I am running trac-all prepocessing using a configuration file. I tried preprocessing a couple of participants, and I keep getting this error: #------------------------------------- #@# Tensor fit Sat Apr 11 21:29:36 PDT 2020 dtifit -k /Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/dwi.nii.gz -m /Volumes/HuaExternal/DTI_FS/S11018a_LGI/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/bvecs -b /Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/bvals -o /Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/dtifit libc++abi.dylib: terminating with uncaught exception of type std::logic_error: Mat::operator(): index out of bounds Abort This is my configuration file: set dtroot = /Volumes/HuaExternal/DTI_FS set subjlist = ( S11018a_LGI ) set dcmroot = /Volumes/HuaExternal/DTI set dcmlist = ( S11018a.nii ) set bvecfile = /Volumes/HuaExternal/DTI/bvecsSPACE.txt set bvalfile = /Volumes/HuaExternal/DTI/bvals.txt set runlist = (1) set doeddy = 1 set dorotbvecs = 1 set usemaskanat = 1 set thrbet = 0.3 set doregflt = 0 set doregbbr = 1 set doregmni = 1 set doregcvs = 0 set mnitemp = /Volumes/HuaExternal/DTI/MNI152_T1_1mm_brain.nii.gz set pathlist = ( lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) Do you know what is going wrong, and how I would fix this issue? Best, Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Freesurfer April 2020