Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

Fw: Freeview problem - can't see surfaces, hidden behind volumes
by Harriet Dempsey-Jones 20 Feb '22

20 Feb '22

External Email - Use Caution Hi there, I am having a weird problem with freeview… When l load some volumes and some surfaces together, I can’t see the surfaces because they are hidden ‘behind’ the volumes. They normally sit on top, but now I can only see them if I toggle off the volumes – which is not useful as I need both at once. They are definitely in alignment as I can see them when I toggle, and when I look at old data that I know I could view properly (and surfaces-volumes are in alignment) I have the same issue. I can't move them up, as you can only move position within volumes and surfaces. I tried to attach a video but my email got bounced for being too large - happy to send directly if it is helpful I am using the below code to load things (though have also manually loaded stuff in freeview). The code has not changed since it worked in the past… I have tried searching the freesurfer help, but can’t find anything on my issue… Any help would be appreciated Thanks! Harriet p.s., I am using freesurfer/ freeview on a remote machine of my university. They inform me no updates have been performed CODE freeview -v mri/T1.mgz \ mri/brainmask.mgz \ mri/wm.mgz:visible=0 \ -f surf/lh.smoothwm:edgecolor=yellow \ surf/lh.pial:edgecolor=red \ -viewport cor -layout 1

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Re: [Freesurfer] Linux Novice (VM_67 root vs. developer permissions)
by fsbuild 20 Feb '22

20 Feb '22

External Email - Use Caution Hello Randy, You can set SUBJECTS_DIR (via export command) to point a directory, e.g., where you have write permission.  You always have permission to write to your home directory, which in the VM is the path /home/developer.  The home directory path is saved in the shell environment variable $HOME. So you could make a writeable directory for subjects under developer’s home directory.  (Below, pwd command = print working directory path). $ echo $SUBEJCTS_DIR/usr/local/freesurfer/7.2.0/subjects$ cd $HOME$ pwd/home/developer$ mkdir subjects_new$ cd subjects_new$ pwd/home/developer/subjects_new$ export SUBJECTS_DIR=$HOME/subjects_new$ echo $SUBJECTS_DIR/home/developer/subjects_new It should work to drag and drop a file *from* Windows Explorer *into* the VM using the Linux file browser GUI in developer’s home directory (or where you have write permission).  That is the example on page 19 of the VBox_load_image.pdf doc found under https://secure-web.cisco.com/12je3qk7PjFfZ8id7gOdQ3NmuWY5iAVuERB… The example is dragging in the single license file (assuming you downloaded it on the Windows side). You can also run a browser directly in the linux VM (uses the Windows host network connection) and download files directly into the VM from any web location, e.g., the license file.  There should be a Firefox browser icon to double click on in the upper left hand corner of the VM window under “Activities”.  Firefox downloads files into /home/developer/Downloads which you can navigate to via “cd” in the LInux terminal or you can go there via the Linux file browser GUI.   If you have some cloud storage, e.g., which comes with a free Google account, then another option besides dragging in files or creating a mount point in the VM from the Windows side - is to use the cloud storage to swap (upload/download) files between the VM and any other computer using the web browsers. - R. On Feb 20, 2022, at 11:21, daedalus39(a)aol.com wrote:        External Email - Use Caution        Dear Freesurfers,I am a Linux novice.  Syntax is my major weakness.  On the other hand, I have been working with Windows for over 30 years.I was able to get the VM_67 up and running.  I had some prior experience using VM for a brief time in 2014 (ver5.3) so I wasn't starting completely from scratch. I figured out how to share with my host (Win 10) and have one of my own test images in my sf-shared folder (I also copied it to the Desktop).I can navigate to /usr/local/... /subjects and I made a directory in "/subjects/" (realized I needed "sudo mkdir, but then I was successful).  However, after having done that, it occurred to me that that wasn't the right thing to do anyway.When I tried using the folder GUIs to drag/drop/copy the image into the test folder (old Windows habit), it simply rejected the action.  I'm assuming this is a permissions issue (everything in FS is "root" and everything in the VM is "developer'), but I am very spooked about using some type of chmod statement here.  If that's the only way to resolve this, would you be able to share some guidance and sample syntax to allow me to import the test image using the GUI?  Thanks in advance for any help you can provide.  This may also help others who need to do the same if I/we can resolve this (i.e., search archives). -Randy_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Linux Novice (VM_67 root vs. developer permissions)
by daedalus39＠aol.com 20 Feb '22

20 Feb '22

External Email - Use Caution Dear Freesurfers, I am a Linux novice. Syntax is my major weakness. On the other hand, I have been working with Windows for over 30 years. I was able to get the VM_67 up and running. I had some prior experience using VM for a brief time in 2014 (ver5.3) so I wasn't starting completely from scratch. I figured out how to share with my host (Win 10) and have one of my own test images in my sf-shared folder (I also copied it to the Desktop). I can navigate to /usr/local/... /subjects and I made a directory in "/subjects/" (realized I needed "sudo mkdir, but then I was successful). However, after having done that, it occurred to me that that wasn't the right thing to do anyway. When I tried using the folder GUIs to drag/drop/copy the image into the test folder (old Windows habit), it simply rejected the action. I'm assuming this is a permissions issue (everything in FS is "root" and everything in the VM is "developer'), but I am very spooked about using some type of chmod statement here. If that's the only way to resolve this, would you be able to share some guidance and sample syntax to allow me to import the test image using the GUI? Thanks in advance for any help you can provide. This may also help others who need to do the same if I/we can resolve this (i.e., search archives). -Randy

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sulc surface error: unit mismatch between FreeSurfer 5.3.0 and 6.0.1
by Guerreiro Fernandes-3, F.D. (Francisco David) 20 Feb '22

20 Feb '22

External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to correlate the sulcal depth information present in the ?h.sulc files with activation in particular brain regions during an overt language task in an fMRI paradigm. For this matter, a dataset was gathered throughout the years with several subjects and the cortical reconstruction process (as described in: https://secure-web.cisco.com/1nqW39ubw2AyrvIfDDZNWB66KB47XSeO6tS5QZO8RBYGIE…) was performed at the time of data acquisition. However, for subjects where recon-all was run in different FreeSurfer versions (5.3.0 or 6.0.1), I get an order of magnitude difference in the sulc values in the ?h.sulc volumes. I've searched the list and the official FreeSurfer Release Notes (https://secure-web.cisco.com/1vUPpLJpZFWtBAPAZsBnTOCfqihx6dgklkyFygBvPMdyx7…) and found no information of a change of magnitude in sulc values. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer versions: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 & freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a 2) Platform: Linux blue 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt11-1+deb8u3 (2015-08-04) x86_64 GNU/Linux Kind Regards, Francisco D. Guerreiro Fernandes [Description: Universitair Medisch Centrum Utrecht] Francisco David Guerreiro Fernandes, PhD Candidate | BCI Group | UMC Utrecht Brain Center Dept. Neurology & Neurosurgery | University Medical Center Utrecht Room STR 4.119 | Heidelberglaan 100 | 3584CX Utrecht | The Netherlands Email: F.GuerreiroFernandes-3(a)umcutrecht.nl<mailto:F.GuerreiroFernandes-3@umcutrecht.nl> | Tel: +31 88 75 50080 De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Running recon-all in parallel error: cannot find sub-101_ses-BL_T1w.nii
by Yuan, Ye 19 Feb '22

19 Feb '22

External Email - Use Caution Dear FreeSurfer Developers, I hope this email finds you well. I'm an MRes student from Imperial College London. I'm attempting to run recon-all in parallel, as described in the FreeSurfer tutorial of Andy's brain book: https://secure-web.cisco.com/1f8N_u253wnYss7NsLFujqzigTyBNU3U_hugHrybuTHK9C… The appropriate way would be: ls .. | grep sub- > subjList.txt # here I deleted the special character of subject number manually, the right format would be `sub-101` for sub in `cat subjList.txt`; do cp ../${sub}/ses-BL/anat/*.gz . done gunzip *.gz SUBJECTS_DIR=`pwd` ls *.nii | parallel --jobs 8 recon-all -s {.} -i {} -all -qcache # the last step However, when running the last step, I've got the following error: ERROR: cannot find sub-101_ses-BL_T1w.nii Linux nhp-System-Product-Name 4.15.0-142-generic #146~16.04.1-Ubuntu SMP Tue Apr 13 09:27:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-101_ses-BL_T1w exited with ERRORS at 2022 02 18 Friday 10:49:24 CST For more details, see the log file To report a problem, see http://secure-web.cisco.com/1TEXQ5EYB9LOX23P4f0QsCWsgDayARXAUE94TZk30GfILIE… In addition, I have attached the dataset that has been processed except for the last step in my last email, the recon-all.log weren't generated in this case. Does anyone have any thoughts on how to trouble-shoot this issue? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: CentOS release 6.7 (Final) 3) uname -a: Linux nhp-System-Product-Name 4.15.0-142-generic #146~16.04.1-Ubuntu SMP Tue Apr 13 09:27:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: were not generated Many thanks in advance! Best regards, Ye

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Re: [Freesurfer] FreeSurfer Issue
by fsbuild 17 Feb '22

17 Feb '22

External Email - Use Caution Hello Anna, You could try the bash shell commands below … freeview should open an empty window. Those commands are documented for the bash shell and also csh/tcsh shells on the help page, https://secure-web.cisco.com/1HXGi2MgGyKrnZsUEDporX-UQ3IrQRAR1UaZSL_m2PtlLk… - R. % bash The default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.cisco.com/1Tcz7fGutzZau6blDkstZVkR5nPiyXBdbX07yX4PuhMcNr… you@Host-Mac:~> export FREESURFER_HOME=/Applications/freesurfer/7.2.0 you@Host-Mac:~> source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.2.0FSFAST_HOME       /Applications/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.2.0/subjectsMNI_DIR           /Applications/freesurfer/7.2.0/mni you@Host-Mac:~> freeview On Feb 17, 2022, at 18:44, Pusok, Anna <anna.pusok(a)yale.edu> wrote:        External Email - Use Caution        Hi,Sorry but this did not fix the issues- could I ask you to help with Freesurfer? I tried to get it work many times, with no success and what you recommended also did not work.Thank you.From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Tim Schäfer <ts+ml@rcmd.org>Sent: Thursday, February 17, 2022 2:10 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] FreeSurfer Issue         External Email - Use Caution        Dear Anna,You should use 'setenv' (for tcsh and related shells) or 'export' (for BASH) when defining environment variables, as listed here:    MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-… setenv FREESURFER_HOME /Applications/freesurfer/7.2.0You should also source (instead of executing) the SetUpFreeSurfer.csh script:    source $FREESURFER_HOME/SetUpFreeSurfer.cshBest,Tim> On 02/17/2022 5:32 PM Pusok, Anna <anna.pusok(a)yale.edu> wrote:> >  > External Email - Use Caution        > > Hi there,> I hope this email finds you well!> I ran into some issues when I tried to use freesurfer. This is the error message I get in my terminal. Could you help me with this issue? If we could set up a Zoom meeting to discuss the issue, that would be helpful as well!> Thank you,> Anna> _______________________________________________> Freesurfer mailing list> Freesurfer(a)nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-…. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, Germany_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
by Edan Daniel 17 Feb '22

17 Feb '22

External Email - Use Caution We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1): recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point) The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on? Would love to hear your thoughts about this. Many thanks!! Edan, Braindevlab@Princeton

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FreeSurfer Issue
by Pusok, Anna 17 Feb '22

17 Feb '22

External Email - Use Caution Hi there, I hope this email finds you well! I ran into some issues when I tried to use freesurfer. This is the error message I get in my terminal. Could you help me with this issue? If we could set up a Zoom meeting to discuss the issue, that would be helpful as well! Thank you, Anna

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mris_preproc error: no source hemi specified
by Koustav Chatterjee 17 Feb '22

17 Feb '22

External Email - Use Caution Dear FreeSurfer experts, I need your help. I am trying to run mris_preproc --fsgd in order to see the effect of cortical volume on velocity, accounting for the effects of eTIV in the analysis. My .fsgd file looks like GroupDescriptorFile 1 Title Vel_vol.glmdir MeasurementName volume Class Main Variables Velocity Totalintracranialvolume Input pt001 Main 57 1233150.571288 Input pt002 Main 44 1441659.580634 Input pt003 Main 60 1534770.256493 Input pt004 Main 55 1374671.330735 Input pt005 Main 29 1252775.397585 Input pt007 Main 42 1466033.251447 Input pt011 Main 82 1565625.985727 Input pt015 Main 30 1255088.0327 Input pt016.nii Main 79 1604469.84187 Input pt018.nii Main 45 1410265.173839 Input pt023 Main 70 1376261.088728 Input pt025 Main 49 1317185.172994 Input pt026 Main 45 1484779.378359 Input pt031 Main 53 1269043.642534 and .mtx file looks like 1 0 I am getting* e**rror: no source hemi specified.* Thanks, KC

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Reconstruct the white and pial from a single brain slice
by 陆玉恒 17 Feb '22

17 Feb '22

External Email - Use Caution Dear, I tried to reconstruct the white and pial surface from a sinlge brain slice (not MRI, it's a histology slice that converted to a nifti file) but failed when using the mris_make_surface. The white matter and grey matter were segmented by in-house tool. I generated the aseg.mgz, filled.mgz, wm.nii.gz from those segmentation masks and ran the "tessellate" "white" steps in "recon" but it reported error when making the ?h.white.I don't know why. I wonder if I could get the pial surface in this way, or you could tell me how to do so. I would appreciate it. Yuheng

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