Freesurfer May 2023

freesurfer@nmr.mgh.harvard.edu

75 participants
109 discussions

Dimension mismatch MRIS PREPROC
by Akansha Mahesh Naraindas 20 Jun '23

20 Jun '23

External Email - Use Caution Hi I am attempting to create a group file using MRIS PREPROC My command is as follows mris_preproc --fsgd brainmorph.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi rh --out mripreproc-rh-thickness.mgh But I am receiving the error ERROR: dimension mismatch between *first two subjects* Would you be able to advise the cause of this error as I am unsure what is causing it Thanks!

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Tksurfer tmp.tcl
by Robert Terziev 20 Jun '23

20 Jun '23

External Email - Use Caution Hello, I am trying to run an old script from the ENIGMA webpage, that was based on freesurfer 5.1 and uses tksurfer. Here is a code excerpt: tksurfer $sub lh pial -tcl tmp.tcl echo "labl_import_annotation \"aparc.annot\"" > tmp.tcl echo "scale_brain 1.35" >> tmp.tcl echo "redraw" >> tmp.tcl echo "save_tiff "$QCdir/$sub/"rh.lat.hr.tif" >> tmp.tcl I have found that I could try to use tksurferfv instead, but then I get the error message “Option 'tcl' not recognized. Run 'freeview -h' for more information.” Running 'freeview -h', I don’t find a solution. Is there a workaround for that problem? Thank you very much in advance. Kind regards Robert Freesurfer Version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b Plattform: macOS Ventura v13.3.1

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[FreeSurfer] Process terminated when talairach was running
by Krystal Xiwing Yau 14 Jun '23

14 Jun '23

External Email - Use Caution Dear FreeSurfer expoerts, I am running recon-all for the subject on a HPC. It exited with error when talairach was running - it indicated "MINC_BIN_DIR: Undefined variable". The log file is attached to this email. I tried to look up the directory, which contains MINC_BIN_DIR as indicated on the <https://secure-web.cisco.com/1Yi_rx3_ryx7Z_5U9Ro-U7Ztjy451lAhdmjzkMKbcgnaOr…> forum <https://secure-web.cisco.com/1Yi_rx3_ryx7Z_5U9Ro-U7Ztjy451lAhdmjzkMKbcgnaOr…> . When I type the command, there was none: echo $MINC_BIN_DIR Any advise would be highly appreciated. Lots of thanks. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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Generate Stats File for fornix.mgz in T1 weighted MRI ?
by Ahsan Ali 12 Jun '23

12 Jun '23

External Email - Use Caution Dear Sir/Madam, I'm having a ADNI T1 weighted MRI database. I have run the recon-all command successfully and got a couple of default stats files in the stats folder. Then fornix.mgz is estimated using command "mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto_CCseg.mgz -f folder_name" successfully. Now what can be done to generate the stats for fornix.mgz? I've been struggling with this for a long time, please help me with this. I'm using ubuntu. [image: IMG-20230526-WA0000.jpg] With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics and Biomedical Engineering (AMBE) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552

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Cortical thickness of elephant brain
by Malav Shah 09 Jun '23

09 Jun '23

External Email - Use Caution Dear freeSurfer team, I am trying to extract cortical thickness in a postmortem elephant (structural) MRI scan. I initiated the process with the segmentation of white (wm) and pial matter, using MATLAB image processing tools. Having satisfied white and pial matter labels, I "tesselated" these volumes to generate pial and wm surfaces. Then, with 'mris_smooth' command, I smoothed these surfaces. When attempted to estimate cortical thickness between these surfaces (lh.pial.smth5 and lh.wm.smth5), I get the following error. command: mris_place_surface --thickness lh.pial.smth5 lh.wm.smth5 20 5 lh.thickness error: No such file or directory error: ERROR: MRISreadVertexPositions(/Volumes/experiment/share/Malav/Ele_ana_cortexMRI/pipelines/dumba_piece/lh.wm.smth5): surfaces differ. Main: 177753 verts 365096 faces, lh.wm.smth5: 145095 verts 298436 faces Surfaces may be out-of-date I understand there is a mismatch in the number of nodes of these surfaces. How can I rectify this issue to get to the thickness? Thanks and regards, malav Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391

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different results for gtmpvc with different tracers
by Federica Di Antonio 09 Jun '23

09 Jun '23

External Email - Use Caution Dear experts, I hope this email finds you well. I run the pvc correction with mri_gtmpvc for subjects data obtained with two different PET tracers. In gtm.stats.dat, for every subject and every region, the number of voxels evaluated for amyloid tracer is approximately twice the volume evaluated for the second tracer. I'd expect that the volume of a region for the same subject doesn't change with the tracer. Do you think this error can result from previous errors in the analysis? Or is it in some way plausible? Thank you for your patience, Federica

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Re: [Freesurfer] Problem installing FreeSurfer
by fsbuild 01 Jun '23

01 Jun '23

External Email - Use Caution Please make sure you have downloaded a freesurfer license.txt file by filling out the form at,https://secure-web.cisco.com/1jgHYKP0gy8_587mR2rxpzl3o6QwcsGjVygS8rScUOs… Place the license.txt file you will receive in your home directory, e.g.,  $ cd $HOME$ head -1 license.txt<email you used to register> Set the FS_LICENSE environment variable manually (and/or in your shell initialization file, e.g., .bashrc) to point to the license file,… here set from a terminal window running bash shell ... $ export FS_LICENSE=$HOME/license.txt Setup the freesurfer environment, $ export FREESURFER_HOME=/Applications/freesurfer/7.4.0$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.4.0-20230504-55dcf98 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.4.0 FSFAST_HOME       /Applications/freesurfer/7.4.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.4.0/subjects MNI_DIR           /Applications/freesurfer/7.4.0/mni $ which freeview/Applications/freesurfer/7.4.0/bin/freeview Then try running freeview with no arguments to see if it brings up an empty window, $ freeview If that works, quit freeview and try running it again with an example volume included in the distribution, $ freeview  $SUBJECTS_DIR/bert/mri/brain.mgz If that works, quit freeview and try your own surface/volume files. - R. On May 31, 2023, at 17:05, Michelangelo Fabbrizzi <michefabb(a)gmail.com> wrote:        External Email - Use Caution        Dear Sirs,I am new to Freesurfer. I installed as shown on website and added the license.txt, however when I open freeview I get an error "/Applications/freesurfer/7.4.0/bin/freeview: riga 2:  2047 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“”Attached the report.Freesurfer version: freesurfer-darwin-macOS-7.4.0-20230510-e558e6ePlatform: MacOS12.6.6Mac: Macbook Pro Intel Core i5 dual-coreXQuartz2..8.15XQuartz2.8.5Can you help me please?Thanks!Michelangelo<report.txt>

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Problem installing FreeSurfer
by Michelangelo Fabbrizzi 31 May '23

31 May '23

External Email - Use Caution Dear Sirs, I am new to Freesurfer. I installed as shown on website and added the license.txt, however when I open freeview I get an error "/Applications/freesurfer/7.4.0/bin/freeview: riga 2: 2047 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“” Attached the report. Freesurfer version: freesurfer-darwin-macOS-7.4.0-20230510-e558e6e Platform: MacOS12.6.6 Mac: Macbook Pro Intel Core i5 dual-core XQuartz2.8.15 XQuartz2.8.5 Can you help me please? Thanks! Michelangelo

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Re: [Freesurfer] source freesurfer error
by fsbuild 31 May '23

31 May '23

External Email - Use Caution Try using $ instead of # to tell the linux shell to expand an environment variable, e.g., here to the path of where freesurfer was installed.   echo $FREESURFER_HOME<output will be path to where installed>   source $FREESURFER_HOME/SetUpFreeSurfer.sh - R. On May 29, 2023, at 07:52, Pedro henrique barradas <phbarradas(a)hotmail.com> wrote:        External Email - Use Caution        Hi everyone!I am trying to run freesurfer on a windows machine using ubuntu but I am having trouble with the source commandWhen I try to source freesurfer i get the following message:source #FREESURFERHOME/SetUpFreeSurfer.sh-bash: source: filename argument requiredsource: usage: source filename [arguments]Thank you very much_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Smoothing with surf2surf
by Akansha Mahesh Naraindas 30 May '23

30 May '23

External Email - Use Caution Hi I have been attempting to perform just the smoothing step on a series of subjects using surf2surf and I seem to be getting an error when attempting to this. My command is as follows mri_surf2surf --hemi lh \ --s fsaverage \ --sval combat_lh-1004.thickness.fwhm0.fsaverage.mgh \ --fwhm 10 \ --cortex \ --tval combatlh.thickness.fwhm10.fsaverage.mgh I get this error ERROR: Option --sval unknown Based on other posts on the mailing list I tried specifying the src and trg subjects but still receive the following error: mri_surf2surf --hemi lh \ --srcsubject fsaverage \ --srcsurfval combat_lh-1004.thickness.fwhm0.fsaverage.mgh \ --fwhm 10 \ --trgsurfval combatlh.thickness.fwhm10.fsaverage.mgh ERROR: Option --srcsubject unknown I was wondering if you might be able to help resolve this issue Thank you very much!

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Freesurfer May 2023