Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

defining input images in a for-loop in recon-all
by Darko Komnenić 29 Mar '18

29 Mar '18

Dear experts, I would like to run a for-loop in FreeSurfer 5.1. so that I can have multiple subjects analyzed over the holiday, without having to come to the lab and start each of them myself. I searched the previous emails in this list and know that I can make a file with a subject list, and then have the loop go through that file. I was wondering, however, how to handle the -i part of recon-all command? Each subject in a loop needs to have one brain image assigned - I don't think FreeSurfer will know where to look for images just by telling it what the subject name is. Thanks in advance for any help!

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Brain volumetry: vessels
by Patrik Krumpolec 28 Mar '18

28 Mar '18

Good morning! I want to ask what type of brain vessels include structure "vessel" (left and right) in result stats file from brain volumetry measurement by freesurfer: artery, vein or booth? Thank You very much! patrik krumpolec

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Information on FS-FAST
by Piero Chiacchiaretta 28 Mar '18

28 Mar '18

Hi list, 601-628 labels in FreeSurferColorLUT or labels obtained by Buckner’s parcellation could be used in FS-Fast to assess the FC of each subfield? The labels should be spatially registrated in a specific space before to procede with FS-FAST? Thanks in advance, Piero Piero Chiacchiaretta, PhD Institute for Advanced Biomedical Technologies - ITAB - University “G. d’Annunzio” of Chieti - Pescara Department of Neuroscience, Imaging and Clinical Sciences Via dei Vestini, 31 66013 Chieti, Italy tel: 39-0871-3556919 fax: 39-0871-3556930 e-mail: p.chiacchiaretta(a)unich.it

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convert labels to volume in MNI?
by gj 27 Mar '18

27 Mar '18

Hi, Newbie question....I want to take FreeSurfer labels (from an atlas in fsaverage space) and convert it into a volumetric NIFTI mask. I ran the following command, but I must be missing something because the output is not in the right space (far too posterior): $FREESURFER_HOME/bin/mri_label2vol \ --label $ll \ --temp $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \ --reg $FREESURFER_HOME/average/mni152.register.dat \ --fillthresh .5 \ --o $wd/${ll}.nii Am I perhaps supposed to first create the volumetric file without mapping into MNI space and then use tkregister2? Thanks in advance for any help or advice! Gina

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Problem with mri_glmfit
by Naiara Aguirre Vidal 27 Mar '18

27 Mar '18

Dear FreeSurfer experts, I have a problem with mri_glmfit. I am using the following script: mri_glmfit \ --y lh.AspergerStudy.thickness.10.mgh \ --fsgd FSGD/AspergerStudy.fsgd dods \ --C Contrasts/AS-HC.mtx \ --C Contrasts/HC-AS.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.thickness.AspergerStudy.10.glmdir But when I run it, I obtain an error: acad1215inv:01_freesurfer_processing acad1215inv$ mri_glmfit \ > --y lh.AspergerStudy.thickness.10.mgh \ > --fsgd FSGD/AspergerStudy.fsgd dods \ > --C Contrasts/AS-HC.mtx \ gdfRead(): reading FSGD/AspergerStudy.fsgd INFO: gd2mtx_method is dods ERROR: must specify GLM output dir acad1215inv:01_freesurfer_processing acad1215inv$ --C Contrasts/HC-AS.mtx \ > --surface fsaverage lh \ > --cortex \ > --glmdir lh.thickness.AspergerStudy.10.glmdir -bash: --C: command not found What could I do for solving this problem? Thanks a lot Naiara -- *Naiara Aguirre Vidal* Neuropsychology and Functional Neuroimaging group Department of Basic and Clinical Psychology and Psychobiology Jaume I University Edificio de Investigación II, Avda. Sos Baynat, s/n E-12071 Castellón de la Plana (Spain)

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tkmedit: no tools window
by gj 27 Mar '18

27 Mar '18

Hi, When I launch tkmedit, I only get the "Display" window with no "Tools" window so I don't have any menus (I wanted to overlay a label file -- not sure how I do that from the command line either). I don't see any errors in the terminal from where I launch tkmedit ------------------------------------------------------------- $ tkmedit -f $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \ -overlay $wd/MPM_rh.FG1.label.nii \ -overlay-reg $FREESURFER_HOME/average/mni152.register.dat \ -fthresh .5 -fmid 1 & [3] 21284 $ tkmedit: Trying to open TOOLBOXES/vcAtlas/NII/MPM_rh.FG1.label.dat Reading /common/apps/freesurfer-6.0.0_x86_64/tktools/tkm_common.tcl Reading /common/apps/freesurfer-6.0.0_x86_64/tktools/tkm_wrappers.tcl Reading /common/apps/freesurfer-6.0.0_x86_64/lib/tcl/fsgdfPlot.tcl Reading /common/apps/freesurfer-6.0.0_x86_64/tktools/tkUtils.tcl ------------------------------------------------------------- Thanks in advance for any help! Gina

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Re: [Freesurfer] Problem running mri_convert
by Hoopes, Andrew 26 Mar '18

26 Mar '18

Hi Jay, as a temporary fix for 6.0, I would suggest disabling SIP and rerunning: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection… best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Jay Edelman <jedelman(a)ccny.cuny.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, March 22, 2018 at 10:02 PM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Problem running mri_convert Dear Freesurfers, I am running the program "mri_convert" within the AFNI script, @SUMA_Make_Spec_FS, and am receiving the error below. I just installed freesurfer from your website and am running this on a Mac running Yosemite. I've looked at the online forums and see this addressed in other contexts, but unfortunately I can't find any fix. Thanks So Much! Jay Edelman Dept. of Biology, The City College of New York mri_convert.bin -ot nii mri/wm.seg.mgz /Users/jedelman/Dropbox/freesurfer/asim/./SUMA/wm.seg.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/wm.seg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /Users/jedelman/Dropbox/freesurfer/asim/./SUMA/wm.seg.nii... -- running 'mris_convert lh.smoothwm lh.smoothwm.asc' Trace/BPT trap dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib

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Error saving a tiff file using tksurfer with NoMachine
by Evans, Jennifer (NIH/NIMH) [F] 26 Mar '18

26 Mar '18

Hi, I’m getting an error when trying to save a tiff file using tksurfer using NoMachine v5.0.47. I’m running the ENIGMA QA pipeline which has a call similar to: tkfsurfer bert lh inflated. Then, trying to save the tiff either from the GUI or using their script doesn’t work and causes the error: pixel read error/resource temporarily unavailable. Is there a way to get this to work? Thanks, Jen

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Tessellation of hippocampus
by pooja prabhu 26 Mar '18

26 Mar '18

Hi list, I was segmented the hippocampus using "recon-all -all -s -hippocampal-subfields-T1" using Freesurfer. Now i want to tessellate the segmented volume. I tried using "mri_tessellate"(Freesurfer) it is not working?? How can i tessellate the hippocampus alone? Please help me Thank You -- Thank You Pooja Prabhu

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lGI values below 1
by Kai Ohmstedt 24 Mar '18

24 Mar '18

Dear all, I am conducting an analysis using the lGI to quantify cortical folding. As advised in the tutorial I checked all reconstructed subjects for errors in reconstruction and lGI-computation. To do I used the pial_lgi-file as an overlay in tksurfer and set the minimal threshold to 1. Using those settings no gray areas showed on the cortex, so I assumed all values had been computed correctly and no values below 1 are present. After the analysis I wanted to create scatter plots for the maximum vertices of the clusters that were found. When I displayed the scatter plots in tksurfer, lGI values below 1 were present in many of my subjects. This only seems to be a problem in vertices that are close to the corpus callosum, vertices that are further away show values well above 1 for all subjects. Have any of you already encountered this problem? If so, do you know if the values are in any way reliable? Could this be caused by the split of the hemispheres during the reconstruction process? Thank you for your help! Best regards, Kai Ohmstedt

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