Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30066 discussions

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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Hippocampal Subfields Module, output error
by Hurtado, Aura Maria 23 Mar '18

23 Mar '18

Hi, I am attempting to use the longitudinal pipeline of the "hippocampal subfields and nuclei of amygdala”, but keep getting a flawed output. My dataset consists of images from a longitudinal study with some dropouts. First, I ran the reconall longitudinal pipeline in fs60 for all subjects. I got no errors. Then, I tried 1. Running the longitudinal pipeline of the hippocampal module, loading Matlab 8.2 to run segmentHA_T1_long.sh SUBJ1_basetemplate segmentHA_T1_long.sh SUBJ2_basetemplate etc I got an error in most of these jobs (mostly for templates of subjects with multiple visits) that read "ERROR: MatlabObjectArray(0x7fd7ce84cea0): Trying to access non-existing object (25) Error in kvlGetOptimizer (line 11) Error in SegmentSubfieldsT1Longitudinal (line 1155)” 2. I then tried running the cross sectional pipeline for each one of the timepoints in subjects already processed by the reconall longitudinal pipeline (i. e. segmentations in the .long. directories) segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_basetemplate segmentHA_T1.sh SUBJ1_timepoint2.long.SUBJ1_basetemplate segmentHA_T1.sh SUBJ2_timepoint1.long.SUBJ2_basetemplate segmentHA_T1.sh SUBJ3_timepoint1.long.SUBJ3_basetemplate etc Most of them ran without errors, but some still did. 3. I then tried to run the cross sectional hippocampal module for all subjects/timepoints without using the reconall longitudinal pipeline segmentHA_T1.sh SUBJ1_timepoint1 segmentHA_T1.sh SUBJ1_timepoint2 segmentHA_T1.sh SUBJ2_timepoint1 segmentHA_T1.sh SUBJ3_timepoint1 etc They were processed without errors. But when inspecting the processing log, there was a message that appeared 4 times in the file "WARNING: Registration did not converge in 5 steps! * Problem might be ill posed. * Please inspect output manually! ……… …….. …... Everything done! It took 766.0135 seconds “ With manual inspection, subfield segmentations output by fs60 seemed fine in all the directories of the reconall cross sectional and longitudinal outputs (hippoSfLabels-T1). For the Hippocampal Module outputs (hippoAmygLabels-T1), the hippocampus was abbruptly cut, sometimes laterally, sometimes dorsally. This was the case for all three analyses. I wonder what is the problem and what I can do to fix it so I can successfully run the longitudinal pipeline of the "hippocampal subfields and nuclei of amygdala” Thanks for your help! Aura M.

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Functional Overlap Map
by nm644 23 Mar '18

23 Mar '18

Hello Freesurfer experts, My question may have already been solved in a previous thread. I have three runs of block-design bold scans. All three are quite similar. They all have only 2 blocks, one for rest and one for task. I’m trying to create a functional map that displays where the functional activation of these three runs overlap. I used the code below with no errors: preproc-sess -s subj01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run mkanalysis-sess \ -fsd bold -stc up -surface fsaverage lh -fwhm 5 \ -event-related -paradigm para.tsv -nconditions 1 \ -spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \ -analysis TaskOverlap.lh -per-run -force mkcontrast-sess -analysis TaskOverlap.lh -contrast con1 -a 1 selxavg3-sess -s subj01 -analysis TaskOverlap.lh And to display: tksurfer-sess -s subj01 \ -analysis TaskOverlap.lh \ -c con1 Or tksurfer-sess -s subj01 \ -analysis TaskOverlap.lh \ -c con1 -map fsig The problem is that when I view the output it seems that there’s far more activation than there should be when trying to find mutual overlap between the three tasks. If anyone has any suggestions it would be much appreciated. Have a great day!

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Re: [Freesurfer] Different DWI protocols
by Yendiki, Anastasia 23 Mar '18

23 Mar '18

Probably not a good idea, depending on how the data are balanced across acquisition protocols. If you find differences between time points of subjects or between subjects, you want to be ensure that those differences are not because of acquisition differences. If, for example time point is always collected with one protocol and time point 2 is always collected with another, you won’t be able to tell. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Cano Catala, Marta" <MCANOCATALA(a)mgh.harvard.edu<mailto:MCANOCATALA@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, March 19, 2018 at 11:20 AM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Different DWI protocols Dear TRACULA experts, I'm running a longitudinal trac-all analysis and I'm wondering whether or not I could include different DWI acquisition protocols both between subjects and within subjects in the same analysis. Thank you, M. Cano

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