Freesurfer January 2018

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

resting state motion censoring
by Adam Martersteck 24 Apr '18

24 Apr '18

Hi Freesurer experts, I’m looking to censor (drop volumes) from my resting state fMRI time series that violate a predetermined motion and signal threshold (FD and DVARS). I've already determined which volumes violate X and Y criteria. Is there a way to to tell FS to "ignore" these time points in the analysis such as in preproc-sess or mkanalysis-sess? If there is not and if I were to drop the volumes directly from the 4D file before starting any pre-processing and analysis – would that be a problem for finding and regressing the auto-correlation in the time series? Thanks! Adam

3 6

mri_glmfi-sim multi-thread
by Dowling, Kevin Francis 08 Apr '18

08 Apr '18

Dear Freesurfer Experts, My apologies for what might be a very simple question, but I have been unable to locate an answer in the archives/wiki. Our group is trying to cut down on our mri_glmfit-sim time (as we are hoping to run mri_glmfit-sim -sim mc-full, rather than -sim mc-z). I know that --bg will split up the larger number of simulations into n background jobs, but I also noted the warning that this option is not to be used on the Martinos launchpad computational cluster. As we are hoping to find a way to use launchpad, I was wondering if mri_glmfit-sim is multi-threaded (or can be multi-threaded similar to -parallel flag in recon-all)? We are currently running Freesurfer 5.3, but can move up to 6.0 if needed. (Our specific command is: mri_glmfit-sim --glmdir $SUBJECTS_DIR/.../glmdir --sim mc-full 2.3 1000 mcfull1000_2.3 --sim-sign abs --cwpvalthresh .05) Thank you in advance for your help! Kind regards, Kevin Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.3215

2 1

Building from source -- autoconf error
by Alle Meije Wink 29 Mar '18

29 Mar '18

I'm trying to build FreeSurfer from source on my Debian 8 (jessie) system. (64 bit, using g++ 4.9 for compilation) After $ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login $ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev $ cd dev $ cvs update -d # just to make sure $ ./setup_configure I get these messages: rm -rf autom4te.cache libtoolize --force libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `config'. libtoolize: linking file `config/ltmain.sh' libtoolize: putting macros in `m4'. libtoolize: linking file `m4/libtool.m4' libtoolize: linking file `m4/ltoptions.m4' libtoolize: linking file `m4/ltsugar.m4' libtoolize: linking file `m4/ltversion.m4' libtoolize: linking file `m4/lt~obsolete.m4' libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.in and libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree. aclocal aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: error: configure.in:2045: file 'm4/autotroll.m4' does not exist Which looks like a not-(anymore)supported use of autoconf? I found one previous message on the list about autotroll https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021854.… that provided another version of configure.in which might solve the issue. And it did in the original case but sadly not for me. I get the same error message also with the new configure.in -- there should probably be a configure.ac? If anyone knows how to make this work (e.g. by modifying the configure script) that would be fantastic.

8 17

Map mask from volume to surface for small volume correction in surface analyses (using my own template)
by Charlotte Grosse Wiesmann 16 Mar '18

16 Mar '18

Dear freesurfer experts, I would like to restrict my surface analyses (cortical thickness and surface area) to a mask from an fMRI meta-analysis using my own subject-specific template that I created with ANTS. So far, I have used Qdec and wanted to correct for cluster size running the Monte Carlo (MC) simulation on my own template. Now I would like to restrict the simulation to my mask to do a small volume correction in my regions of interest. I mapped the mask to my own template (in volume space) using ANTS (WarpImageMultiTransform) but how can I get this mask to the surface space to run the MC simulation on my own template within this mask? I was planning to do: mri_mcsim --o my_template/mult-comp-cor/my_template/lh/mymask --base mc-z --surface my_template ?h --nreps 10000 --mask mymask.mgz How do I get mymask.mgz in the correct space for this? And can I continue using Qdec or do I have to use glmfit for these analyses? In addition: is it also possible to do a small volume correction using FDR rather than cluster-size correction? Thanks for your help! Charlotte

3 6

thickness measure in basal ganglia
by Giovanni de Marco 27 Feb '18

27 Feb '18

Hello, In stats-table, I did'n t find the thickness of basal ganglia. Please, c an we get thickness in basal ganglia? ( Ma ybe freesurfer measures only the cortical thickness) Many thanks for your response. Giovanni -- Tel: +33 (0) 6 74 61 01 65 demarco.giovanni(a)gmail.com

3 8

mris_flatten error: bad vertex
by Ji Won Bang 20 Feb '18

20 Feb '18

Dear. Freesurfer experts. Hi. I'm having a problem with mris_flatten (version 5.3.0) Could you please help me fix this problem? My command line is: mris_flatten -w 0 -distances 12 7 $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat It returns the error: using write iterations = 0 sampling 7 neighbors out to a distance of 12 mm reading patch /home/jbang/Projects/replay/mri//replay06/surf/lh.oc.patch.3d with 30434 vertices (20.5% of total) MRISreadPatch: bad vertex # (148517) found in patch file No such file or directory When making the patch lh.oc.patch.3d, I followed the processes below: tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast UpperLower select 3 points along a boundary between upper and lower visual fields (near calcarine sulcus) and press "Cut line". Then, select 4 points to define the cutting plane: 1 on lower side of the line, 2 on upper side of the line, 3 on the opposite surface (use rotation tool), and 4 to specify which portion of surface is kept, and press "Cur plane". File->Patch->Save Patch As lh.oc.patch.3d So I think I made the patch correctly. ! weird thing that I suspect is that when I click save patch as, the default location is $SUBJECTS_DIR/fsaverage/surf/ , so I had to change it to $SUBJECTS_DIR/$SUBJECT/surf Could you please help me? Thanks a lot! Best, Ji Won

3 4

Re: [Freesurfer] IndexError: list index out of range
by Maksimovskiy, Arkadiy 16 Feb '18

16 Feb '18

Hi Doug, I sent you the tar files, but just wanted to update you that I tried running this with just one subjects and am still getting an error but a different one. The two inputs and output errors in the terminal are pasted below: [arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] amaksimovskiy% asegstats2table --subjects SILVA030 --meas volume --stats aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt SUBJECTS_DIR : /Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits Parsing the .stats files Traceback (most recent call last): File "/Applications/freesurfer/bin/asegstats2table", line 548, in <module> id_name_map, measurelist = parsed.parse(options.meas) File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse seg = strlst[1] # segmentation id is in the 2nd field IndexError: list index out of range [arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] amaksimovskiy% asegstats2table --subjects SILVA040 --meas volume --stats aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt SUBJECTS_DIR : /Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits Parsing the .stats files Traceback (most recent call last): File "/Applications/freesurfer/bin/asegstats2table", line 548, in <module> id_name_map, measurelist = parsed.parse(options.meas) File "/Applications/freesurfer/bin/fsutils.py", line 122, in parse self.measurelist.append( float(strlst[self.measure_column_map[measure]] )) ValueError: could not convert string to float: Left-Cerebellum-Cortex Let me know if any further info is needed to troubleshoot. Thank you for helping with this. -arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

3 6

Volume to Surface mapping looks great for Vols created in FSL but not SPM
by Rita Elena Loiotile 15 Feb '18

15 Feb '18

Hi, I'm trying to compare analyses that I've done entirely on the surface to analyses I've done in the volume. I'm comparing the analyses by projecting the volume analyses to the surface (HCP's 32k_fs_LR). The commands I'm using are: mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} --projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii; mri_surf2surf --srcsubject fsaverage --srcsurfval ${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval ${giftiFile}.$hemi.gii --hemi ${hemi}; It seems that the FSL volumes look identical to the surface analysis, when mapped. (Our surface analysis is mainly FSL-based, so this makes sense.) The SPM mapping, however, looks very odd. It isn't just that the intensity differs, but the localization of high intensity areas also varies. It seems that everything is shifted a bit superior and, possibly, posterior to the true location (as seen on the surface analysis). I'm wondering if I'm doing anything obviously wrong in my command usage. The brains were normalized to the MNI ICBM 152 template in SPM. I *think* it's suitable to use the -mni152reg flag in the command. I can attach pictures of the comparison if you'd like. Thanks in advance, Rita

3 5

[freesurfer] Extracting values of cortical thickness in each vertex.
by 박경일 09 Feb '18

09 Feb '18

Dear FS experts, I could get QDEC image comparing two groups. However, is there a way to get numerical values of cortical thickness in each vertex? Thank you Best, Kyung

3 10

mri_aparc2aseg labelwm not labelling wm
by Sims, Sara A 09 Feb '18

09 Feb '18

Freesurfers, I am trying to use a cortical label to label wm. I am using the following command line: mri_aparc2aseg --s $patient --annot 8V1 –labelwm And most of the time in most subjects this works, however sometimes the output file doesn’t label any wm with the 3000+N or 4000+N like it usually does. I have tried changing the -wmparc-dmax, -hypo-as-wm, -smooth_normals. Basically everything I could find but it won’t budge even though doing other labels in the same person works fine. Fyi: The original cortical label is also correctly place in the cortical ribbon. Any ideas? Please! Thanks, Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 snolin(a)uab.edu

3 6

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Freesurfer January 2018