Freesurfer July 2018

freesurfer@nmr.mgh.harvard.edu

112 participants
165 discussions

Re: [Freesurfer] Cortical Thickness at Individual Vertices (fwd)
by Bruce Fischl 18 Jul '18

18 Jul '18

from Tom.... ---------- Forwarded message ---------- Date: Thu, 12 Jul 2018 16:51:31 +0100 From: Thomas Nichols <thomas.nichols(a)bdi.ox.ac.uk> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cortical Thickness at Individual Vertices External Email - Use Caution Hi Bruce! James: I don't have any particular deep thoughts except, all things equal, if you have a tenable continuous summary of the mTBI deficits it will probably be more sensitivity than a discrete count-based summary of the deficits. Bruce's idea of comparing distributions is sound but probably will only work well for mTBI effect that are diffuse. For localised effects (that are not spatially consistent), finding some summary measure of the deficits are probably the best way forward. -Tom On Thu, Jul 12, 2018 at 4:31 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: Hi James you could use techniques that compare the whole distribution of thicknesses across subject populations. You could do a t-test or something non-parametric like a Kolmogorov-Smirnov or use permutation testing. I'll cc Tom Nichols so he can chime in with something more sophisticated or specific. cheers Bruce On Wed, 11 Jul 2018, James Gullickson wrote: > > External Email - Use Caution > > All, > I am comparing cortical thickness between subjects with and without mild traumatic brain injury > (mTBI). So far the contrasts in QDEC have not been significant after correcting for multiple > comparisons. I am not necessarily surprised at this due to the heterogeneous nature of mTBI in our > sample, i.e. we do not expect any two subjects to have damage in the same area. I am interested in > ways to compare cortical thickness that are not dependent on a single ROI having an effect across > subjects. One way I have tried is calculating z-scores for the values in the aparc.stats file, and > using the number of abnormally low ROIs as a dependant variable to compare between groups. > > Is there a way to look at thickness differences at an even more general level? E.g. by comparing the > number of vertices with abnormally low thickness? If so how would one go about that with Freesurfer > data? > > This paper takes a similar approach with DTI. I'd like to do something analogous to their "number of > voxels with low FA" analysis. > https://www.sciencedirect.com/science/article/pii/S1053811911012146 > > Thanks, > > James > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- __________________________________________________________ Thomas Nichols, PhD Professor of Neuroimaging Statistics Nuffield Department of Population Health | University of Oxford Big Data Institute | Li Ka Shing Centre for Health Information and Discovery Old Road Campus | Headington | Oxford | OX3 7LF | United Kingdom T: +44 1865 743590 | E: thomas.nichols(a)bdi.ox.ac.uk W: http://nisox.org | http://www.bdi.ox.ac.uk

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tar extraction problem
by Francis Houde 17 Jul '18

17 Jul '18

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to extract the freesurfer program from (http://freesurfer.net/fswiki/DownloadAndInstall) but I get the following error when I run the tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz command (i changed the /usr/local to my path where i want my freesurfer folder) : tar: freesurfer/subjects/fsaverage5/surf/lh.inflated: Cannot hard link to ‘freesurfer/subjects/fsaverage5/surf/lh.inflated-from-fsaverage’: Operation not permitted tar: Exiting with failure status due to previous errors I've searched the log for errors with the (tar -xzf reesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz command). I also tried using sudo before the tar command without success. The same error comes back. I've run the steps proposed by (http://freesurfer.net/fswiki/DownloadAndInstall) to see if the program is working fine. I can convert the sample001 to nifty but the recon-all command ends up with errors. These are the errors that I get (See attached) Does anyone have any thoughts on how to trouble-shoot this? Can you help me ? Thank you Francis Houde Étudiant au doctorat en sciences des radiations et imagerie biomédicale Centre de recherche sur le vieillissement (Université de Sherbrooke) (819) 780-2220 # 45423 CIUSSS de l'Estrie CHUS 1036, rue Belvédère Sud - local 3441 Sherbrooke (Québec) J1H 4C4

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Exvivio stats?
by Jason Bruggemann 17 Jul '18

17 Jul '18

External Email - Use Caution Hello, I ran a batch in order to tabulate the FreeSurfer stats from our data set, but error logs indicated that the usual "?h.BA.stats" files were missing. It appears that these files were not generated, and instead we have "?h.BA_exvivo.stats" and "?h.BA_exvivo.thresh.stats". So I am not exactly sure what these are, but a mail archive search suggested that these are associated with the developer version of FreeSurfer? ...or perhaps this is just something new in FS Version 6.0.0? We are currently running: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Any advice appreciated... Best Regards, Jason

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segmentHA_T2.sh
by 墨初 17 Jul '18

17 Jul '18

External Email - Use Caution Dear freesurfer experts, when i run the command“segmentHA_T2.sh subject001 T2.nii T2 1” ,it runs as following: -------------- Making Left-Thalamus-Proper map to reduced label 10 -------------- Making Left-choroid-plexus map to reduced label 11 -------------- Making Left-VentralDC map to reduced label 12 -------------- Making Left-Accumbens-area map to reduced label 13 -------------- Making Unknown map to reduced label 14 Computing hyperparameters for estimation of Gaussians parameters znzreadInt: znzread failed No such file or directory Estimating typical intensities of molecular layer and alveus numberOfLabels: 2 Rasterizing mesh...here: 2 here2: 2 done Smoothing mesh collection with kernel size 1.500000 ...Smoothing class: 0 Smoothing class: 1 Smoothing class: 2 Smoothing class: 3 Smoothing class: 4 Smoothing class: 5 Smoothing class: 6 Smoothing class: 7 Smoothing class: 8 Smoothing class: 9 Smoothing class: 10 Smoothing class: 11 Smoothing class: 12 Smoothing class: 13 done numberOfImages = 2 Image: 0 Image: 2 Iteration 1 of 7 1 0.00035804 2 0.089592 fianally,it stop here and can't run anymore,no error reported。I didn't know what‘s wrong？ What can i do？ Thanks very much Fiona Ding

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across-subject overlap
by Elisa Castaldi 17 Jul '18

17 Jul '18

External Email - Use Caution Dear experts, I would like to show the across-subject overlap of voxels by creating a map with color coding indicating the number of subjects activating corresponding voxels. For each subject I have run the first level model in spss and saved the 1000 most activated voxels for a given contrast as an roi (binary file). Now with freesurfer I am trying to : 1) display the saved roi on the subject's surface (which has been obtained with recon all) - this step worked 2) align each subject's surface to fsaverage - this step gave me the problem 3) add all subjects together and create the map showing how many subjects activated each location To do so I have done the following: 1) this first step worked fine and I could display the roi on my subject's surface mri_vol2surf --mov ${DATA_DIR}/sub01/vois/1000vox_IPS.nii \ --reg ${DATA_DIR}/sub01/fmri/register.dat \ --hemi rh \ --o ${DATA_DIR}/sub01/probmap/testIPS.rh.mgh \ --projfrac ${thisprojfrac} 2) this step crashed mri_surf2surf --hemi rh --s fsaverage --fwhm 3 --cortex \ --sval ${DATA_DIR}/sub01/probmap/testIPS.rh.mgh --tval ${DATA_DIR}/sub01/probmap/testIPSfs.mgh The error is: Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 163842 Number of value vertices = 133030 Do you have any idea why? 3)Then I was planning to use fscalc and add all subjects together, is this correct? If there is another/easier way to do the same thing, please let me know Thanks in advance for your help, Best Elisa

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After v.5.3 to v.6.0 update octave set up doesn't work
by Patrycja Naumczyk 17 Jul '18

17 Jul '18

External Email - Use Caution Hi all, I just switched from FS 5.3 to 6.0 on Gentoo Linux. Previously Freesurfer worked fine under octave setup (as specified here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.…) but after the update, when I tried testing a MATLAB related function I get an error: mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 INFO: Found 2 Non-Null Conditions INFO: Found 3 Delays Condition Weights: 1.00000000000000000000 0 mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ cmtxfile PASAT.sm5.lh/test.mat nconds 2, wcond 1.00000000000000000000 0 ndelays 3, wdelay 1 0 0 ndelays 3, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR: cannot find matlab. Is it in your path? ERROR running mkcontrast mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave Fri Jun 29 21:21:16 CEST 2018 It seems that the environment variable (FS_USE_OCTAVE) is recognized correctly (the function runs with "-octave" flag), but somehow is omitted during execution? What can I do about it? I checked that v.5.3 used mkcontrast, whereas v.6.0 uses mkcontrast2 which does not seem to support octave? Is it possible to force calling mkcontrast instead of mkcontrast2? Best regards, Patrycja

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question about the GLM power
by Ting Li 16 Jul '18

16 Jul '18

External Email - Use Caution Hi Freesurfer Expert, How can I know the power of my GLM test after I did the clusterwise correction? I got this question because I had a problem like this. I have 21 subjects for group A and B. Once I delete one subject from group A, one of the clusterwise correction results has disappeared. Can you help me on this? Thanks a lot! Best wishes, Ting Li

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Multiple comparison - permutation
by Ting Li 16 Jul '18

16 Jul '18

External Email - Use Caution Dear Freesurfer Experts, I am running the multiple comparison (permutation) on a MAC with the following code. It has taken 8 hours and has not finished yet. It gives me Poll jobs information without end. According to tutorial information, it will only take around 20 minutes. Do you know what should I do if I want to use this perm multiple comparison? I have attached my MAC system information and the Poll jobs information. Thanks a lot! Best wishes, Ting mri_glmfit-sim \ > --glmdir lh.volume_70_sTIV_perm.glmdir \ > --perm 1000 4.0 neg \ > --cwp 0.05\ > --2spaces \ > --bg 2

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fthresh documentation
by srishti goel 16 Jul '18

16 Jul '18

External Email - Use Caution Hello, I am trying to decide what fthresh values should I be using for viewing my mkda maps on surface. Where could I find some theoretical explanation of how to figure that out the freesurfer wiki? I have read a lot of different things on the archive but didn't figure out my answer. It's great appreciated. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig(a)email.unc.edu skype: srishti.goel12

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recon-all -s 1 exited with ERRORS
by Bernardo Regal 16 Jul '18

16 Jul '18

External Email - Use Caution Hello FreeSurfer Developers, I have a problem to convert the files using the recon-all. It appears, recon-all -s 1 exited with ERRORS. Before I had the last version (stable v6.0.0). As I did not find a solution of how to fix this problem, so I decided to make a downgrade to the previous version (5.3.0 stable). I thought that maybe the oldest version of this program was solved. But no, I still have the same problem. How I can fix this problem permanently? My code is: $ export SUBJECTS_DIR=/home/regal/Data/Subjects/test_old_version $ recon-all -s 1 /home/regal/Data/Subjects/test_old_version/01C_dislebi_T1.nii -autorecon-all than: " ERROR: Flag /home/regal/Data/Subjects/test_old_version/01C_dislebi_T1.nii unrecognized. -s 1 /home/regal/Data/Subjects/test_old_version/01C_dislebi_T1.nii -autorecon-all Linux genedys2 4.15.0-2-amd64 #1 SMP Debian 4.15.11-1 (2018-03-20) x86_64 GNU/Linux recon-all -s 1 exited with ERRORS at Tue Jul 3 18:47:19 CEST 2018 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting " 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Linux genedys2 4.15.0-2-amd64 #1 SMP Debian 4.15.11-1 (2018-03-20) x86_64 GNU/Linux Thank you for your help, Best regards -- Bernardo Regal [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 07/03/18, 7:27:54 PM

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Freesurfer July 2018