Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

Monte Carlo in mri_glmfit-sim
by smcl＠u.washington.edu 03 Nov '15

03 Nov '15

Hi experts, I am having trouble performing a Monte Carlo correction using mri_glmfit-sim. My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I then ran mri_glmfit on the data. I want to do my analysis/correction only in auditory cortex (AC) so I did my own simulation in AC of each hemisphere using mri_mcsim (as per http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo) So far, so good. But when I try to run: mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it didn't help. Any thoughts? Also, can you clarify which comparison neg vs pos will give me? Thank you, Susan McLaughlin, PhD Research Scientist Laboratory for Auditory Brain Sciences & Neuroengineering Institute for Learning & Brain Sciences (I-LABS) Portage Bay Bldg. Room 204 University of Washington, Box 357988 Seattle, WA 98195-7988 Ph: (206) 616-0102 Fx: (206) 221-6472 Cell: 206-850-8638 E-mail: smcl(a)uw.edu

2 8

First-level analysis (native vs fsaverage)
by Rodriguez-Thompson, Anais 03 Nov '15

03 Nov '15

Hi freesurfer experts, I have a question about how running first-level analyses in either native space or fsaverage space changes activation. My original analysis was a per-session analysis run on native space. The command used to make the analysis was ANALYSIS 1: mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_050514 -TR 2 -paradigm slopepar -event-related -runlistfile runlistfile -tpef tpef_1.5mm.txt -native -fwhm 5 -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 However, my lab was interested in running our analyses -per-run, so I created a new per-run analysis on the fsaverage brain using the command: ANALYSIS 2: mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_072915_lh -TR 2 -paradigm slopepar -event-related -runlistfile runlistfile -tpef tpef_1.5mm.txt -surface fsaverage lh -fwhm 5 -per-run -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refevendur 2 -fsd bold The group maps for the two looked comparable. However, I covaried those maps with performance on our task. The maps looked significantly different, and while 9 cluster survived MC correction from analysis 1 (3 LH, 6 RH), only 3 survived MC correction from analysis 2 (0 LH, 2 RH). I thought that the difference could have been due to per-run vs. per-session MC, but I created a test analysis (per-session, fsaverage space), and this analysis looked more like the 2nd analysis than the 1st, leading me to believe that the difference in activation was due to running the first-level analysis on fsaverage space rather than native space. The command I used for the test analysis was: mkanalysis-sess -analysis TEST_fsaverage_persession_lh -TR 2 -paradigm slopepar -surface fsaverage lh -event-related -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 -fwhm 5 -per-session Do you know why running first-level analyses on fsaverage space rather than native space would decrease activation effects, leading to fewer significant clusters after MC correction? I've attached a pdf file with the maps in question. Thanks, Anais

2 5

R: Re: average z-score of each subject from a common cluster
by stdp82＠virgilio.it 03 Nov '15

03 Nov '15

Thanks.I have obtained: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg z.nii.gz --annot Control21_FS rh aparc --i z.nii.gz --sum summaryfile sysname Darwin hostname iMac-di-Stefano.local machine x86_64 user Stefano UseRobust 0 Loading z.nii.gz Loading z.nii.gz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 22 segmentations Computing statistics for each segmentation 0 -7 2 2.000 1 -6 110 110.000 2 -5 255 255.000 3 -4 518 518.000 4 -3 1190 1190.000 5 -2 1692 1692.000 6 -1 4104 4104.000 7 0 61577 61577.000 8 1 42598 42598.000 9 2 28146 28146.000 10 3 14859 14859.000 11 4 5845 5845.000 12 5 1899 1899.000 13 6 485 485.000 14 7 116 116.000 15 8 75 75.000 16 9 74 74.000 17 10 78 78.000 18 11 65 65.000 19 12 104 104.000 20 13 45 45.000 21 14 5 5.000 How I can know the meaning of this number? Where is z? I have tried also with:mri_segstats --seg z.nii.gz --annot Control_21 rh aparc --i z.nii.gz --sum summaryfile --mask .../fc.ramgseed.surf.rh/R_Amygdala/my-glm.wls/group.diff/cache.th13.neg.sig.masked.nii.gz --avgwfvol mrivol but I have problem with interpretation. Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 30-ott-2015 16.17 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] average z-score of each subject from a common cluster On 10/30/15 7:16 AM, stdp82(a)virgilio.it wrote: Hi list, I have two queries, please. I'd like to have the z-score from my rsfMRI data (seed-analyis). 1) I have extract the z-score from the Vtx Max In details, after groups comparison analysis, I have opened the cache.th13.pos.sig.cluster.summary contained in group.diff folder and I have read the Vtx Max coordinates. Next, I have open the z.nii.gz of each subject and I have expected the z-score from the vertex which have the Vtx Max coordinates. Is this procedure corrected? Yes 2) z-score of each subject from a common cluster I would like to use the cluster which shows the group difference (cache.th13.pos.sig.cluster.nii.gz) as ROI mask. Thus, I would extract from it the average of the z-score which is contained in each subject. How should I do? Use mri_segstats passing the z map as the input (--i) and the cluster map as the seg. The output will be --sum. Run with --help for more info Thanks. Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

R: Re: error vcsf.config
by stdp82＠virgilio.it 03 Nov '15

03 Nov '15

Yes, the ventricle is very small. The segmentation in aparc and aseg is nice.How can I do to analyze this subject? I need to include it in the analysis.Many thanks, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 30-ott-2015 16.03 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] error vcsf.config That means it could not find any CSF voxels. Try checking the registration. It could also be that this is a subject with really small ventricles. On 10/30/15 3:57 AM, stdp82(a)virgilio.it wrote: Hi list, During fcseed-sess -s subj -cfg vcsf.config a subject produces the follow error. I have rerun recon-all, cheched aparc+aseg with tkmedit. They seem to be ok. Why this error is produced? Thanks Stefano Creating output directory /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm Loading y from /Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz Saving design matrix to /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/Xg.dat Normalized matrix condition is 61.5872 Matrix condition is 1e+08 Pruning voxels by thr: 0.000000 Found 0 voxels in mask Saving mask to /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/mask.mgh search space = 0.000000 DOF = 297 Starting fit and test Fit completed in 0.0008 minutes Computing temporal AR1 Writing results Computing FSNR mean maxvox sig=0 F=0 at index 0 0 0 seed=1446518089 linear maxvox sig=0 F=0 at index 0 0 0 seed=1446518089 quad maxvox sig=0 F=0 at index 0 0 0 seed=1446518089 Computing PCA (300) ERROR: no voxels in mask _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

reproducing sig.mgh
by Eric Cunningham 03 Nov '15

03 Nov '15

Hello Freesurfer Experts, I am trying to reproduce the values in sig.mgh using matlab, just to confirm that I know what is going on. My numbers do not match exactly, and I am hoping someone can explain my error, or point me in the right direction. With Qdec, I built a model with one discrete factor (A) with groups (A1) and (A2), one continuous covariate (B), and one nuisance factor (C). I extracted the values from sig.mgh from the folder: lh-Diff-A1-A2-Cor-area-B at a specific vertex. I also extracted the values from y.mgh at the same vertex. I then ran an anova with contrast matrix, and expected the -log10(p-value) of the A*B term to match that of sig.mgh. [1 0 0;... (A) 0 1 0;... (B) 0 0 1;... (C) 1 1 0]; (A*B) Thank you for your time, -E

2 1

FreeSurfer and OpenMP
by Linda BOUMGHAR 03 Nov '15

03 Nov '15

I would like to use freesurfer with OpenMP, with 4 processors. I wrote this : recon-all -all -i /mnt/linuxwin/lboumgha/data/CENTER_TBI/tro/suj1/T1.nii.gz -subjid subj1 -openmp <8> and I got this error message : bash: syntax error near unexpected token `8' What is the good syntax if I want tu use OpenMP, please? Great regards, Linda Boumghar ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

4 4

Voxel based vs surface based
by John Anderson 03 Nov '15

03 Nov '15

4 3

Differences in the asc and FreeSurfer format of the surface data
by Razlighi, Qolamreza R. 03 Nov '15

03 Nov '15

Hi Guys, Why converting a surface to .asc format changes its spatial orientation? Specifically, I have converted lh.while to lh.white.asc (using: mris_convert lh.white lh.white.asc) and plot both of them using freeview but they are not corresponding. In fact, lh.white corresponds to the volume image (e.g orig.mgz) but the lh.white.asc doesn't. See the attached screenshot. The red curve is the lh.white.asc. Any explanation would be greatly appreciated. Best -- Ray Razlighi, Ph.D. Assistant Professor Quantitative Neuroimaging Laboratory Division of Cognitive Neuroscience Department of Neurology Columbia University Alt: razlighi(a)gmail.com Office Phone: 212-342-1352 Office Fax: 212-342-1838 Website: http://www.columbia.edu/cu/qnl/

3 5

using ADNI preprocessed files in FS
by Riphagen Joost (NP) 03 Nov '15

03 Nov '15

Hi, Sorry for the very basic question but I have not been able to find the answer in the archives, nor anywhere else. I want to use ADNI data in FS ADNI data is available in either original DICOM or has been preprocessed in the following manner: Phillips Systems: unpreprocessed DICOM N3 corrected GE and Siemens systems with transmit-receive head RF coils: unpreprocessed DICOM gradwarped gradwarp plus N3 GE and Siemens systems with receive-only head RF coils: unpreprocessed DICOM gradwarped gradwarp plus B1 plus N3 I reality there are quite a few more options available. Question is which one to use best for FS (plan is to rerun in a newer FS version) I suppose that using the files that are gradwarped and B-1 corrected is sensible for using in FS. However the "best" files after quality control have been N3 corrected which makes it a lot easier for me to extract these files from the database (I need a few hundred, meaning I have many thousands of files to extract from). Would running recon all, but omitting the N3 step be correct ? Thanks a lot, JM Joost Riphagen, MD Phd candidate Maastricht University.

1 0

comparison of subcortical volume with 1.5 T and 3T...
by Gonzalo Rojas Costa 03 Nov '15

03 Nov '15

Hi: I have some longitudinal study of a patient with 1.5 T images... now, we have 3T mprage images of the same patient... how can I do the comparison of the subcortical volume of the patient ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Freesurfer November 2015