Freesurfer

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30132 discussions

selxavg3-sess error
by stdp82＠virgilio.it 16 May '17

16 May '17

Hi list, this error occurs during selxavg3-sess in FS-FAST fcMRI meanval --i stem2fname stem Looks for stem.fmt where fmt is mgh mgz nii nii.gz bhdr img w, then returns stem.fmt. See also stem2fmt, fname2stem The file needs to exist on disk. --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.datERROR: cannot find stem2fname I have already run for this folder other seed. The error occurs only on it (amygdala). Thanks Stefano

2 1

perirhinal volumes
by Antoniades, Mathilde 16 May '17

16 May '17

Dear Freesurfer experts, I would like to obtain perirhinal cortex volumes from structural images that have undergone recon-all. I see that the label subfolder contains left and right perirhinal cortex labels but the stats file does not. So a first step seems to be "converting" the label to a stats file!? Is there a command for this? Thank you, Mathilde. PhD student in Psychosis studies.

1 0

probability maps
by Trisanna Sprung-Much 16 May '17

16 May '17

Hi there I have generated some anatomical probabilistic maps as overlays on the fsaverage pial surface. Is there a way to automatically find the vertex coordinates of the vertex with the highest probability of overlap? Or does this have to be done manually in Freeview? Many thanks Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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2 stage model longitudinal data analysis
by Maria A Infante 16 May '17

16 May '17

Hi, I am interested in looking at groups differences (3 groups) in percent thickness change. I want to use mri_glmfit to analyze but I am unclear on what I should include on my fsgd file. Can you please provide an example? Also The example provided on the fswiki under Option mri_glmfit doesn't call for an fsgd file. long_mris_slopes --qdec long.testretest.qdec \ --meas thickness \ --hemi lh \ --sd $SUBJECTS_DIR \ --do-pc1 --do-label \ --generic-time \ --fwhm 15 \ --qcache fsaverage \ --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \ --isec-labels lh.testretest.fsaverage.cortex.label mri_glmfit --osgm \ --glmdir lh.testretest.thickness-pc1.fwhm15 \ --y lh.testretest.thickness-pc1.stack.fwhm15.mgh \ --label lh.testretest.fsaverage.cortex.label \ --surf fsaverage lh

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mri_convert
by John Anderson 15 May '17

15 May '17

Dear Freessurfer experts, i want to convert IMA files to nifti using mri_convert I did the following: mri_convert 54365413.ima output.nii I got this error WARNING: bad orientation matrix (determinant = 0) in nifti1 file ... ... continuing. if I run mri_info on output.nii I see voxel-to-ras determinant 0 ras to voxel transform: mat = NULL! MatrixFree: NULL mat POINTER! How can I correctly convert IMA to nifti Thank you for any suggestion John

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Cortical Thickness
by Limachia, Gaurang (NIH/NINDS) [F] 15 May '17

15 May '17

Hello Freesurfer Experts, I finished running the qdec analysis on our patient and healthy control populations. While looking at the clusters I am having a hard time telling which group -controls or patients have a larger cortical thickness? Additionally, I wanted to know if it would be possible to save the images created by qdec as a jpeg or png file. I would greatly appreciate your help. Thanks, Gaurang

2 1

mri_surf2vol cannot recognize the type of surf/lh.inflated
by Lukas Pezenka 15 May '17

15 May '17

Hi all, I need a volume that maps my sulci. So first I've run recon-all on my data. Worked like a charm. Visual verification in freeview shows that the inflated surface looks just about right (although it does not seem to be registered to the aparc+aseg volume). However, when I try to run mri_surf2vol, I get the error message "ERROR: cannot recognize the type of surf/lh.inflated". My precise syntax was mri_surf2vol --o out.nii --identity casestudy2 --surf inflated --hemi --lh --surfval surf/lh.inflated Can anyone advise me on this? Best regards, Lukas PS :I'm running on FS version 5.3.0. PPS: Is it possible to achieve this from freeview rather than from the command line?

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mri_glmfit mask.mgh for mri_surfcluster
by Ryan Muetzel 15 May '17

15 May '17

Dear Experts, This is partially a follow-up question to another thread related to the mask.mgh generated by mri_glmfit (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50691.html <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50691.html>). We would like to use the mri_surfcluster tool on a log10p map. I’m wondering — for vertex-wise analyses that use freesurfer-specific output (e.g., thickness, surface area, lgi, etc, not FMRI or DTI data)….can we rely on a single mask image for each hemisphere that comes from the fsaverage ?h.cortex.label? Or, should we be creating a mask that is specific to a given analysis/dataset, as is done with mri_glmfit? If the latter, is there a way to create this mask outside of mri_glmfit? Thank you in advance for your time and help! Best, Ryan

2 2

Calculating effect sizes using an older version of Freesurfer
by Clint Johns 15 May '17

15 May '17

Using Freesurfer 5.3.0, we assessed correlations. between behavioral measures (e.g., working memory, IQ) and grey matter thickness in a single group of participants. We obtained some results - a significant correlation between measure X and cortical thickness in, say, IFG. We would like to include the Pearson's r or some other measure of the effect size. Newer versions of Freesurfer allow this (pcc.mgh), but we are not sure what to use. We have the contrast effect size file gamma.mgh, and the gamma values are "C*beta, where beta are the regression coefficients, so gamma is a type of regression coeff" (per Doug G. in this old thread: https://mail.nmr.mgh. harvard.edu/pipermail//freesurfer/2016-April/045135.html) So how do we use these values in a table? They're not Pearson's r, or Cohen's d, obviously. Do we just label the column "peak contrast effect size", naming the values after the gamma.mgh file? Thanks! (We're very confused.) clint -- I remain... Clinton L. Johns, Ph.D. Research Scientist, Haskins Laboratories 300 George Street New Haven CT 06511 speech: 203-865-6163 x240 fax: 203-865-8963 net: johns(a)haskins.yale.edu

2 1

Create thresholded annotations without recon-all?
by Michael Bannert 15 May '17

15 May '17

Dear FreeSurfer community, I would like to perform a ROI analysis using an anatomical mask. I was thinking of using the thresholded masks in the annotations file created from running recon-all. Now I noticed that a few of my older datasets do not seem to have thresholded annotation files, but only the unthresholded ones. Is it possible to create these files (e.g., l/rh.BA.tresh.annot) again without having to run recon-all over again? Maybe from manually thresholding the unthresholded annotation files (l/rh.BA.annot)? How would I go about this? Thanks and best, Michael

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