Re: [Freesurfer] mri_glmfit-sim --grf question

On 7/24/17 4:12 PM, Jiahe Zhang wrote: That makes sense. And thanks for the suggestion! I tried running permutation test with the following command: mri_glmfit-sim --glmdir r_PCC_glm --sim perm 1 1.3 perm.abs.1.3 --sim-sign abs The results are empty maps for all the contrasts I have,

Re: [Freesurfer] mri_glmfit-sim --grf question

That makes sense. And thanks for the suggestion! I tried running permutation test with the following command: mri_glmfit-sim --glmdir r_PCC_glm --sim perm 1 1.3 perm.abs.1.3 --sim-sign abs The results are empty maps for all the contrasts I have, which I did not expect, since some of the

Re: [Freesurfer] converting vertex numbers in .label files to R, A, S coordinates

Try using mri_label2label with the --paint option. I think the vertex numbers need to be -1 (not random numbers). You will also need to convert the RAS to "tkregisterRAS", one of our internal coordinate systems. See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems, you'll need to

Re: [Freesurfer] Cerebral White Matter vs Cortical White Matter

They are the same measures. We changed the name because "Cortical" WM does not make sense:). In v6, we slightly changed the way it is computed, but the difference should be pretty small. On 7/24/17 3:52 PM, Dowling, Kevin Francis wrote: Dear Freesurfer Experts, My apologies for what is

[Freesurfer] Cerebral White Matter vs Cortical White Matter

Dear Freesurfer Experts, My apologies for what is admittedly a very simple question, however I have not been able to find an answer on the forum. We are running some analyses in an older version of Freesurfer (5.0) to compare the results to some earlier work. When I run asegstats2table for all

Re: [Freesurfer] Segmentation Violation problem in surface files

Hi Idil, we only store surface overlays in .mgz not surfaces themselves. Try loading a surface (like lh.inflated) then load whatever you were looking at as an overlay on the surface cheers Bruce On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote: > Hello freesurfer experts, > > I am trying to use

Re: [Freesurfer] help with finding exact and detailed coordinates of brain areas

HI Adiel we distribute all our matlab scripts as part of FreeSurfer cheers Bruce On Mon, 24 Jul 2017, עדיאל חרבש wrote: Hi Bruce, It may really help to shorten and ease the procedure, thanks. I see that I should clone all your matlab repository to use this function? I will look over

Re: [Freesurfer] help with finding exact and detailed coordinates of brain areas

If you want all the coordinates for a given segment (eg, left hippo), then you can run mri_cor2label --i aparc+aseg.mgz --id 17 --l file.label 17 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt The coordinates will be in "tkregister space" which you can convert to MNI305 using the info

Re: [Freesurfer] Monte-Carlo in LME

yes On 7/21/17 5:24 AM, Jordi Pegueroles wrote: > Thank you Doug. So, instead of running mri_surfcluster I should run > mri_glmfit-sim with the --fwhm-override with the smoothing obtained > from the residuals of the lme model. > > Thanks again, > > A 2017-07-18 22:09, Douglas N Greve escrigué:

[Freesurfer] Segmentation Violation problem in surface files

Hello freesurfer experts, I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up; freadFloat: fread

Re: [Freesurfer] help with finding exact and detailed coordinates of brain areas

Hi Bruce, It may really help to shorten and ease the procedure, thanks. I see that I should clone all your matlab repository to use this function? I will look over mri_extract_labels as well. Best, Adiel 2017-07-24 17:02 GMT+03:00 Bruce Fischl : > Hi Adiel > > in

Re: [Freesurfer] help with finding exact and detailed coordinates of brain areas

Hi Adiel in matlab you could do something like: cd $SUBJECTS_DIR//mri matlab [v,M,mr] = load_mgh('aseg.mgz'); left_hippo_indices = find(v == 17); where the '17' comes from $FREESURFER_HOME/FreeSurferColorLUT.txt and is the index for left hippocampus. Is that would you mean? Or you could

Re: [Freesurfer] help with finding exact and detailed coordinates of brain areas

Hi again, I figured it out- converted .mgz to nii.gz with "mri_convert", then gunzip the nii.gz files, and get the file with the labels as a brain map. Thanks for the direction! Adiel -- Forwarded message -- From: עדיאל חרבש Date: 2017-07-24 9:11 GMT+03:00

[Freesurfer] Clarification for aseg edits in longitudinal phase

Hello, I have made edits to aseg files in the longitudinal outputs (participantID.long.participantID-temp). I am beginning the reconstruction phase and as suggested by a response to an earlier post I am running: recon-all -long tpN1 template ID -autorecon2-noaseg -autorecon3, where tpN1 is

Re: [Freesurfer] help with finding exact and detailed coordinates of brain areas

Hi Bruce, Thanks for the reply. By "coordinates" I mean all the voxels that belong to a certain structure. I think it's called "labels"? I interest in the main structures like Hippocampus, Thalamus, Cerebellum, Amygdala, corpus callosum, etc. If the standard segmentation segments in that