[Freesurfer] Extracting values via mri_segstats from middle of the cortex

Hi, I have a MT and T1W volume (processed through recon-all). I would like to extract all MT values that lie in the middle surface of the cortex, and run that through mri_segstats so I get average MT values for each cortical region in the DK-atlas. My workflow is as follows: 1. mri_vol2suf --mov

[Freesurfer] Extracting values via mri_segstats from middle of the cortex

Hi, I have a MT and T1W volume (processed through recon-all). I would like to extract all MT values that lie in the middle surface of the cortex, and run that through mri_segstats so I get average MT values for each cortical region in the DK-atlas. My workflow is as follows: 1. mri_vol2suf --mov

Re: [Freesurfer] Extracting values via mri_segstats from middle of the cortex

Update - Solved the issue. A better way to extract values from a surface overlay is by using mri_segstats with --annot subject hemi parc. Thanks On Sat, Oct 7, 2017 at 11:45 AM, Yash Patel wrote: > Hi, > > I have a MT and T1W volume (processed through recon-all). I would like to >

[Freesurfer] mri_segstats - CTABWriteFileASCII; could not open file for writing

Hello FreeSurfer experts, I am attempting to run "mri_segstats --annot [subjectid] lh aparc --sum [outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035" Whenever I try, I receive the following error (in error.log file); CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15

Re: [Freesurfer] mri_segstats - CTABWriteFileASCII; could not open file for writing

Yes, I made sure I had permission to write into /tmp. On Wed, Feb 28, 2018 at 12:23 PM, Douglas N Greve wrote: > do you have write permission to /tmp ? > > > On 02/27/2018 03:25 PM, Yash Patel wrote: > > Hello FreeSurfer experts, > > > > I am attempting to run &q

Re: [Freesurfer] mri_segstats - CTABWriteFileASCII; could not open file for writing

Yash Patel wrote: > Yes, I made sure I had permission to write into /tmp. > > On Wed, Feb 28, 2018 at 12:23 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> do you have write permission to /tmp ? >> >> >> On 02/27/2018 03:25 PM, Yash Patel wr

[Freesurfer] Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?

Dear all, I am using mri_segstats to obtain intensity values from each of the 34 cortical parcellations in the Desikan-Killiany Atlas; this provides metrics such as mean, min, max, range, and standard deviation. Is there a way to extract information such as the *mode*, or information to create a h

Re: [Freesurfer] Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?

Any updates or ideas in extracting histogram data from mri_segstats? On Sun, Mar 11, 2018 at 1:16 PM Yash Patel wrote: > Dear all, > > I am using mri_segstats to obtain intensity values from each of the 34 > cortical parcellations in the Desikan-Killiany Atlas; this provides metri

[Freesurfer] Lateral Geniculate Nucleus (LGN) roi or volume measures?

Hi all, Is there any way to obtain (automatically, n~1000 subjects), LGN volumes from the Freesurfer set of tools? Or somehow transform the ROI from an atlas into subject space, then extract volume data? Thanks, Yash ___ Freesurfer mailing list Freesurf

Re: [Freesurfer] Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?

g.vol == SegNo); > > segmode = mode(input.vol(ind)); > > [h x] = hist(input.vol(ind),100); > > > > On 03/13/2018 07:58 PM, Yash Patel wrote: > > Any updates or ideas in extracting histogram data from mri_segstats? > > > > On Sun, Mar 11, 2018 at 1:16 PM Yash

Re: [Freesurfer] Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?

You should be able to use it to generate histograms of > each parcel in 5-10 lines of matlab code > > cheers > Bruce > > > On Wed, 22 Aug 2018, Yash Patel wrote: > > >> External Email - Use Caution >> >> >> Hi FS experts, >> >>

Re: [Freesurfer] Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?

wrote: > Hi Yash > > try something like: > > seg = MRIread('aparc+aseg.mgz'); > norm = MRIread('norm.mgz'); > ind = find(seg.vol == 1002); > segmode = mode(norm.vol(ind)) > > > cheers > Bruce > > On Wed, 22 Aug 2018, Yash Patel wrote:

[Freesurfer] Mapping labels from left hemisphere to right hemisphere in fsaverage space

External Email - Use Caution Hi all, I have manually drawn roi onto fsaverage space on the left hemisphere. Is there a way to transfer these labels to the right? The end goal is to extract cortical measures from labels in both hemispheres and then will be averaged for further an

[Freesurfer] Working with cortical surface area - parcellation size?

External Email - Use Caution Hi Freesurfer colleagues, I want to analyze regional profiles of differences in cortical surface area (SA). However, SA and its group differences in SA depend on parcellation size. In order to mitigate this effect, should I create a parcellation that

Re: [Freesurfer] Visualization of data

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