Re: [Freesurfer] Get Atlas surfaces in subject space

External Email - Use Caution I don't see how it's possible I got a comparable list of points when the input was in the order of 300k verts, and the ouput was 180k verts - I would need the number of output verts to be exactly the same as the number of input verts. On 07/05/2020

[Freesurfer] tracula stats summary

External Email - Use Caution Hi, Is it possible to collect all 18 tracts stats into a single file? Has tried: "tractstats2table --load-pathstats-from-file paths.txt --overall --tablefile tractAll.txt" Path.txt contains all the subjects' 18 paths' full path directory Error message:

[Freesurfer] Hippocampal subfield tool for 6.0.0 data

External Email - Use Caution Hello, Would you be able to point me to the right version of the hippocampal subfield tool as described here: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala? The data have been processed in 6.0.0, but the stable p

Re: [Freesurfer] flirt.fsl error (NEWMAT::SingularException) when running bbregister in Freesurfer 7.0.0

External Email - Use Caution Hi Andrew, Thanks for looking into this. Yes, copying the binary from the v6 to the v7 installation does solve the issue. Julien ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nm

Re: [Freesurfer] Hippocampal subfield tool for 6.0.0 data

If you look at that page, you will find installation instructions On 5/8/2020 10:37 AM, O'Shea,Andrew wrote: External Email - Use Caution Hello, Would you be able to point me to the right version of the hippocampal subfield tool as described here: https://surfer.nmr.mgh.harvard.edu/

Re: [Freesurfer] tracula stats summary

If you're not happy with the output of tractstats2table and want something custom, you can just do a search in the stats files. They're simple text files. You can see how these files are named and what their contents look like here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStat

Re: [Freesurfer] tracula stats summary

External Email - Use Caution Already Solved. Thank you so much! Best, Qi On Fri, May 8, 2020 at 10:46 AM Yendiki, Anastasia wrote: > If you're not happy with the output of tractstats2table and want something > custom, you can just do a search in the stats files. They're simple

[Freesurfer] Parcellation of files containing within subject summary measures

External Email - Use Caution Dear experts, I calculated vertex-wise standard deviation across multiple thickness (lh.thickness.fwhm10.fsaverage.mgh) and volume files (lh.volume.fwhm10.fsaverage.mgh) of one individual,calculated from scans at different time points. I used the f

Re: [Freesurfer] Parcellation of files containing within subject summary measures

You can use mri_segstats. Run it with --help and modify example 6 On 5/8/2020 12:18 PM, Martin Gell wrote: External Email - Use Caution Dear experts, I calculated vertex-wise standard deviation across multiple thickness (lh.thickness.fwhm10.fsaverage.mgh) and volume files (lh.volume

[Freesurfer] averaging timecourses

Hi Freesurfer experts I have extracted the time course of a task fMRI data in a specific contrast and within a specific ROI, in 7 subjects. Consider my specific ROI has 1200 voxels and I extracted the time course for a duration of 5 TRs. After extracting the timecourse, I have a matrix of 1200x

[Freesurfer] segmentHA_T1.sh outputs "Error using myMRIread (line 16)"

External Email - Use Caution Hello. I am testing freesurfer 7.0.0 with segmentHA processing. I've run recon-all successfully, and now I am trying to run "segmentHA_T1.sh". When I do, it generates the following error message. $ segmentHA_T1.sh output . > --