[Freesurfer] how to read/import .m3z warp files

Dear FreeSurfer, I am trying to visualize and compare multiple subjects from the mri_cvs_registration. Therefore I need to work with the .m3z file. Is there a way to read this file format in python or is there a way to convert it into an other file format ? There are just a few information on

Re: [Freesurfer] how to read/import .m3z warp files

Hi Daniel I don't know if there is a python converter, but you can do: mri_convert file.m3z file.mgz or mri_convert file.m3z file.nii.gz and it will convert it to a 3-frame volume with the dense vector field. You lose information that way though about source and target geometry and such chee

Re: [Freesurfer] computing euler number error

Hi Amanda can you check to make sure you haven't run out of disk space? mris_euler_number does very little except read the surface and report some arithmetic on it. I would use -make all to restart, but you will need a patch as this feature had a bug in 6.0. I think Andrew posted it a week or

Re: [Freesurfer] how to read/import .m3z warp files

Dear Bruce, the loss of information about the source and target geometry is not tolerable. I found similar request (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-February/049834.html). There is an matlab script, which is able to read the .m3z files. Lilla Zollei replied the scr

[Freesurfer] hemisphere analysis

Dear experts, I have two questions about hemisphere analysis: 1) When I run left-right hemisphere paired t-test, can I add age as covariate? If use fsgd to add covariate, to this paired t-test analysis, how to make the fsgd table? 2) I want to reorganize the hemisphere from left-right to symptom-

[Freesurfer] surface based fMRI gorup analysis from spm

Dear Freesurfer users, I would like to perform surface based fMRI gorup analysis in Freesurfer starting from SPM first level output files, but I am not succeding. I have already preprocessed the data in spm and used Freesurfer for boundary based registration, I have succesfully ran the recon -all

Re: [Freesurfer] mask volume calculation

Thanks Bruce Thanks Doug that was a great help. I was able to run it as you mentioned. I also tried to see if I can get the same values as aseg.stats file that you mentioned. I created a binarized mask from aseg.mgz for a structure and ran the same command. However, the values that I get are a lit

Re: [Freesurfer] surface based fMRI gorup analysis from spm

Use --target fsaverage instead of giving the full path On 11/06/2017 01:27 PM, Elisa Castaldi wrote: > Dear Freesurfer users, > > I would like to perform surface based fMRI gorup analysis in > Freesurfer starting from SPM first level output files, but I am not > succeding. > I have already pr

Re: [Freesurfer] Trans. : VBM question

Hi Mohamed, please remember to post to the list. As for your question, what aparc files are you looking at? Those measures are in, eg, lh.aparc.stats On 11/06/2017 04:05 AM, Mohamed Ali Bahri wrote: > > Dear Douglas, > > Many thanks for your answer! > > We are interested on one region belonging

Re: [Freesurfer] hemisphere analysis

On 11/06/2017 12:03 PM, lanbo Wang wrote: > Dear experts, > > I have two questions about hemisphere analysis: > > 1) When I run left-right hemisphere paired t-test, can I add age as > covariate? If use fsgd to add covariate, to this paired t-test > analysis, how to make the fsgd table? use this

Re: [Freesurfer] hemisphere analysis

Dear FDs, I encountered an odd situation: My free surfer will always shut down when I run command. My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel Core i5 I don’t know if the compatibility is fine with my download version (MacOS Lion OS X 10.7 (64b intel)Stable v6.0.0) Please ki