Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

If you've already run qcache, then it will be in the subject/surf folder with a name like lh.thickness.fsaverage.fwhm10.mgz On 2/6/18 11:22 PM, 박경일 wrote: Thanks, Bruce. From that, I got thickness data (vertex#, location x/y/z, thickness value). But, amount and location of vertex are

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

Thanks, Bruce. >From that, I got thickness data (vertex#, location x/y/z, thickness value). But, amount and location of vertex are different among subjects. As far as i understand, it is the subject space, not common space. is that right? If so, how can i get the thickness values in common space

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

Hi Kyung you should look at the mris_convert help. It has an example of how to convert a scalar overlay like a curv file to ascii: Convert a scalar overlay file to ascii: mris_convert -c lh.thickness lh.white lh.thickness.asc it needs the surface as an input to do the conversion

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

Hi Bruce I found a directory having a file with ".curv", open terminal and run following command. [root@localhost surf]# mris_convert rh.curv rh.curv.asc nquads=4587523, nvertices=476 ERROR: MRISread: file 'rh.curv' has many more faces than vertices! Probably trying to use a scalar data file as

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

Hi Kyung the thickness values are stored as "curvature" file format that you can load into matlab with read_curv.m. Alternatively, you can convert them to ascii with mris_convert and do what you want with them. For each index, you can look up its location on the white or pial (or whatever

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

Hi Bruce, I am very new for FS, so did not understand you comments completely. sorry.. For cortical thickness from each vertex in one subject, which scripts should follow "mris_convert"? And another question is how to recognize the location of each vertex in brain finally. thank you so much

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

p.s. if you want the vertices to correspond, first run recon-all -qcache for each subject. That will generate a set of thickness maps in fsaverage space at predefined smoothing levels (so that the vertex numbers correspond across subjects) On Mon, 13 Nov 2017, 박경일 wrote: Hi Bruce,What I

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

yes. You can use mris_convert to make an ascii file, or read_curv.m to read them into matlab. cheers Bruce On Mon, 13 Nov 2017, 박경일 wrote: Hi Bruce,What I want is the values of cortical thickness in each vertex in each subject. Is that possible? Thanks so much. Kyung   2017-11-13 0:43

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

Hi Bruce, What I want is the values of cortical thickness in each vertex in each subject. Is that possible? Thanks so much. Kyung 2017-11-13 0:43 GMT+09:00 Bruce Fischl : > Hi Kyung > > you can load them into matlab or convert them to ascii if you want > Bruce > >

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

Hi Kyung you can load them into matlab or convert them to ascii if you want Bruce On Sun, 12 Nov 2017, 박경일 wrote: Dear FS experts, I could get QDEC image comparing two groups. However, is there a way to get numerical values of cortical thickness in each vertex? Thank you Best, Kyung