Mishkin,

You can view the contents of the file with this command:

mris_convert -c ./lh.thickness.fsaverage.mgh \ $SUBJECTS_DIR/fsaverage/surf/lh.white \ lh.thickness.fsaverage.asc

which creates an ascii file listing the thickness value at each vertex, where the vertex number is the first number on the line in the ascii file, then next three numbers are the x,y,z coords of the white surface (pial if the second arg is lh.pial), and the last number is thickness. The .mgh file is just encoding surface data in a 'volume' format for convenience.

Nick

On Wed, 2008-10-08 at 15:25 -0400, Mishkin Derakhshan wrote:

Thanks.

Just as a follow up. What is the format of lh.thickness.fsaverage.mgh? Is this how I would view the entire contents of it:

mri_convert --ascii lh.thickness.fsaverage.mgh lh.thickness.fsaverage.mgh.asc

And am I right in assuming that the contents of this file, are my thickness stats of my subject, after being aligned to fsaverage space, and that each line is in the correct order that corresponds to each vertex in fsaverage/surf/lh.{pial,white} ?

mishkin

On Tue, Oct 7, 2008 at 7:36 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:

...

Mishkin,

Yes, mris_preproc is a wrapper script that calls mris_vol2surf, mris_surf2surf and mri_concat. You can view mris_preproc in a text editor.

In answer to 2a, in this case tester2.1.mgh should be the same as lh.thickness.fsaverage.mgh. In answer to 2b, one file is always 'concatenated', as mris_preproc is used by the -qcache. In other usages of mris_preproc, it is possible to concatnate multiple files.

Nick

On Tue, 2008-10-07 at 17:16 -0400, Mishkin Derakhshan wrote:

...

Hi, I am trying to understand what happens when you run the recon-all -qcache command I noticed these three commands get run:

mris_preproc --s tester2 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh

mri_surf2surf --hemi lh --srcsubject tester2 --surfreg sphere.reg --sval /lab1/FreeSurfer/4.0.5/ms-mni/testing/tester2/surf/lh.thickness --sfmt curv --trgsubject fsaverage --tval ./tmp.mris_preproc.12176/tester2.1.mgh --noreshape

mri_concat ./tmp.mris_preproc.12176/tester2.1.mgh --o lh.thickness.fsaverage.mgh

My questions are:

1. Am I right to assume that the first command (mris_preproc) is just

a wrapper script that calls the 2nd and 3rd commands? 2a. In the case above, does the 3rd command (mri_concat) simply copy the contents of tester2.1.mgh into lh.thickness.fsaverage.mgh. 2b. Is there a case when mri_concat will actually concat more than one thing into lh.thickness.fsaverage.mgh?

thanks, mishkin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer