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:
- 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