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
<[EMAIL PROTECTED]> 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
>> _______________________________________________
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>>
>>
>
>
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