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Hi Douglas,
I have tried to follow your suggestion to use the transformed thickness file
like this:
mris_preproc --fsgd xxx.fsgd \
--meas $meas.fwhm$smoothing.xformed.mgz \
--target fsaverage \
--hemi $hemi \
--out $hemi.$meas.$smoothing.mgh
But it says $meas.fwhm$smoothing.xformed.mgz does not match surface
(163842,166904).
My files $meas.fwhm$smoothing.xformed.mgz come from
$meas.fwhm$smoothing.fsaverage (just by multiplying it with a weight). If I
use "--cache-in" in the mris_preproc like below:
mris_preproc --fsgd xxx.fsgd \
--cache-in $meas.fwhm$smoothing.fsaverage \
--target fsaverage \
--hemi $hemi \
--out $hemi.$meas.$smoothing.mgh
The above command line runs fine.
I know the problem in the first command line might be that the files
$meas.fwhm$smoothing.xformed.mgz are already on the fsaverage surface, not
the subject surface. But mris_preproc is still trying to use mri_surf2surf
to resample those mgh file from the subject surface to fsaverage surface,
which leads to the "does not match surface" error.
My question is: How can I tell mris_preproc to regard those transformed
files to be on the fsaverage surface already (instead of subject's surface),
just like the second command line where the "-cache-in" option is used?
You know, my transformed files are Just derived from cached files
$hemi.$meas.fwhm$smoothing.fsaverage.mgh in the $subject/surf directories. I
do not want to use mri_surf2surf to transform them to the subject surface
first, and then let mris_preproc transform them back to fsaverage surface
again.
Thanks!
Xiao
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from
:%22Douglas+N.+Greve%22>
Douglas N. Greve
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date
:20200511> Mon, 11 May 2020 14:14:42 -0700
Just call your thickness file some other name, eg, lh.xformed.thickness.mgz,
the just specify --meas xformed.thickness.mgz
On 5/11/2020 3:52 PM, Xiaojiang Yang wrote:
External Email - Use Caution
Thank you Douglas!
If I apply my transform to both the healthy controls and the patient, I
guess I would lose the convenience of using mri_glmfit, which eventually
loses the convenience of using mri-glmfit-sim (I don't care not using
mri_glmfit, but I want to use mri_glmfit-sim to do multiple comparisons
correction). That is because mri_glmfit uses the prepared output from
mris_preproc, which I have no control over to use the transformed subject.
The only way I can circumvent this is to use my transformed thickness file
to overwrite the FS calculated thickness file, but that is what I am
hesitant to do. If you have good suggestions regarding this, please let me
know. Thanks!
Xiao
On Mon, May 11, 2020 at 12:25 PM Douglas N. Greve <dgr...@mgh.harvard.edu <
<mailto:dgr...@mgh.harvard.edu> mailto:dgr...@mgh.harvard.edu>> wrote:
I guess you could apply your transform to both the healthy
controls and to your patient, can then create an FSGD file with
two classes as before but no continuous variable. Then just have a
contrast that computes the diff between the patient and the mean
of the controls.
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