Did you try specifying your xformed file as the argument to --cached-in ?
If that does not work, then transform the thickness in the native
surface,then run mris_preproc, then smooth with mris_fwhm
On 5/12/2020 11:37 PM, Xiaojiang Yang wrote:
External Email - Use Caution
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
Douglas N. Greve
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N.+Greve%22>Mon,
11 May 2020 14:14:42 -0700
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20200511>
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 losethe convenience of using mri_glmfit, whicheventually
loses the convenience of using mri-glmfit-sim (I don't carenot
usingmri_glmfit, but I want to use mri_glmfit-sim to do
multiplecomparisonscorrection). That is because mri_glmfit uses the
preparedoutput from mris_preproc, which I have no control over to use
thetransformed subject. The only way I can circumvent this is to use
mytransformed thickness file to overwrite the FS calculated
thicknessfile, but that is what I am hesitant to do. If you have
goodsuggestions regardingthis, 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>> 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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