You need to specify a format for the output (eg, ...thickness.mgz)
On 2/26/2024 10:31 AM, Asuka Toyofuku wrote:
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Hi, many thanks for your reply.
Here's the terminal output;
asuka@rigi:/media/.../FS7_Teen$ for d in Teen* EPK* epk*
> do mris_preproc --surfreg sphere.reg.teenheart_average_template --s
$d --hemi lh --out lh.surfreg.teenheart_average_template.thickness
--meas thickness
> done
ERROR: format for lh.surfreg.teenheart_average_template.thickness not
recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not
recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not
recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not
recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not
recognized
....
Error continued so I stopped running at a certain point.
What do you think?
Best regards,
Asuka
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* 23 February 2024 19:30
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Creating a custom registration template
with FreeSurfer template
Can you include the full terminal output for one of the mris_preproc
commands that is failing?
On 2/22/2024 7:12 AM, Asuka Toyofuku wrote:
* External Email - Use Caution *
Dear Freesurfer experts,
I have issues with creating a custom registration template. (I'm
following this instruction: *MailScanner has detected a possible
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claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates
<https://secure-web.cisco.com/1_qfYxT5WNAR-lGRNh895Kl4pqE513hIRdGqZt0w-oDRR8NwLSUh8ataurmByizdN5-6NPpWldetuOVhBt0OSuQVw_fTGTUnlfnRy5cZOC8gQ6xkn-I0sETntn5X7pssvIBMvxipctrdnnR0sdsJ_SEe-szwdE6WbG2z6qSW6mRoR1O_TSBtVJN6id4aZVTo30KwQes1T6AeGXG7volizYQI0te7HhF9DiqFp19oym11wqmrG8OvtY5FBou3V7ihQabCPQZdP81Qr6NFvLvkDT-D9iLBlRl7VIvT9MFviOs55EDcMS1LivQnETY_fTpuV_tnuLQHAkyphGLkrH_xwYA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates>
)
According to the instructions, we need to
1) Create an average subject (Creates $SUBJECTS_DIR/newtemplate)
2) Register each subject to the new template (do for both lh and
rh), resulting in lh.sphere.reg.newtemplate and
rh.sphere.reg.newtemplate
3) Get thickness values in the newtemplate space for GLM analysis
4) Create another average template based on the previous one:
(Creates $SUBJECTS_DIR/newnewtemplate)
I'm stuck with the 3) command.
Instruction suggests:
mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2
--s subj3 ...
and this is my code:
for d in Teen*
do mris_preproc --surfreg sphere.reg.teenheart_average_template
--s $d --hemi lh --out
lh.surfreg.teenheart_average_template.thickness --meas thickness
done
( I specified hemi and output because, without it, I got ERROR: no
source hemi specified)
My command led to an error saying:
ERROR: format for lh.surfreg.teenheart_average_template.thickness
not recognized
So my questions are:
a) what does it mean that "format for
lh.surfreg.average_template.thickness not recognised"? Any ideas
on how to fix this?
b) Does this mris_preproc --surfreg command produce different
smoothing mgh files? (e.g., fwhm10, fwhm15, fwhm20...?)
Because standard mris_preproc before GLM analysis(*MailScanner has
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are done with previously qcashed data (e.g., need
thickness.fwhm10.fsaverage to run mris_preproc), but at this
point, I don't have any of these thickness files with different
smoothing levels.
c ) If this mris_preproc --surfreg command does not generate a set
of thickness maps in **newtemplate space** at different smoothing
levels, what kind of command should I run?
Any input is appreciated!
Best regards,
Asuka
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