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:
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Dear Freesurfer experts,
I have issues with creating a custom registration template. (I'm
following this instruction: *MailScanner has detected a possible fraud
attempt from "secure-web.cisco.com" 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
detected a possible fraud attempt from "secure-web.cisco.com" claiming
to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
<https://secure-web.cisco.com/1lH2n5girv1pSO3WmL3I9nDeL07oFU0ViiAmz_tUClrPQjFwGxFIj8Uw-HpRNXN4_ADUrXeK8GQcI91O76PQUoilqcBBTuz_cbBfg2BUYMoPChwgcqvL5jiL3mJuCIhROFLqmz6Ay1m-Mt3VqQfQiArWs7KPRzGvA7altNpSDzxPE8sB-_TlC3JKVV06-mzVggUwD3kS7BkRaXe1z174NmNbHyzHlcoUEX12pXebgZgGEv6bLiKxH2Wrka404J_vPCmOb8me-0QbLp1HJJdw_vbklt9SSNhdXnR2XCQ-vZeRZep_w5lp7gvo-TBU4Fdow4MtnGe-Oy6yM7OBUf0230w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis>)
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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