It looks like if you don't specify a subject (--target subject) as common
space, it will default to 'fsaverage'. See
https://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc
The input to -surfreg <> is the surface registration to the common space. I
think it should be a surface file not in .mgh format.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Asuka Toyofuku
Sent: Wednesday, February 28, 2024 8:07 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Creating a custom registration template with
FreeSurfer template
External Email - Use Caution
Hi, thanks for your suggestion.
I added .mgh at the end of the input and output file, but I got a different
type of error.
for d in Teen*
> do mris_preproc --surfreg sphere.reg.teenheart_average_template.mgh --s $d
> --hemi lh --out lh.surfreg.teenheart_average_template.thickness.mgh --meas
> thickness
> done
ERROR: cannot find fsaverage in /media/m-ssd5/FS7_Teen
ERROR: cannot find fsaverage in /media/m-ssd5/FS7_Teen
ERROR: cannot find fsaverage in /media/m-ssd5/FS7_Teen
...
Do we need the fsaverage folder when creating a custom template?
There is for example, lh.fsaverage.sphere.reg file in addition to
sphere.reg.teenheart_average_template.
The previous error was ; ERORR: format for
lh.surfreg.teenheart_average_template.thickness not recognized.
This time, the problem seems to lie in not having fsaverage folder, rather than
the format for the thickness template?
Any input is appreciated.
Best,
Asuka
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>
Sent: 26 February 2024 18:22
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Creating a custom registration template with
FreeSurfer template
You need to specify a format for the output (eg, ...thickness.mgz)
On 2/26/2024 10:31 AM, Asuka Toyofuku wrote:
External Email - Use Caution
Hi, many thanks for your reply.
Here's the terminal output;
asuka@rigi:/media/.../FS7_Teen$<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: 23 February 2024 19:30
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto: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 fraud attempt from
"secure-web.cisco.com" claiming to
be<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>MailScanner
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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://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>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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