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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 $d --hemi lh --out lh.surfreg.teenheart_average_template.thickness.mgh --meas thickness done
ERROR: cannot find fsaverage in /media/m-ssd5/FS7_Teen ERROR: cannot find fsaverage in /media/m-ssd5/FS7_Teen ERROR: cannot find fsaverage in /media/m-ssd5/FS7_Teen ...
Do we need the fsaverage folder when creating a custom template? There is for example, lh.fsaverage.sphere.reg file in addition to sphere.reg.teenheart_average_template.
The previous error was ; ERORR: format for lh.surfreg.teenheart_average_template.thickness not recognized. This time, the problem seems to lie in not having fsaverage folder, rather than the format for the thickness template?
Any input is appreciated.
Best, Asuka ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU> Sent: 26 February 2024 18:22 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Creating a custom registration template with FreeSurfer template
You need to specify a format for the output (eg, ...thickness.mgz) On 2/26/2024 10:31 AM, Asuka Toyofuku wrote:
External Email - Use Caution Hi, many thanks for your reply. Here's the terminal output;
asuka@rigi:/media/.../FS7_Teen$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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Sent: 23 February 2024 19:30 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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 behttps://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%2FSurfaceRegAndTemplatesMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplateshttps://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 behttps://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%2FGroupAnalysisMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysishttps://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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