External Email - Use Caution Dear Freesurfer experts,
I have issues with creating a custom registration template. (I'm following this instruction: 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(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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