External Email - Use Caution Hello FreeSurfer Developers,
I am trying to run the mri_surf2surf command as shown in this MRtrix tutorial on page 35 (https://secure-web.cisco.com/1IRfOd9DbtoZ73ePUy1kNxDjehQaayodvb_Pq3LttY1M2YqbKQhQ1UWIVGQmivIOeHqfZlJkiIPiENR9fGdSkObi00qtpoSZ8Jm9wwwQnxRhQm6hmGs6MvMportB8LLrr13nsIVJlGNgmDmVt2i_k6NqxieH97jsKyaWkKiulCv5J5ZWicVbSHhRfriTWUMfd88okHhuEhZqcDvEV0Hjlj2dOCZkdDjAYskYfmLgKCfunXsyywJZzs5SXHSYMHohUoO6chopWkH8GfYpBIEEGnVOaE9SeVAYRJWq1-wdIYO-YuJdIiLvOpah94FyrtBHuRNt0RS9IJYxQp6dPlEh5pw/https%3A%2F%2Fosf.io%2Fpm9ba%2F) in order to map the annotation files of the HCP MMP 1.0 atlas. I keep running into a “No such file or directory” error when the code tries to read the “lh.orig” file, but the file is clearly in the required directory. Below is the output of my code: (base) salmasalhi@SalmasMacbookAir 100307_F26-30 % mri_surf2surf --srcsubject fsaverage --trgsubject subject_100307 --hemi lh --sval-annot $SUBJECTS_DIR/fsaverage/label/lh.glasser.annot --tval $SUBJECTS_DIR/subject_100307/label/lh.hcpmmp1.annot Setting mapmethod to nnf 7.2.0 setenv SUBJECTS_DIR /Users/salmasalhi/my_code/HumanBrain_v2/reconall cd /Users/salmasalhi/my_code/HumanBrain_v2/100307_F26-30 mri_surf2surf --srcsubject fsaverage --trgsubject subject_100307 --hemi lh --sval-annot /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/label/lh.glasser.annot --tval /Users/salmasalhi/my_code/HumanBrain_v2/reconall/subject_100307/label/lh.hcpmmp1.annot sysname Darwin hostname SalmasMacbookAir.local machine x86_64 user salmasalhi srcsubject = fsaverage srcval = (null) srctype = trgsubject = subject_100307 trgval = /Users/salmasalhi/my_code/HumanBrain_v2/reconall/subject_100307/label/lh.hcpmmp1.annot trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/surf/lh.sphere.reg Loading source data Reading surface file /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/surf/lh.orig error: No such file or directory error: could not read annot file /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/label/lh.glasser.annot If I cd into the surf directory and check the files, this is the output: (base) salmasalhi@SalmasMacbookAir surf % ls lh.area lh.sphere.reg rh.inflated_avg lh.avg_curv lh.sphere.reg.avg rh.inflated_pre lh.avg_sulc lh.sulc rh.orig lh.avg_thickness lh.thickness rh.orig.avg.area.mgh lh.cortex.patch.3d lh.white rh.orig_avg lh.cortex.patch.flat lh.white.avg.area.mgh rh.pial lh.curv lh.white_avg rh.pial.avg.area.mgh lh.fsaverage_sym.sphere.reg lh.white_avg.H rh.pial_avg lh.inflated lh.white_avg.K rh.pial_semi_inflated lh.inflated.H mris_preproc.surface.lh.log rh.smoothwm lh.inflated.K mris_preproc.surface.rh.log rh.sphere lh.inflated_avg rh.area rh.sphere.reg lh.inflated_pre rh.avg_curv rh.sphere.reg.avg lh.orig rh.avg_sulc rh.sulc lh.orig.avg.area.mgh rh.avg_thickness rh.thickness lh.orig_avg rh.cortex.patch.3d rh.white lh.pial rh.cortex.patch.flat rh.white.avg.area.mgh lh.pial.avg.area.mgh rh.curv rh.white_avg lh.pial_avg rh.fsaverage_sym.sphere.reg rh.white_avg.H lh.pial_semi_inflated rh.inflated rh.white_avg.K lh.smoothwm rh.inflated.H lh.sphere rh.inflated.K (base) salmasalhi@SalmasMacbookAir surf % pwd /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/surf The “lh.orig” file is clearly in the right place. I tried to check the format of the file by typing mri_info lh.orig but the output was “ERROR: could not determine type of lh.orig”. Below are more details about my setup: 1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0 2) Platform: macOS Monterey 12.3.1 (M1 chip) Thank you very much for your help, I greatly appreciate it. Salma Salhi
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