I am trying to run the mri_surf2surf command as shown in this BATMAN MRtrix tutorial on page 35 (OSF | BATMAN_tutorial_update2020.pdf) 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
However, when I check the
surf directory, the
lh.orig file is in fact inside that folder. 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.
Apologies if this is off topic; I know this is more of a FreeSurfer issue, but I haven’t yet heard back from the FreeSurfer forum so I was hoping someone here might be able to help.
Thank you very much,