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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_Pq3LttY1M2Yq...) 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