Hi Salma,

I think mri_surf2surf was complaining /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/label/lh.glasser.annot. Can you check if the file exists?

The reason for “ERROR: could not determine type of lh.orig” is that mri_info doesn’t handle surface file.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Salma Salhi
Sent: Sunday, May 22, 2022 10:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_surf2surf error: No such file or directory (but file exists)

        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 (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://osf.io/pm9ba/) 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