Can you confirm that /subjects/CI_01/mri/orig.mgz exists? Usually, your SUBJECTS_DIR would not be directly in root, especially on a mac, but it is not impossible.
On 10/14/2022 7:17 AM, Wandschneider, Britta wrote:
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Hello,
I am trying to map tumour+oedema lesion masks (generated with ITKSnap) to subjects' freesurfer surface (in native space) using mri_vol2surf.
This is an example of the command I am using for a specific subject:
mri_vol2surf --mov CI_01_t+oedema_corrected.nii\
--fwhm 0 \
--regheader CI_01 \
--hemi lh --surf pial \
--projdist-max 0 1 0.1 \
--interp trilinear\
--surfreg sphere.reg \
--icoorder 5 \
--out CI_01_t+oedema_corrected_lh.mgh
However, I get this error message:
IcoOrder = 5, nIcoVtxs = 10242
srcvol = CI_01_t+oedema_corrected.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = pial
hemi = lh
ProjDist = 0.5
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 1
INFO: float2int code = 0
INFO: this is an unsiged short. I'll try to read it, but
it might not work if there are values over 32k
INFO: using NIfTI-1 qform
INFO: changing type to float
Done loading volume
Computing registration from header.
Using /subjects/CI_01/mri/orig.mgz as target reference.
error: mghRead(/subjects/CI_01/mri/orig.mgz, -1): could not open file
klp32e:7.1.1 Britta$
I have tried the same command with a different freesurfer version (6.0.0), which lead to the same problem. The /mri/orig.mgz loads in freeview and looks fine to me. I searched the mailing list but have not found a post with this error being reported.
I am using version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 on MacOS Mojave version 10.14.6
I would be very grateful for any advice.
Best wishes Britta
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer