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:
External Email - Use Caution
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
