External Email - Use Caution
Dear Freesurfer experts,
I am currently trying to use mri_vol2surf on my bold data. I typed this
commandline :
"
mri_vol2surf --mov
${dir1}/${subject}/${subject}${scan}_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
\
--mni152reg \
--projfrac-avg 0.2 0.8 0.1 \
--trgsubject fsaverage5 \
--interp nearest \
--hemi ${hemi} \
--surf-fwhm 6.0 --cortex --noreshape \
--o ${dir1}/${subject}/${subject}${scan}.fsa5.${hemi}.mgz
"
However, when trying to run it, I obtain the following error: ERROR: could
not read .. as type 24
detail:
"
srcvol =
/mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
srcreg = /home/loic.daumail/freesurfer/average/mni152.register.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = fsaverage5
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
niiRead(): error opening file
/mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
ERROR: could not read
/mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
as type 24
"
but when converting from nii.gz to mgz, I obtain the following :
"
mri_convert
/mnt/data/loic2/embedding/recon_all_success/fmriprep/sub-002/func/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
/mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/mnt/data/loic2/embedding/recon_all_success/fmriprep/sub-002/func/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz...
niiRead(): error opening file
/mnt/data/loic2/embedding/recon_all_success/fmriprep/sub-002/func/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
srcvol =
/mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz
srcreg = /home/loic.daumail/freesurfer/average/mni152.register.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = fsaverage5
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
mghRead(/mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz,
-1): could not open file
ERROR: could not read
/mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz
as type 3
"
I also copied the output from mri_info on my bold image in .nii.gz format:
"
mri_info
sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
Volume information for
sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
type: nii
dimensions: 91 x 109 x 91 x 200
voxel sizes: 2.0000, 2.0000, 2.0000
type: FLOAT (3)
fov: 182.000
dof: 0
xstart: -91.0, xend: 91.0
ystart: -109.0, yend: 109.0
zstart: -91.0, zend: 91.0
TR: 3220.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
0.00 degrees
nframes: 200
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r =
0.5000
: x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a =
-17.5000
: x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s =
18.5000
Orientation : RAS
Primary Slice Direction: axial
voxel to ras transform:
2.0000 0.0000 0.0000 -90.5000
0.0000 2.0000 0.0000 -126.5000
0.0000 0.0000 2.0000 -72.5000
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 8
ras to voxel transform:
0.5000 -0.0000 -0.0000 45.2500
-0.0000 0.5000 -0.0000 63.2500
-0.0000 -0.0000 0.5000 36.2500
0.0000 0.0000 0.0000 1.0000
"
Thanks in advance for your help,
Sincerely,
Loïc Daumail
Université Lyon 1
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