External Email - Use Caution
Dear Doug Greve,
Sorry, issue solved!
I had used a wrong path directory in the commandline... it’s now working
perfectly well.
Thanks for your help,
Sincerely,
Loïc Daumail
Le mer. 17 avr. 2019 à 17:25, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :
> can you send the full terminal output of the mri_surf2vol command?
>
> On 4/17/19 5:59 AM, Loïc Daumail wrote:
> >
> > 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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>
>
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