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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