Dear all,
I am trying to convert 4D volume time series to GIFTI surface time series.
Following the instructions given in a previous post, so far, I have tried
using mri_vol2surf and mris_convert, with no success (i.e. when I try to
open the surface file in freeview I get Failed to load Surface
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_time_series_white_lh.gi
i). I would really appreciate if anyone could give me an advise on how to
make it work. I give below the logs of each process.
Thank you,
Prokopis
osboxes@osboxes:~$ mri_vol2surf --mov
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet.
feat/filtered_func_data.nii --reg
$SUBJECTS_DIR/AL_subject/AL_registrations/AL.mat --hemi lh --o
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_surface_time_series_lh.
mgh --projfrac 0.5 --interp nearest
srcvol =
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet.
feat/filtered_func_data.nii
srcreg =
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_test//AL_subject/AL_registratio
ns/AL.mat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Reading surface
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_test//AL_subject/AL/surf/lh.whi
te
Done reading source surface
Reading thickness
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_test//AL_subject/AL/surf/lh.thi
ckness
Done
Mapping Source Volume onto Source Subject Surface
1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 11976
Writing to
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_surface_time_series_lh.
mgh
Dim: 139848 1 1
osboxes@osboxes:~$ mri_info
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_surface_time_series_lh.
mgh
Volume information for
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_surface_time_series_lh.
mgh
type: MGH
dimensions: 139848 x 1 x 1 x 400
voxel sizes: 1., 1., 1.
type: FLOAT (3)
fov: 139848.000
dof: 0
xstart: -69924.0, xend: 69924.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.5
TR: 3000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 400
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = -1., y_r = 0., z_r = 0., c_r =
-3.2031
: x_a = 0., y_a = 1., z_a = 0., c_a =
3.2031
: x_s = 0., y_s = 0., z_s = 1., c_s =
72.
talairach xfm :
Orientation : LAS
Primary Slice Direction: axial
voxel to ras transform:
-1. 0. 0. 69920.7969
0. 1. 0. 2.7031
0. 0. 1.71.5000
0. 0. 0. 1.
voxel-to-ras determinant -1
ras to voxel transform:
-1. 0. 0. 69920.7969
-0. 1. -0.-2.7031
-0. -0. 1. -71.5000
0. 0. 0. 1.
osboxes@osboxes:~$ mris_convert -f
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_surface_time_series_lh.
mgh $SUBJECTS_DIR/AL_subject/AL/surf/lh.white
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_time_series_white_lh.gi
i
freeview log:
osboxes@osboxes:~$ mriseadGIFTIfile: mris is NULL! found when parsing file
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_time_series_white_lh.gi
i
MRISread failed
mriseadGIFTIfile: mris is NULL! found when parsing file
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_time_series_white_lh.gi
i
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