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: 1.0000, 1.0000, 1.0000
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 = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -3.2031
: x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 3.2031
: x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 72.0000
talairach xfm :
Orientation : LAS
Primary Slice Direction: axial
voxel to ras transform:
-1.0000 0.0000 0.0000 69920.7969
0.0000 1.0000 0.0000 2.7031
0.0000 0.0000 1.0000 71.5000
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 0.0000 0.0000 69920.7969
-0.0000 1.0000 -0.0000 -2.7031
-0.0000 -0.0000 1.0000 -71.5000
0.0000 0.0000 0.0000 1.0000
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