Dear Freesurfers,
I have problems converting .nii.gz files into .mgh files needed e.g. for
performing ROI analysis.
I used mri_vol2surf and mri_vol2vol to produce .mgh files either to visualize
contrast estimates and significance maps on volumes or surfaces
I think the problem is due to voxel resolution mismatches between source and
registration files but I don't know how to solve this problem.
I worked with different registration files: the register.dof6.dat (originally
outpu from the preproc-sess) as well as register.dat and register.lta by
running bbregister for the template.nii.gz
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here is an example command:
# resample to surface
mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg
$sub/bold/register.lta --projfrac 0.5 \
--interp nearest --hemi lh --o $sub/bold/lh.sig.mgh
mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg
$sub/bold/register.lta --projfrac 0.5 \
> --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh
srcvol = PM_04001/bold/EX.sm5.lh/EX/sig.nii.gz
srcreg = PM_04001/bold/register.lta
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
regio_read_register: loading lta
reading extra input line subject PM_04001
reading extra input line fscale 0.150000
WARNING: the voxel resolution in the source volume (1,1,1) differs
from that listed in the registration file (2.29167,2.29167,2.99)
Reading surface /home/christopher/subjects/PM_04001/surf/lh.white
Done reading source surface
Reading thickness /home/christopher/subjects/PM_04001/surf/lh.thickness
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 = 5
Writing to PM_04001/bold/lh.sig.mgh
Dim: 126553 1 1
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Thanks,
Christopher
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