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Hello,
I’m trying to reconstruct an old pipeline that I don’t completely understand
(so sorry if this is very elementary or out of date), and one step is to
convert the freesurfer T1 segmentation ribbon.mgz to .nii format using
mri_convert.
Through freesurfer interface I see the T1 and the segmentation are fine; but
mri_convert seems to fail on looking for the T1:
The command (from inside Matlab) is:
mri_convert --reslice_like
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt
nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz
/Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii
Output looks like:
mri_convert --reslice_like
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt
nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz
/Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii
reading from /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
reading template info from volume
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii...
error: niiRead(): error opening file
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii*****
It is failing to read the T1 and then it does not save the output file.
But the input files (T1.nii and ribbon.mgz) are all where they should be.
What could I be doing wrong?
thanks,
-Andrew
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