I'm trying to average multi-subject tractographies (with sample data from fdt1/tbss directory), but am having trouble getting the required steps to execute probtracx. I continue to be truly grateful for all your help and want to make this work. Thanks a lot again!
Questions I have so far:
1) The link I have referred for probtracx which is : http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide suggested running dtifit, and then bedpostx which would generate the files required for probtracx. bedpostx seems to require data directory, bvecs and bval. But I am using .nii files and don't have bvals and bvec. I understand that those files get generated when I convert .dcm using dcm2nii tool, but I already have .nii files. I am unable to proceed without bvals and bvec. a) I tried copying bval and bvec from the samples directory just to unblock, but not sure if that's the right thing to do. b) Should I copy nodif_brain_mask from fdt1/subj1 directory? Should I generate this on my own and if so how? b) bedpostx still looks for data dir and even if I rename the FA directory as data dir, it doesn't seem to find the data dir. The steps (below) that I used generated FA, origdir and stats dir but not data dir which bedpostx seems to be expecting.
2) Got failure in Linear Registration via FEAT in GUI. (Details below)
Below are the steps I have executed so far :
1) Eddy correction via the GUI, which generated _ecc file
2) BET via the GUI, which generated _brain file
3) Pre-processing:
a) tbss_1_preproc *.nii.gz
b) tbss_2_reg -T
c) tbss_3_postreg -S
d) tbss_4_prestats 0.2
I see the FA, stats and origdir sub directories.
4) Invoked FEAT from the GUI for non-linear registration and entered the following info.
a) Data tab: Specified input data as 1260_FA. Got message: " Input has a TR of 1: If the data was generated with an older MRI sequence, this may be incorrect and need to be fixed in the header"
b) Registration tab: Selected non-linear. Entered 1260_FA_brain for non-structural image.
c) Got the following error on hitting Go:
"Problem with processing the model: libc+ +abi.dylib: terminating the uncaught exception of type NEWMAT::IndexException.
Kindly advice what I may be missing and how to proceed. Thanks a lot!
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