Dear FSL experts,
I am trying to run probtrackx2, with the following syntax:
probtrackx2 --seed=${subrois}/${sub}_ListofSeeds.txt --omatrix1 --samples=${subject}/merged --mask=${subject}/nodif_brain_mask --nsamples=50 --pd --forcedir --dir=${outdir}/${sub}
I however encounter the error:
Running in network mode
load seeds
error: inv(): matrix appears to be singular
libc++abi.dylib: terminating with uncaught exception of type std::runtime_error: inv(): matrix appears to be singular
Abort trap: 6
I already addressed this problem in another thread and I still haven't a solution, so I thought I would provide more details on my pipeline hoping for some advice/ideas on where this error might originate from.
Because my data does not have a field map nor reversed phase encoding, I registered the first b0 volume to each subject's T1 image to correct for EPI-induced distortions. I then applied the transform to all volumes of the DWI data.
I used this data (i.e. diffusion now in T1 space) as input for bedpostx, the output of which is then used in my probtrackx2 command.
As for my seeds, I registered each subject's T1 to MNI and I then used the inverse transform to warp the ROIs from standard to T1 space, all of which are listed per subject in the ${sub}_ListofSeeds.txt.
Of note, I performed all these registration steps in ANTs.
I now wonder whether something is wrong because my diffusion data is in T1 space? Do I need to input any kind of transform in my probtrackx2?
I am quite lost in this, so any help would be greatly appreciated!
Thanks in advance
Best,
Samantha
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