Hi
I am getting segmentation fault error after creating the WM_FODs and also a warning “Diffusion encoding of input file does not match number of image volumes; omitting gradient information from output image” while performing mrconvert WM_FODs.mif … and then "segmentation fault " in mrview WM_FODs.mif and in “tckgen WM_FODs.mif 1M.tck -act TT.mif -backtrack -crop_at_gmwmi -seed_dynamic WM_FODs.mif -maxlength 250 -number 1M -cutoff 0.06”.
I have also put the mrinfo of WM_FODs,mif. But I am not be able to interpret what is causing the error “segmentation fault”.
I have done these steps before with same set of HCP data (subject 100307) and it was successful. Now only thing which is different is ubuntu 16. 04, does that cause anything?
The commands execution snippet:
DQ77MK:~/HCP_Data/2016-09-20/100307$ dwi2fod msmt_csd DWI.mif RF_WM.txt WM_FODs.mif RF_GM.txt GM.mif RF_CSF.txt CSF.mif -mask nodif_brain_mask.nii.gz
dwi2fod: [100%] uncompressing image "nodif_brain_mask.nii.gz"
dwi2fod: [100%] performing multi-shell, multi-tissue CSD
DQ77MK:~/HCP_Data/2016-09-20/100307$ mrconvert WM_FODs.mif - -coord 3 0 | mrcat CSF.mif GM.mif - tissueRGB.mif -axis 3
mrconvert: [WARNING] Diffusion encoding of input file does not match number of image volumes; omitting gradient information from output image
mrconvert: [100%] copying from “WM_FODs.mif” to "/tmp/mrtrix-tmp-vQLG1q.mif"
mrcat: [100%] concatenating "CSF.mif"
mrcat: [100%] concatenating "GM.mif"
mrcat: [100%] concatenating "/tmp/mrtrix-tmp-vQLG1q.mif"
DQ77MK:~/HCP_Data/2016-09-20/100307$ mrview tissueRGB.mif -odf.load_sh WM_FODs.mif
Segmentation fault (core dumped)
DQ77MK:~/HCP_Data/2016-09-20/100307$ tckgen WM_FODs.mif 1M.tck -act 5TT.mif -backtrack -crop_at_gmwmi -seed_dynamic WM_FODs.mif -maxlength 250 -number 1M -cutoff 0.06
tckgen: [100%] resampling ACT 5TT image to fixel image space
tckgen: [100%] segmenting FODs
Segmentation fault (core dumped)
DQ77MK:~/HCP_Data/2016-09-20/100307$ mrinfo WM_FODs.mif
Image: “WM_FODs.mif”
Dimensions: 145 x 174 x 145 x 45
Voxel size: 1.25 x 1.25 x 1.25 x 1
Data strides: [ -2 3 4 1 ]
Format: MRtrix
Data type: 32 bit float (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 1 0 0 -90
-0 1 0 -126
-0 0 1 -72
comments: FSL5.0
dw_scheme: [ 288 entries ]
mrtrix_version: 0.3.15-266-g2bf78387