Hi,
I’m still trying to follow this tutorial : http://userdocs.mrtrix.org/en/latest/tutorials/hcp_connectome.html
I had first problems with 5ttgen but that has been solved (for more details see 5ttgen).
I was next able to run all subsequent “Structural image processing” steps.
Regarding, the “Diffusion image processing” steps, I encountered a problem at the first step :
$ mrconvert data.nii.gz DWI.mif -fslgrad bvecs bvals -datatype float32 -stride 0,0,0,1
mrconvert: [100%] uncompressing image "data.nii.gz"
mrconvert: [ERROR] error allocating memory to hold mmap buffer contents
Does that mean I don’t have enough memory on my computer (8GB) for a file data.nii.gz of 1.2GB. If yes, is there anyway I can split the data in order to do the conversion on smaller portions ?
Interestingly, in spite of this error, the file DWI.mif has been generated (but I don’t know if it is corrupted or not).
Anyway, I proceeded up to step 3, where I got the following error :
$ dwi2response msmt_5tt DWI.mif 5TT.mif RF_GM.txt RF_WM.txt RF_CSF.txt -voxels RF_voxels.mif
dwi2response:
dwi2response: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
dwi2response:
dwi2response: Generated temporary directory: /tmp/dwi2response-tmp-8YI12J/
Command: mrconvert 5TT.mif /tmp/dwi2response-tmp-8YI12J/5tt.mif -quiet
Command: mrconvert DWI.mif /tmp/dwi2response-tmp-8YI12J/dwi.mif -stride 0,0,0,1 -quiet
dwi2response: Changing to temporary directory (/tmp/dwi2response-tmp-8YI12J/)
Command: dwi2mask dwi.mif mask.mif -quiet
Command: dwi2tensor dwi.mif - -mask mask.mif -quiet | tensor2metric - -fa fa.mif -vector vector.mif -quiet
Command: mrtransform 5tt.mif 5tt_regrid.mif -template fa.mif -interp linear -quiet
Command: mrconvert 5tt_regrid.mif - -coord 3 0 -axes 0,1,2 -quiet | mrcalc - 0.95 -gt fa.mif 0.2 -lt -mult mask.mif -mult gm_mask.mif -quiet
Command: mrconvert 5tt_regrid.mif - -coord 3 2 -axes 0,1,2 -quiet | mrcalc - 0.95 -gt mask.mif -mult wm_mask.mif -quiet
Command: mrconvert 5tt_regrid.mif - -coord 3 3 -axes 0,1,2 -quiet | mrcalc - 0.95 -gt fa.mif 0.2 -lt -mult mask.mif -mult csf_mask.mif -quiet
dwi2response: Calling dwi2response recursively to select WM single-fibre voxels using 'tournier' algorithm
Command: dwi2response -quiet tournier dwi.mif wm_ss_response.txt -mask wm_mask.mif -voxels wm_sf_mask.mif
fixel2voxel: [ERROR] fixel image is empty
dwi2response: [ERROR] Command failed: fixel2voxel iter0_peaks.msf split_value iter0_amps.mif -quiet
dwi2response: [ERROR] Command failed: dwi2response -quiet tournier dwi.mif wm_ss_response.txt -mask wm_mask.mif -voxels wm_sf_mask.mif
dwi2response: Changing back to original directory (/home/cdeledal/brainware/hcp/structural_connectome)
dwi2response: Deleting temporary directory /tmp/dwi2response-tmp-8YI12J/
Thanks for your help,
Cheers
Charles