MRtrix Team,
I’m facing a weird error while following the HCP Connectome Tutorial [http://mrtrix.readthedocs.io/en/latest/tutorials/hcp_connectome.html]
If I just copy and paste the tutorial everything works perfect, the streamlines are created and I can visualize them with fibernavigator/trackvis without problem.
The problem comes when I try to use a seed mask. Even if I try to use the whole white matter as seeds. More precisely, for the following code:
wb_command -volume-math “(w>=2)*(w<=2)+(w>=41)*(w<=41)+(w>199)*(w<301)” my_wmmask.nii.gz -var w wmparc.nii.gz
tckgen WM_FODs.mif -maxlength 250 -output_seeds used_seeds.txt -seed_image *my_wmmask.nii.gz’ -number 1000 ‘test.tck’
The output is:
tckgen: [ 100%] N generated, 0 selected
Where N is some big number. This also happens with the parameters:
-seed_grid_per_voxel my_wmmask.nii.gz 10
-seed_random_per_voxel my_wmmask.nii.gz 1000
But again, if I simply do:
tckgen WM_FODs.mif test.tck -seed_dynamic WM_FODs.mif -maxlength 250 -number 1000
This works perfectly, and all the streamlines are there, in the test.tck file.
Checked:
-
mrinfo WM_FODs.mif and mrinfo my_wmmask.nii.gz report the same Affine matrix (Transform).
-
mrview DWI.mif my_wmmask.nii.gz shows that the created wmmask and the DWI are well aligned.
- The white matter in my_wmmask.nii.gz corresponds well with the one in the file vis.mif.
- The error persists if I use -nthreads 0 or the Anatomically-Constrained Tractography options.
- The error persists if I transform the wmmask with mrconvert.
You’re making a great work with this toolkit, thanks!.
Best Regards,
Guillermo.
That’s indeed pretty odd… I just had a go with your commands on some data I have on my laptop, everything seems to work as it should…
A few things to check:
-
is this an up to date install?
-
is the intensity within the mask as reported by MRView greater than one (or at least, greater than 0.5)?
-
is your my_wmmask.nii.gz stored using an integer type? What happens if you convert to bitwise or uint8 type first, like this:
$ mrconvert my_wmmask.nii.gz -datatype bit my_wmmask.mif
and use that file in your tckgen command?
(you can use uint8 instead of bit, and also store in NIfTI if you want to, that should work fine).
-
what happens if you use the MRtrix3 equivalent command to generate that mask? I assume it would be:
$ mrcalc wmparc.nii.gz 2 -eq wmparc.nii.gz 41 -eq wmparc.nii.gz 200 -ge wmparc.nii.gz 300 -le -mult -mult -mult my_wmmask.nii.gz
mrcalc: [100%] uncompressing image "wmparc.nii.gz"
mrcalc: [100%] computing: ((wmparc.nii.gz == 2) * ((wmparc.nii.gz == 41) * ((wmparc.nii.gz >= 200) * (wmparc.nii.gz <= 300))))
mrcalc: [100%] compressing image "my_wmmask.nii.gz"
-
what happens if you use dwi2mask to generate a rough brain mask from the RAW images, and use that as the seed image? Is it just your wm_mask.nii.gz image that tckgen struggles with, or does the -seed_image option simply not work no matter what image you provide?
Problem solved.
Actually, there was an error in how I was creating the DWI.mif. The bvals file was incorrect. One of my old scripts had changed them to use the Dipy library. The HCP subjects have a bval=5 for the b0 image. Dipy throws an error if it doesn’t find at least one bval=0. In the folder I was using, the subjects were already preprocessed to be compatible with Dipy.
Your answer make me doubt of my files, so I went to double check them. Thanks for your time and help.
Best Regards,
Guillermo.