oh yes I see, I have renamed the dpath/${TRACT[$num_tract]} directories to have a backup, so the name is not correct anymore. Actually I didn't need to do that, I can just set a different name for the outputs pathpathstats.byvoxel.txt and pathstats.overall.txt Thanks Celine
Hi Celine - This command assumes that --intrc is a tracula output directory, containing all the files that tracula saves in such a directory. What are you trying to get stats from?
a.y
On Mon, 3 Mar 2014, Celine Louapre wrote:
Hi Anastasia I have finally managed to coregister and resample all lesion masks on DTI images :-), and as you suggested I set the lesion voxels to 0 in dtifit_FA.nii.gz (as well as L1 L2 L3 and MD volumes)
Then the command I found in the trac-all log was the one below (where TRACT is the full name of the tract and SHORT_TRACT is the short name)
./freesurfer-stable5_3_0-05152013/bin/dmri_pathstats --intrc ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]} --dtbase ${PATH_3T}${SUBJECTS_3T[$subj]}/dmri/dtifit --path ${SHORT_TRACT[$num_tract]} --subj ${SUBJECTS_3T[$subj]} --out ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]}/pathstats.overall.txt --outvox ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]}/pathstats.byvoxel.txt
However I got this error message and couldn't find in the log file how to set the output type ERROR: fio_pushd: ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr ERROR: fio_pushd: ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr ERROR: must specify at least one type of output
Would you have some idea about that? Thank you very much Celine
Hi Celine - That's an interesting question. There's nothing implemented in there right now that would allow you to skip part of the tract in the along-the-tract stats. One (not very elegant) way to try to do something like this is:
- Set the lesion voxels in the dmri/dtifit_FA.nii.gz volume to zero.
(You'll want to save the original volume under some other name for backup first.) If you want the same for the diffusivities, repeat for the also for the MD, L1, L2, L3 volumes.
- Run the dmri_pathstats command line that you'll find in trac-all.log
for that subject.
This will regenerate all the pathstats.* files, but now the parts of the tract that go through the lesions will have zero values (or very low, if they're mixed in with some neighboring voxels).
Let us know if this worked! If not I may be able to implement something.
a.y
On Tue, 11 Feb 2014, Celine Louapre wrote:
Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine
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