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:
>
> 1. 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.
>
> 2. 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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