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:
>>
>> 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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>
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