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:
>>>
>>> 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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