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 >>> >>> >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.