Hi Minjie - There was no attachment to your email. The fmajor issue that you're describing sounds like an initialization issue. That single curve that you describe is where the algorithm starts at and b/c something is wrong with it, it doesn't move from there. Does the curve seem to go into a low anisotropy area? Can you rerun the dmri_paths command for just one of these fmajor paths with --debug and send us the log.txt file?
Thanks! a.y On Mon, 20 Feb 2012, Minjie Wu wrote: > Hi Priti, > > Thank you very much for the detailed instructions. The tracts with > empty pathstat.byvoxel.txt files are slfp, slft, and unc tracts. > After your email, I have checked all 10+ subjects with such problems. > They all share similar motion problems (the parietal or temporal part > of brain is cut due to motion), which may be why TRACULA is not > working. > > The other issue is with fmajor. For many subjects (almost 1/3 of > overall subjects), the fiber tracking for fmajor (path.pd.nii.gz) > looks like a single fiber (or 2,3 fibers) instead of a bundle of > fibers. The volume from pathstats.overall.txt (195 voxels) is > significantly lower than the mean fmajor volume (1000 voxels) from the > population (see attached file). These brain images are complete (no > cutting issue at fmajor). Also I have checked the FA-MNI > co-registration, and the registration seems to be accurate. Any idea > of how to avoid this problem will be really appreciated. > > Thanks, > Minjie > > > > > [minjiewu@ccmfsl1 fmajor_PP_avg33_mni_bbr]$ more pathstats.overall.txt > # Title Pathway Statistics > # > # generating_program /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats > # cvs_version > # cmdline /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats --intrc > /ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr > --dtbase /ccm/pavuluri/rest/DTI/data/20191/dmri/dtifit --path > fmajor --subj 20191 --out > /ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt > --outvox > /ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr/pathstats > .byvoxel.txt > # sysname Linux > # hostname ccmfsl2.psych.uic.edu > # machine x86_64 > # user minjiewu > # anatomy_type pathway > # > # subjectname 20191 > # pathwayname fmajor > # > Count 1000 > Volume 195 > Len_Min 136 > Len_Max 179 > Len_Avg 149.767 > Len_Center 164 > AD_Avg 0.00145274 > AD_Avg_Weight 0.00149492 > AD_Avg_Center 0.00165127 > RD_Avg 0.000615351 > RD_Avg_Weight 0.00058665 > RD_Avg_Center 0.000529699 > MD_Avg 0.00089448 > MD_Avg_Weight 0.000889406 > MD_Avg_Center 0.000903556 > FA_Avg 0.475963 > FA_Avg_Weight 0.507926 > FA_Avg_Center 0.610243 > > > > > > > On Wed, Feb 15, 2012 at 9:25 AM, Priti Srinivasan > <rspr...@nmr.mgh.harvard.edu> wrote: >> Hi Minjie, >> >> The pathstats.byvoxel.txt gives the statistics of the higest probability >> streamline of the posterior distribution of the tract and the >> pathstats.overall.txt gives you average diffusion values for the whole >> tract. >> >> Please refer to the following: >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics >> >> Your pathstats.overall.txt does not look right. For instance the center >> streamline's length (Len_Center = 0). Did you open the posterior >> probability distribution of this tract? >> >> You can use the following command to do the same: >> >> freeview <path/to/your/data>/dpath/path.pd.nii.gz >> >> If it does not look right then something probably went wrong during the >> path reconstruction. If you can send us your trac-all.log, we can check >> for anything that went wrong. >> >> Hope this is helpful., >> >> Priti >> >> >>> Hello Tracula Developer & User, >>> >>> I found a few subjects have pathstat.overall.txt information but with >>> blank voxel information in pathstats.byvoxel.txt. For such tracts, >>> they usually len_min = len_max = len_avg. Anyone know what happened >>> for the fiber tracking? Is it possible to extract the byvoxel >>> information along the tract? >>> >>> Thanks, >>> Minjie >>> >>> For example: >>> >>> [minjiewu@ccmfsl1 data]$ more >>> 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt >>> # Title Pathway Statistics >>> # >>> # generating_program /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats >>> # cvs_version >>> # cmdline /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats --intrc >>> /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr >>> --dtbase /ccm/pavuluri/rest/DTI/data/223 >>> 31/dmri/dtifit --path rh.slfp --subj 22331 --out >>> /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt >>> --outvox /ccm/pavuluri/rest/DTI/data/ >>> 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.byvoxel.txt >>> # sysname Linux >>> # hostname ccmfsl2.psych.uic.edu >>> # machine x86_64 >>> # user minjiewu >>> # anatomy_type pathway >>> # >>> # subjectname 22331 >>> # pathwayname rh.slfp >>> # >>> Count 1000 >>> Volume 86 >>> Len_Min 86 >>> Len_Max 86 >>> Len_Avg 86 >>> Len_Center 0 >>> AD_Avg 0.00112029 >>> AD_Avg_Weight 0.00112029 >>> AD_Avg_Center nan >>> RD_Avg 0.000783836 >>> RD_Avg_Weight 0.000783836 >>> RD_Avg_Center nan >>> MD_Avg 0.000895987 >>> MD_Avg_Weight 0.000895987 >>> MD_Avg_Center nan >>> FA_Avg 0.264347 >>> FA_Avg_Weight 0.264347 >>> FA_Avg_Center nan >>> _______________________________________________ >>> 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. >> > _______________________________________________ > 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
