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 rspriti@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.

Thanks Anastasia! The pathstats.allvoxel.txt was pasted at the end of this email as in the previous one.

I will rerun dmri_paths command for the fmajor path and will send you the log.txt file.

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 Mon, Feb 20, 2012 at 9:08 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

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 rspriti@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