Hi John - The values are weighted (multiplied) by the probability distribution (path.pd.nii.gz) at the same voxel. So they are the expected values, from a probabilistic standpoint. The distribution is thresholded at 20% of its maximum by default (this is a parameter in dmri_pathstats).
Best, a.y
On Wed, 16 Sep 2015, John Anderson wrote:
Hi Anastasia, How the script "dmri_pathstats" compute the weighted FA, MD, AD, and RD values? I checked the command "dmri_pathstats" inside the file "trac-all.log" but I was unable to figure out how this weighting is working. Is it by multiplying the mean DTI metrics by the number of voxel? If my FA maps is "dtifit_FA.nii.gz" and my probabilistic distribution map for the cortico spinal tract is "path.pd.nii.gz" and I want to compute FA value using the command "fslstats" like: fslstats dtifit_FA.nii.gz -k path.pd.nii.gz -m ==== >This command will output the mean FA for the probabilistic distribution map. How can I weight this FA value using the previous command line? Bests, John Anderson
Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
HI Anastasia,
I'm new to tracula. I was able to get the stats of each diffusion parameter for each tract, as shown below. However, when I try and use waypoint in freeview to display the mean paths, using the command here:
freeview -w /data/bil-mb2/fMRI/CAST/all_freesurfer_subjectsdir/stats/*.path.mean.txt ------------------------------------------------------------------------ I get the below error. Please let me know if you have any ideas as to what could be wrong here.
Thanks very much.
Karuna
advaita.129> cd /data/bil-mb2/fMRI/CAST/all_freesurfer_subjectsdir/stats/ advaita.130> ls *.path.mean.txt fmajor_PP.avg33_mni_bbr.path.mean.txt lh.cst_AS.avg33_mni_bbr.path.mean.txt rh.atr_PP.avg33_mni_bbr.path.mean.txt rh.slfp_PP.avg33_mni_bbr.path.mean.txt fminor_PP.avg33_mni_bbr.path.mean.txt lh.ilf_AS.avg33_mni_bbr.path.mean.txt rh.cab_PP.avg33_mni_bbr.path.mean.txt rh.slft_PP.avg33_mni_bbr.path.mean.txt lh.atr_PP.avg33_mni_bbr.path.mean.txt lh.slfp_PP.avg33_mni_bbr.path.mean.txt rh.ccg_PP.avg33_mni_bbr.path.mean.txt rh.unc_AS.avg33_mni_bbr.path.mean.txt lh.cab_PP.avg33_mni_bbr.path.mean.txt lh.slft_PP.avg33_mni_bbr.path.mean.txt rh.cst_AS.avg33_mni_bbr.path.mean.txt lh.ccg_PP.avg33_mni_bbr.path.mean.txt lh.unc_AS.avg33_mni_bbr.path.mean.txt rh.ilf_AS.avg33_mni_bbr.path.mean.txt
advaita.131> freeview -w /data/bil-mb2/fMRI/CAST/all_freesurfer_subjectsdir/stats/*.path.mean.txt ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig... ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named advaita.radiology.ucsf.edu by karunas Thu Jan 28 21:33:23 2016 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-i386/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Mon Jun 16 12:09:46 2008 [0]PETSC ERROR: Configure options --with-debugging=0 --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Hi Karuna - I haven't seen this before. Can you check which version of freeview you have? Is it the one that came with freesurfer 5.3 or a newer version of freeview that you downloaded separately from the web site?
a.y
On Thu, 28 Jan 2016, Karuna Subra wrote:
HI Anastasia,
I'm new to tracula. I was able to get the stats of each diffusion parameter for each tract, as shown below. However, when I try and use waypoint in freeview to display the mean paths, using the command here:
freeview -w /data/bil-mb2/fMRI/CAST/all_freesurfer_subjectsdir/stats/*.path.mean.txt
I get the below error. Please let me know if you have any ideas as to what could be wrong here.
Thanks very much.
Karuna
advaita.129> cd /data/bil-mb2/fMRI/CAST/all_freesurfer_subjectsdir/stats/ advaita.130> ls *.path.mean.txt fmajor_PP.avg33_mni_bbr.path.mean.txt lh.cst_AS.avg33_mni_bbr.path.mean.txt rh.atr_PP.avg33_mni_bbr.path.mean.txt rh.slfp_PP.avg33_mni_bbr.path.mean.txt fminor_PP.avg33_mni_bbr.path.mean.txt lh.ilf_AS.avg33_mni_bbr.path.mean.txt rh.cab_PP.avg33_mni_bbr.path.mean.txt rh.slft_PP.avg33_mni_bbr.path.mean.txt lh.atr_PP.avg33_mni_bbr.path.mean.txt lh.slfp_PP.avg33_mni_bbr.path.mean.txt rh.ccg_PP.avg33_mni_bbr.path.mean.txt rh.unc_AS.avg33_mni_bbr.path.mean.txt lh.cab_PP.avg33_mni_bbr.path.mean.txt lh.slft_PP.avg33_mni_bbr.path.mean.txt rh.cst_AS.avg33_mni_bbr.path.mean.txt lh.ccg_PP.avg33_mni_bbr.path.mean.txt lh.unc_AS.avg33_mni_bbr.path.mean.txt rh.ilf_AS.avg33_mni_bbr.path.mean.txt
advaita.131> freeview -w /data/bil-mb2/fMRI/CAST/all_freesurfer_subjectsdir/stats/*.path.mean.txt
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig... ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named advaita.radiology.ucsf.edu by karunas Thu Jan 28 21:33:23 2016 [0]PETSC ERROR: Libraries linked from/autofs/space/lyon_006/pubsw/Linux2-2.3-i386/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c- opt [0]PETSC ERROR: Configure run at Mon Jun 16 12:09:46 2008 [0]PETSC ERROR: Configure options --with-debugging=0 --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Hi Anastasia,
Yes, it's the one that came with freesurfer 5.3. Is it possible to use the GUI to get waypoint to display the paths rather than command line? I have all the mean path outputs in the stats folder as shown here but somehow am getting this weird error below.
Thanks.
Karuna
On Fri, Jan 29, 2016 at 4:37 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Karuna - I haven't seen this before. Can you check which version of freeview you have? Is it the one that came with freesurfer 5.3 or a newer version of freeview that you downloaded separately from the web site?
a.y
On Thu, 28 Jan 2016, Karuna Subra wrote:
HI Anastasia,
I'm new to tracula. I was able to get the stats of each diffusion parameter for each tract, as shown below. However, when I try and use waypoint in freeview to display the mean paths, using the command here:
freeview -w /data/bil-mb2/fMRI/CAST/all_freesurfer_subjectsdir/stats/*.path.mean.txt
I get the below error. Please let me know if you have any ideas as to what could be wrong here.
Thanks very much.
Karuna
advaita.129> cd /data/bil-mb2/fMRI/CAST/all_freesurfer_subjectsdir/stats/ advaita.130> ls *.path.mean.txt fmajor_PP.avg33_mni_bbr.path.mean.txt lh.cst_AS.avg33_mni_bbr.path.mean.txt rh.atr_PP.avg33_mni_bbr.path.mean.txt rh.slfp_PP.avg33_mni_bbr.path.mean.txt fminor_PP.avg33_mni_bbr.path.mean.txt lh.ilf_AS.avg33_mni_bbr.path.mean.txt rh.cab_PP.avg33_mni_bbr.path.mean.txt rh.slft_PP.avg33_mni_bbr.path.mean.txt lh.atr_PP.avg33_mni_bbr.path.mean.txt lh.slfp_PP.avg33_mni_bbr.path.mean.txt rh.ccg_PP.avg33_mni_bbr.path.mean.txt rh.unc_AS.avg33_mni_bbr.path.mean.txt lh.cab_PP.avg33_mni_bbr.path.mean.txt lh.slft_PP.avg33_mni_bbr.path.mean.txt rh.cst_AS.avg33_mni_bbr.path.mean.txt lh.ccg_PP.avg33_mni_bbr.path.mean.txt lh.unc_AS.avg33_mni_bbr.path.mean.txt rh.ilf_AS.avg33_mni_bbr.path.mean.txt
advaita.131> freeview -w /data/bil-mb2/fMRI/CAST/all_freesurfer_subjectsdir/stats/*.path.mean.txt
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig... ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message
[0]PETSC ERROR: Signal received! [0]PETSC ERROR:
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:
[0]PETSC ERROR: Unknown Name on a linux-gnu named advaita.radiology.ucsf.edu by karunas Thu Jan 28 21:33:23 2016 [0]PETSC ERROR: Libraries linked from/autofs/space/lyon_006/pubsw/Linux2-2.3-i386/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c- opt [0]PETSC ERROR: Configure run at Mon Jun 16 12:09:46 2008 [0]PETSC ERROR: Configure options --with-debugging=0 --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR:
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
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.
You need to specify some volume to display the paths over. The paths are just text files with a list of point coordinates, so it has no idea in what space to display them if you don't specify a volume. Check the tracula tutorial, too.
On Tue, 9 Feb 2016, Karuna Subra wrote:
Hi Anastasia,
Yes, it's the one that came with freesurfer 5.3. Is it possible to use the GUI to get waypoint to display the paths rather than command line? I have all the mean path outputs in the stats folder as shown here but somehow am getting this weird error below.
Thanks.
Karuna
On Fri, Jan 29, 2016 at 4:37 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Karuna - I haven't seen this before. Can you check which version of freeview you have? Is it the one that came with freesurfer 5.3 or a newer version of freeview that you downloaded separately from the web site? a.y On Thu, 28 Jan 2016, Karuna Subra wrote: HI Anastasia, I'm new to tracula. I was able to get the stats of each diffusion parameter for each tract, as shown below. However, when I try and use waypoint in freeview to display the mean paths, using the command here: freeview -w /data/bil-mb2/fMRI/CAST/all_freesurfer_subjectsdir/stats/*.path.mean.txt ------------------------------------------------------------------------ I get the below error. Please let me know if you have any ideas as to what could be wrong here. Thanks very much. Karuna advaita.129> cd /data/bil-mb2/fMRI/CAST/all_freesurfer_subjectsdir/stats/ advaita.130> ls *.path.mean.txt fmajor_PP.avg33_mni_bbr.path.mean.txt lh.cst_AS.avg33_mni_bbr.path.mean.txt rh.atr_PP.avg33_mni_bbr.path.mean.txt rh.slfp_PP.avg33_mni_bbr.path.mean.txt fminor_PP.avg33_mni_bbr.path.mean.txt lh.ilf_AS.avg33_mni_bbr.path.mean.txt rh.cab_PP.avg33_mni_bbr.path.mean.txt rh.slft_PP.avg33_mni_bbr.path.mean.txt lh.atr_PP.avg33_mni_bbr.path.mean.txt lh.slfp_PP.avg33_mni_bbr.path.mean.txt rh.ccg_PP.avg33_mni_bbr.path.mean.txt rh.unc_AS.avg33_mni_bbr.path.mean.txt lh.cab_PP.avg33_mni_bbr.path.mean.txt lh.slft_PP.avg33_mni_bbr.path.mean.txt rh.cst_AS.avg33_mni_bbr.path.mean.txt lh.ccg_PP.avg33_mni_bbr.path.mean.txt lh.unc_AS.avg33_mni_bbr.path.mean.txt rh.ilf_AS.avg33_mni_bbr.path.mean.txt advaita.131> freeview -w /data/bil-mb2/fMRI/CAST/all_freesurfer_subjectsdir/stats/*.path.mean.txt ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named advaita.radiology.ucsf.edu by karunas Thu Jan 28 21:33:23 2016 [0]PETSC ERROR: Libraries linked from/autofs/space/lyon_006/pubsw/Linux2-2.3-i386/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c- opt [0]PETSC ERROR: Configure run at Mon Jun 16 12:09:46 2008 [0]PETSC ERROR: Configure options --with-debugging=0 --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0The 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@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Karuna Subra