Hi Lucia - You can probably do that with mri_segstats. Try something like:

mri_segstats --seg dlabel/diff/aparc+aseg.bbr.nii.gz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --sum output.txt --i dpath/lh.unc_AS_avg32_mni_flt/path.pd.nii.gz

And similarly for any other pathway. See the mri_segstats help for more usage info. Let me know if this gives you what you need.

a.y

On Fri, 18 Oct 2013, Lucia Billeci wrote:

Thanks Anastasia, this is useful for visualization. But to construct a table

with for each tracts the parcellation regions that it connects do I need to

look at the image?

Lucia

On Oct 18, 2013, at 3:48 PM, Anastasia Yendiki wrote:

     Hi Lucia - You can look at the tracula output over the cortical

     parcellation and subcortical segmentation in the individual's

     diffusion space like this:

     freeview dmri/dtifit_FA.nii.gz

     dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.5 -tv

     dpath/merged_avg33_mni_bbr.mgz

     Hope this helps,

     a.y

     On Fri, 18 Oct 2013, Lucia Billeci wrote:

           Dear Anastasia and all,

           how can I understand which are the region of the

           brain in which the brain

           base been parecellated that each tract generated by

           TRACULA connect?

           For example  if I look at the left uncinate

           fascicles how can I know which

           are the ROIs of the statistical output from the

           cortical parcellation that

           it connects?

           Thanks

           Lucia

           On Oct 14, 2013, at 11:08 PM, Lucia Billeci wrote:

                Hi Anastasia,

           thanks for you answer. Now I have understood the

           meaning of that

           parameter.

           Best regards

           Lucia

           On Oct 14, 2013, at 10:58 PM, Anastasia Yendiki

           wrote:

                Hi Lucia - It's how many sample paths were

           drawn to

                produce the probability distribution of the

           path

                (path.pd.nii.gz). It depends on the

           configuration

                parameters (nsample, nkeep), so it'll be the

           same if these

                configuration parameters are the same.

                Hope this helps,

                a.y

                On Mon, 14 Oct 2013, Lucia Billeci wrote:

                      Dear all,

                      I noticed that in the TRACULA statistics

                      output files (pathstats.overall.txt) the

                      variable "Count" that

                      should indicate the number of sample

           paths in

                      the WM tract is the same for all the

           computed

                      tract. Could

                      anyone tell me why this happen?

                      Thanks a lot

                      Regards

                      Lucia

                      _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

           _

                      Dr. Lucia Billeci, PhD

                      Institute of Clinical Physiology (IFC)

                      National Research Council (CNR)

                      via Moruzzi 1, 56124, Pisa

                      ITALY

                      Tel: +39-0506213204

                      e-mail: lucia.billeci@ifc.cnr.it

                      _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

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           Dr. Lucia Billeci, PhD, Engineer 

           National Research Council of Italy (CNR)

           Institute of Clinical Physiology (IFC)

           via Moruzzi, 1 Pisa - Italy

           http://www.ifc.cnr.it

           Tel. +39-050-3152182 Cell. +39-339-1863902

           Email: lucia.billeci@ifc.cnr.it

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           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.

           Dr. Lucia Billeci, PhD, Engineer 

           National Research Council of Italy (CNR)

           Institute of Clinical Physiology (IFC)

           via Moruzzi, 1 Pisa - Italy

           http://www.ifc.cnr.it

           Tel. +39-050-3152182 Cell. +39-339-1863902

           Email: lucia.billeci@ifc.cnr.it

Dr. Lucia Billeci, PhD, Engineer 

National Research Council of Italy (CNR)

Institute of Clinical Physiology (IFC)

via Moruzzi, 1 Pisa - Italy

http://www.ifc.cnr.it

Tel. +39-050-3152182 Cell. +39-339-1863902

Email: lucia.billeci@ifc.cnr.it