Hi Lucia - The columns "NVoxels Volume_mm3" in the mri_segstats output are the volumes of each of the structures in the aparc+aseg, so those columns have nothing to do with the path. The last few columns, "Mean StdDev Min Max Range", are related to the values in path.pd.nii.gz.

Hope this helps,
a.y

On Wed, 23 Oct 2013, Lucia Billeci wrote:

Dear Anastasia,

I tried the command you suggested me and i obtained the output I attach to the mail.

I would like to ask you if I understood well shot it means. In this case left uncinatus connects the following cortex areas:

ctx-lh-fusiform

ctx-lh-inferiortemporal

ctx-lh-lateralorbitofrontal

ctx-lh-medialorbitofrontal

ctx-lh-middletemporal

ctx-lh-rostralanteriorcingulate

ctx-lh-superiortemporal

ctx-lh-temporalpole

ctx-lh-insula

and for each area I have the volume of the path. Is it correct?

Thanks

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

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

Il giorno 18/ott/2013, alle ore 17:32, Anastasia Yendiki ha scritto:

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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          National Research Council of Italy (CNR)

          Institute of Clinical Physiology (IFC)

          via Moruzzi, 1 Pisa - Italy

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          and properly

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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

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