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.bill...@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.bill...@ifc.cnr.it >> >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> _ >> >> 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. >> >> 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.bill...@ifc.cnr.it >> >> _______________________________________________ >> >> 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. >> >> 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.bill...@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.bill...@ifc.cnr.it _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
