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
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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 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 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.billeci@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.billeci@ifc.cnr.itDr. 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