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.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
