Dear Bruce, Thank you for your quick and precise answer.
One last question. Is it possible to segment the Nucl. Subthalamicus? It is a subcortical anatomical structure, and is a part of the basal ganglia. It is not included in the output following the command: asegstats2table --subjects 1_T1W_recon-all 2_T1W_recon-all 3_T1W_recon-all 4_T1W_recon-all 5_T1W_recon-all --meas volume --tablefile Subcortical.txt Kind regards Morten -----Oprindelig meddelelse----- Fra: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne af Bruce Fischl Sendt: 22. marts 2016 14:02 Til: Freesurfer support list Emne: Re: [Freesurfer] Asegstats2table: insula and Substantia nigra volumes are not reported Hi Morten the insula you should be able to get out of the cortical labels in the various *.annot files. The substantia nigra we don't segment at the moment, and I suspect it would be hard to do so from only a T1-weighted scan. cheers Bruce On Tue, 22 Mar 2016, Morten Sejer Hansen wrote: > > Dear Experts, > > > > I am interested in retrieving the volume of the insula and substantia > nigra from T1W structural scans converted to nii.gz files. All scans > have undergone the recon-all process without error. > > I have seen volume estimations of Insula and substantia nigra > performed in several studies, but I can’t seem to figure out how I retrieve > these volumes. > > > > I ran the command: > > > > asegstats2table --subjects 1_T1W_recon-all 2_T1W_recon-all > 3_T1W_recon-all 4_T1W_recon-all 5_T1W_recon-all --meas volume > --tablefile Subcortical.txt > > > > SUBJECTS_DIR : /Applications/freesurfer/subjects > > Parsing the .stats files > > Building the table.. > > Writing the table to Subcortical.txt > > > > following this I get at fine output with several volume estimation of > subcortical structures, but without the Insula (left and right), and > without the substantia nigra (left and right). > > > > I tried to run the same command on “Bert”, and ended up with the same > result (with the insula and substania nigra still missing). I also > tried to add the > > > > --all-segs > > > > But without any change in the output. > > > > On the > FreeSurferColorLUT(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutoria > l/AnatomicalROI/FreeSurferColorL > UT) I can see that the structures I am interested in have the > following numbers: 19, 27, 55 and 59. > > > > Could you provide me answers on how to extract the volumes of the > insula and substantia nigra? > > > > Thanks a lot! > > > > Kind regards > > > > Morten Sejer Hansen > > > > > > > > Morten Sejer Hansen > > MD > Direct: + 45 26373611 > > Mail: morten.sejer.han...@regionh.dk / morten.sejer.han...@dadlnet.dk > > Department of anaesthesiology 4231 > > Centre of head and orthopaedics > > Copenhagen University Hospital, Rigshospitalet > > Blegdamsvej 9 > 2100 Copenhagen > > > > Tel: +45 35 45 35 45 > Web: www.regionh.dk > > This e-mail and any attachment may contain confidential and privileged > material intended for the addressee only. If you are not the > addressee, you are notified that no part of the e-mail or any > attachment may be disclosed, copied or distributed, and that any other > action related to this e-mail or attachment is strictly prohibited, > and may be unlawful. If you have received this e-mail by error, please notify > the sender immediately by return e-mail, and delete this message. > > > > > ______________________________________________________________________ > _______________ > > > Denne e-mail indeholder fortrolig information. Hvis du ikke er den > rette modtager af denne e-mail eller hvis du modtager den ved en > fejltagelse, beder vi dig venligst informere afsender om fejlen ved at > bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme uden at > videresende eller kopiere den. > > ________________________________ Denne e-mail indeholder fortrolig information. Hvis du ikke er den rette modtager af denne e-mail eller hvis du modtager den ved en fejltagelse, beder vi dig venligst informere afsender om fejlen ved at bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme uden at videresende eller kopiere den. _______________________________________________ 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.
