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/FsTutorial/AnatomicalROI/FreeSurfe...) 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.hansen@regionh.dk / morten.sejer.hansen@dadlnet.dkmailto:morten.sejer.hansen@regionh.dk%20/%20morten.sejer.hansen@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.dkhttp://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.
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/FsTutorial/AnatomicalROI/FreeSurfe... 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.hansen@regionh.dk / morten.sejer.hansen@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.
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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.hansen@regionh.dk / morten.sejer.hansen@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.
Hi Morten
not yet. The STN is on our list of things to segment (as is the SN), although both will likely require good T2* (or maybe T2) weighted images.
cheers Bruce On Tue, 22 Mar 2016, Morten Sejer Hansen wrote:
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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.hansen@regionh.dk / morten.sejer.hansen@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
Hi Bruce,
Again, thank you for the quick response!
I will be looking forward to the upgrade then.
Kind regards
Morten
-----Oprindelig meddelelse----- Fra: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] På vegne af Bruce Fischl Sendt: 22. marts 2016 16:16 Til: Freesurfer support list Emne: Re: [Freesurfer] Asegstats2table: insula and Substantia nigra volumes are not reported
Hi Morten
not yet. The STN is on our list of things to segment (as is the SN), although both will likely require good T2* (or maybe T2) weighted images.
cheers Bruce On Tue, 22 Mar 2016, Morten Sejer Hansen wrote:
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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/FsTutori a 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.hansen@regionh.dk / morten.sejer.hansen@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
________________________________
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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Morten Sejer Hansen