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Hi Eugenio

So I ran the new Amygdala and hippocampus tool on my longitudinal data and from that I got the three output files as described on the wiki( the FS60, HBT and the CA) which these mgz files are in the long mri directories for each subject.

This all looks fine. The issue is that I want to look at the FS 60 version of the subfields and export these rather than the HBT versions. When I use the script to extract all the measures to a file, it works fine and I have the amygdala volumes but for the hippocampus, I get the HBT versions. How do you get the extract script to output the FS60 subfield measures? Is it possible? If not can I simply add the HBT sections for each subfield to equate to the FS 60 measures?

Thanks for your prompt reply. Much appreciated

Erik

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@MGH.HARVARD.EDU Sent: Friday 27 August 2021 22:02 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal subfields

Dear Erik I’m not sure I understand. What does your output file look like? Cheers, /Eugenio

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://secure-web.cisco.com/1lOExJeky8AFqkFfrzJ79hMnVWS5jkY1XvPoEM7_fiDyZiO2...

On Aug 27, 2021, at 16:14, Erik O'Hanlon <OHANLOER@tcd.iemailto:OHANLOER@tcd.ie> wrote:

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Dear FS experts,

I've run a lognitudinal hippocampal and amygdala analysis. I jave managed to extract the amygdala and the head body tail subfields bui I'm wondering how to extract the regular FS60 volume measures? I have the three versions (FS60, HBT and CA mgz files in my long mri directories but I just keep getting the HBT volumes.

I tried

quantifyHAsubregions.sh hippoSf T1.long Outputfilename

and that gives me the HBT measures

What command do I use to pull out the FS60 subfield measures from my long mri directories?

Thanks for any help.

Erik _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1KpjtWxWHIKAUquh4Uydr2e7YoRAgRF-HVDiv4BqhdUa-0X...

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Hi Eugenio,

Thanks so much for you reply. I will do that so. Just by way understanding the outputs I have , so the extract script only pulls the HBT automatically, and you need to simply add these together for the FS60 measures ? You can't modify the extract tool to read the FS60 data automatically?

Thanks again for your help. I will follow your instructions.

Best regards

Erik

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@MGH.HARVARD.EDU Sent: Monday 30 August 2021 11:05 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal subfields

Oh, now I understand.

Yeah you can add the head, body and tail segments of each subfield to get 6.0 type of measurements ;-)

Cheers,

/Eugenio

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://secure-web.cisco.com/1knFRpDOFuoCvGaipHjXiJ2cPhPsiPMOeHi81MNBHC1pYD-x...

On Aug 28, 2021, at 08:20, Erik O'Hanlon <OHANLOER@tcd.iemailto:OHANLOER@tcd.ie> wrote:

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External Email - Use Caution

Hi Eugenio

So I ran the new Amygdala and hippocampus tool on my longitudinal data and from that I got the three output files as described on the wiki( the FS60, HBT and the CA) which these mgz files are in the long mri directories for each subject.

This all looks fine. The issue is that I want to look at the FS 60 version of the subfields and export these rather than the HBT versions. When I use the script to extract all the measures to a file, it works fine and I have the amygdala volumes but for the hippocampus, I get the HBT versions. How do you get the extract script to output the FS60 subfield measures? Is it possible? If not can I simply add the HBT sections for each subfield to equate to the FS 60 measures?

Thanks for your prompt reply. Much appreciated

Erik

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@MGH.HARVARD.EDUmailto:JIGLESIASGONZALEZ@MGH.HARVARD.EDU> Sent: Friday 27 August 2021 22:02 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampal subfields

Dear Erik I’m not sure I understand. What does your output file look like? Cheers, /Eugenio

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1knFRpDOFuoCvGaipHjXiJ2cPhPsiPMOeHi81MNBHC1pYD-x...http://secure-web.cisco.com/1lOExJeky8AFqkFfrzJ79hMnVWS5jkY1XvPoEM7_fiDyZiO2NCivnLmj1kLuPRm2w88EDcWDJFNg74iZ5sXiGABC3n_oKlQ0uGC_9nPN9HjPWymVUYBrBeTboJSI7XzVHe1kg37ir15P16T7suVpnbFAkPhobCBTQwqWnq4d9hmBt5I1ybk3_w9_yFktbjWWuVl6uJ_6k6IUCsPgYNWjI5LqC-dobHYl3W_y6GhIsiANkJk6bKdBmRwDZDkB7o8lLevPO3On0jPYRQRhL13Rhgg/http%3A%2F%2Fwww.jeiglesias.com

On Aug 27, 2021, at 16:14, Erik O'Hanlon <OHANLOER@tcd.iemailto:OHANLOER@tcd.ie> wrote:

External Email - Use Caution

External Email - Use Caution

Dear FS experts,

I've run a lognitudinal hippocampal and amygdala analysis. I jave managed to extract the amygdala and the head body tail subfields bui I'm wondering how to extract the regular FS60 volume measures? I have the three versions (FS60, HBT and CA mgz files in my long mri directories but I just keep getting the HBT volumes.

I tried

quantifyHAsubregions.sh hippoSf T1.long Outputfilename

and that gives me the HBT measures

What command do I use to pull out the FS60 subfield measures from my long mri directories?

Thanks for any help.

Erik _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1KpjtWxWHIKAUquh4Uydr2e7YoRAgRF-HVDiv4BqhdUa-0X...

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1OrxGESnJasDMCX8Gy49ujB7Y2HMjR6jb8Cq5qabxvZx69e...