Re: [Freesurfer] HSF in 5.3

Hi Eugenio: Here is the list of files in the 'mri' directory of a given subject: afrancis-mac:HSF afrancis$ cd Smoke_d004/ afrancis-mac:Smoke_d004 afrancis$ cd mri afrancis-mac:mri afrancis$ ls -la total 93464 drwxrwxr-x 47 afrancis staff 1598 Dec 23 01:05 . drwxr-xr-x 13 afrancis staff

Re: [Freesurfer] HSF in 5.3

Got it! All you need to do is to replace Smoke_e024 by T1, which is the ID of the analysis: quantifyHippocampalSubfields.sh T1 Nicotine_HSF.txt Let me know if it doesn't work! Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal

Re: [Freesurfer] HSF in 5.3

Works beautifully - Thanks so much Eugenio. Have a great weekend. On Fri, Jan 29, 2016 at 10:33 AM, Eugenio Iglesias wrote: > Got it! All you need to do is to replace Smoke_e024 by T1, which is the ID > of the analysis: > > quantifyHippocampalSubfields.sh T1 Nicotine_HSF.txt

Re: [Freesurfer] HSF in 5.3

Hi Alan, can you please list the files in the mri directory of any of the subjects and send me the output? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From:

Re: [Freesurfer] HSF in 5.3

Hi Eugenio: As you advised, I ran the following command: afrancis-mac:HSF afrancis$ quantifyHippocampalSubfields.sh Smoke_e024 Nicotine_HSF.txt Gathering results from subjects in: /Users/afrancis/Desktop/Connectome/HSF/ Using the suffix name: Smoke_e024 And writing them to:

Re: [Freesurfer] HSF in 5.3

Hi Alan, the subfield module is not present in 5.3; you'll need to download the development version (or wait until 6.0 is released, which should be pretty soon=. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso

Re: [Freesurfer] HSF in 5.3

Thanks for the very quick reply Eugenio. Will download the 6.0 beta. Alan On Fri, Dec 11, 2015 at 12:51 PM, Eugenio Iglesias wrote: > Hi Alan, > the subfield module is not present in 5.3; you'll need to download the > development version (or wait until 6.0 is released,

Re: [Freesurfer] HSF in 5.3

: Eugenio Iglesias <e.igles...@bcbl.eu> To: Alan Francis <alandarkene...@gmail.com> Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Sent: Fri, 11 Dec 2015 12:51:24 -0500 (EST) Subject: Re: [Freesurfer] HSF in 5.3 Hi Alan, the subfield module is not present in 5.3; you'l