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External Email - Use Caution
Yes, it looks like that. You can try ~/Desktop/pruebaHipocampo.txt
you should be able to write there.
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
From: <freesurfer-bounces@nmr.mgh.
harvard.edu > on behalf of Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Date: Tuesday, 29 May 2018 at 15:47
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Subject: Re: [Freesurfer] Command to export hippocampal subfields segmentations
External Email - Use Caution
Hi Eugenio,
I ran the command and fs gave me the following error in all subjects
Collecting data for subject: 5250
/Applications/freesurfer/bin/
quantifyHippocampalSubfields. sh: line 94: pruebahipocampo.txt: Permission denied
In order to gathering the hippocampus volumes I used this command
rmnlab1:~ neucoga$ quantifyHippocampalSubfields.
sh T2_3D_SAG pruebahipocampo.txt /Applications/freesurfer/ subjects
Could be motivated this error due to read & write permissions on Mac folders?
Thanks
Best,
2018-05-29 10:54 GMT+02:00 Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk>:
External Email - Use Caution
The results should be in pruebahipocampo.txt, which will be located in the directory from which you ran the command.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
From: <freesurfer-bounces@nmr.mgh.
harvard.edu > on behalf of Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Date: Tuesday, 29 May 2018 at 09:46
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Subject: Re: [Freesurfer] Command to export hippocampal subfields segmentations
External Email - Use Caution
Hi Eugenio,
I want to export the volumnes of all subjects, I used the quantifyHippocampalSubfields.
sh command and apparently it did work but now I can´t find where Freesurfer saved the file.
Here is the response of Freesurfer
rmnlab1:~ neucoga$ quantifyHippocampalSubfields.
sh T1-T2_3D_SAG pruebahipocampo.txt /Applications/freesurfer/ subjects
Gathering results from subjects in:
/Applications/freesurfer/subjects
Using the suffix name:
T1-T2_3D_SAG
And writing them to:
pruebahipocampo.txt
I looked for it in the subjects folder but I can not find the file anywhere.
Thanks in advance
2018-05-29 10:34 GMT+02:00 Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk>:
External Email - Use Caution
Hola Miguel Ángel,
What do you mean by exporting? The volumes? There is a command to gather the volumes from all subjects in the subjects directory, which is:
quantifyHippocampalSubfields.
sh (in FreeSurfer 6.0) quantifyHAsubregions.sh (in dev version)
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
From: <freesurfer-bounces@nmr.mgh.
harvard.edu > on behalf of Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Date: Tuesday, 29 May 2018 at 09:32
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Subject: [Freesurfer] Command to export hippocampal subfields segmentations
External Email - Use Caution
Hi Freesurfer developers,
I was looking for the freesurfer command to export hippocampal sufields segmentations but I did not found. What is the command to export this measures and in what folder are exported the file?
Thanks a lot.
Best,
--Miguel Ángel Rivas Fernández
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--
Miguel Ángel Rivas Fernández
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The information in this e-mail is intended only for the person to whom it is
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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.