Re: [Freesurfer] Command to export hippocampal subfields segmentations

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Yes!

-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

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 16:26 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Command to export hippocampal subfields segmentations

External Email - Use Caution Thank you Eugenio, it works but now I have a "absurd" question, the volume values that I obtained are mm with six decimals?

For example, for the left_Hippocampal_tail I obtained 498.117062

Sorry for this absurd question but I would like be sure about this.

Thanks in advance,

Best

2018-05-29 16:50 GMT+02:00 Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk>:

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 http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.commailto:miguelrivasfdez@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, 29 May 2018 at 15:47

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto: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 http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.commailto:miguelrivasfdez@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, 29 May 2018 at 09:46 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto: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 http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.commailto:miguelrivasfdez@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, 29 May 2018 at 09:32 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Command to export hippocampal subfields segmentations

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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 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.

-- Miguel Ángel Rivas Fernández

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.

-- Miguel Ángel Rivas Fernández