[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* ___ Freesurfer mailing list 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.
Re: [Freesurfer] Command to export hippocampal subfields segmentations
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: on behalf of Miguel Ángel Rivas Fernández Reply-To: Freesurfer support list Date: Tuesday, 29 May 2018 at 09:32 To: Freesurfer support list 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 ___ Freesurfer mailing list 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.
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 : > 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: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Tuesday, 29 May 2018 at 09:32 > *To: *Freesurfer support list > *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* > > ___ > Freesurfer mailing list > 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* ___ Freesurfer mailing list 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.
Re: [Freesurfer] Command to export hippocampal subfields segmentations
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: on behalf of Miguel Ángel Rivas Fernández Reply-To: Freesurfer support list Date: Tuesday, 29 May 2018 at 09:46 To: Freesurfer support list 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 mailto:e.igles...@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: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Miguel Ángel Rivas Fernández mailto:miguelrivasf...@gmail.com>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday, 29 May 2018 at 09:32 To: Freesurfer support list mailto: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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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 ___ Freesurfer mailing list 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.
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 : > 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: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Tuesday, 29 May 2018 at 09:46 > *To: *Freesurfer support list > *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.igles...@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: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Tuesday, 29 May 2018 at 09:32 > *To: *Freesurfer support list > *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* > > > ___ > Freesurfer mailing list > 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* > > ___ > Freesurfer mailing list > 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
Re: [Freesurfer] Command to export hippocampal subfields segmentations
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: on behalf of Miguel Ángel Rivas Fernández Reply-To: Freesurfer support list Date: Tuesday, 29 May 2018 at 15:47 To: Freesurfer support list 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 mailto:e.igles...@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: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Miguel Ángel Rivas Fernández mailto:miguelrivasf...@gmail.com>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday, 29 May 2018 at 09:46 To: Freesurfer support list mailto: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 mailto:e.igles...@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: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Miguel Ángel Rivas Fernández mailto:miguelrivasf...@gmail.com>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday, 29 May 2018 at 09:32 To: Freesurfer support list mailto: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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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 c
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 : > 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: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Tuesday, 29 May 2018 at 15:47 > > *To: *Freesurfer support list > *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.igles...@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: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Tuesday, 29 May 2018 at 09:46 > *To: *Freesurfer support list > *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.igles...@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: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Tuesday, 29 May 2018 at 09:32 > *To: *Freesurfer support list > *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 > segmentati
Re: [Freesurfer] Command to export hippocampal subfields segmentations
External Email - Use Caution 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: on behalf of Miguel Ángel Rivas Fernández Reply-To: Freesurfer support list Date: Tuesday, 29 May 2018 at 16:26 To: Freesurfer support list 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 mailto:e.igles...@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: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Miguel Ángel Rivas Fernández mailto:miguelrivasf...@gmail.com>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday, 29 May 2018 at 15:47 To: Freesurfer support list mailto: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 mailto:e.igles...@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: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Miguel Ángel Rivas Fernández mailto:miguelrivasf...@gmail.com>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday, 29 May 2018 at 09:46 To: Freesurfer support list mailto: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 mailto:e.igles...@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: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Miguel Ángel Rivas Fernández mailto:miguelrivasf...@gmail.com>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday, 29 May 2018 at 09:32 To: Freesurfer support list mailto: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. Be
