External Email - Use Caution
Hi Emily, You need to download the dev version, but run the subfield/amygdala volume on cases reconned with FS6.0. Cheers, /Eugenio
-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Emily Schwartz emily.schwartz@einstein.yu.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 April 2019 at 15:44 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal subfield version
External Email - Use Caution Hello FS experts,
I was planning to use the hippocampal subfield segmentation module in FreeSurfer 6.0 on a Linux ubuntu computer. I also would like to use the nuclei of the amygdala segmentation, but realized I need to download the development version in order to do that. Is there any reason why I shouldn't use the development version over the 6.0 release?
Thank you in advance.
Best, Emily
External Email - Use Caution
Hi Eugenio,
Thank you so much. I downloaded the development version, but when I run "segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]," it says command not found.
After I download the runtime2014 version, I get the MCRv84 folder, but when I try to run a subject through the hippocampal subfield it gives me an error and tells me to download runtime2012b. Once I do that I also get the MCRv80 folder and am able to run the hippocampal segmentation, but I assume this is the 2017 version since I cannot run the amygdala segmentation. I am not sure what I am doing wrong when I download the 2018 dev version.
Best, Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.iglesias@ucl.ac.uk] Sent: Thursday, April 04, 2019 5:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfield version
External Email - Use Caution Hi Emily, You need to download the dev version, but run the subfield/amygdala volume on cases reconned with FS6.0. Cheers, /Eugenio
-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Emily Schwartz emily.schwartz@einstein.yu.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 April 2019 at 15:44 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal subfield version
External Email - Use Caution Hello FS experts,
I was planning to use the hippocampal subfield segmentation module in FreeSurfer 6.0 on a Linux ubuntu computer. I also would like to use the nuclei of the amygdala segmentation, but realized I need to download the development version in order to do that. Is there any reason why I shouldn't use the development version over the 6.0 release?
Thank you in advance.
Best, Emily
External Email - Use Caution
Hi Emily, I suspect that you’re mixing versions. Please make sure that you source the dev version. Cheers, /E
-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Emily Schwartz emily.schwartz@einstein.yu.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, 11 April 2019 at 13:02 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal subfield version
External Email - Use Caution Hi Eugenio,
Thank you so much. I downloaded the development version, but when I run "segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]," it says command not found.
After I download the runtime2014 version, I get the MCRv84 folder, but when I try to run a subject through the hippocampal subfield it gives me an error and tells me to download runtime2012b. Once I do that I also get the MCRv80 folder and am able to run the hippocampal segmentation, but I assume this is the 2017 version since I cannot run the amygdala segmentation. I am not sure what I am doing wrong when I download the 2018 dev version.
Best, Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.iglesias@ucl.ac.uk] Sent: Thursday, April 04, 2019 5:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfield version
External Email - Use Caution Hi Emily, You need to download the dev version, but run the subfield/amygdala volume on cases reconned with FS6.0. Cheers, /Eugenio
-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Emily Schwartz emily.schwartz@einstein.yu.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 April 2019 at 15:44 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal subfield version
External Email - Use Caution Hello FS experts,
I was planning to use the hippocampal subfield segmentation module in FreeSurfer 6.0 on a Linux ubuntu computer. I also would like to use the nuclei of the amygdala segmentation, but realized I need to download the development version in order to do that. Is there any reason why I shouldn't use the development version over the 6.0 release?
Thank you in advance.
Best, Emily
External Email - Use Caution
Hi Eugenio,
Thanks! I am able to run it now.
Best, Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.iglesias@ucl.ac.uk] Sent: Thursday, April 11, 2019 1:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfield version
External Email - Use Caution Hi Emily, I suspect that you’re mixing versions. Please make sure that you source the dev version. Cheers, /E
-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Emily Schwartz emily.schwartz@einstein.yu.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, 11 April 2019 at 13:02 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal subfield version
External Email - Use Caution Hi Eugenio,
Thank you so much. I downloaded the development version, but when I run "segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]," it says command not found.
After I download the runtime2014 version, I get the MCRv84 folder, but when I try to run a subject through the hippocampal subfield it gives me an error and tells me to download runtime2012b. Once I do that I also get the MCRv80 folder and am able to run the hippocampal segmentation, but I assume this is the 2017 version since I cannot run the amygdala segmentation. I am not sure what I am doing wrong when I download the 2018 dev version.
Best, Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.iglesias@ucl.ac.uk] Sent: Thursday, April 04, 2019 5:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfield version
External Email - Use Caution Hi Emily, You need to download the dev version, but run the subfield/amygdala volume on cases reconned with FS6.0. Cheers, /Eugenio
-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Emily Schwartz emily.schwartz@einstein.yu.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 April 2019 at 15:44 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal subfield version
External Email - Use Caution Hello FS experts,
I was planning to use the hippocampal subfield segmentation module in FreeSurfer 6.0 on a Linux ubuntu computer. I also would like to use the nuclei of the amygdala segmentation, but realized I need to download the development version in order to do that. Is there any reason why I shouldn't use the development version over the 6.0 release?
Thank you in advance.
Best, Emily
freesurfer@nmr.mgh.harvard.edu
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Emily Schwartz -
Iglesias Gonzalez, Eugenio