Dear Vanessa,
1. No changes were made in the hippocampal module between 7.0 and 7.1, so you don’t need to rerun (as the subjects were reconned-all with 6.0, which doesn’t have any problems). 2. Yeah it may not be as easy to reproduce as running everything with the same version, but it’s perfectly fine to write in your paper that you reconned the brains with 6.0 and then processed the hippo and amygdala with 7.1. People (even reviewers!) understand that some labs don’t have the CPU cycles to quickly rerun all their data with FS every time a new version comes out. 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 Vanessa Cropley vcropley@unimelb.edu.au Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, May 20, 2020 at 01:35 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer version 7.0.0 and hippocampal segmentation
External Email - Use Caution Hello Freesurfer team,
I have just become aware of the release notes concerning v7.0.0 being recalled and not to be used, with the recommendation to use v7.1.0 instead: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
I have a couple of questions about the implications of this recall.
We have processed a large dataset using freesurfer version 6, with all subjects being processed (recon-all) with the same version/platform.
We would now like to segment the hippocampal subfields using the enhanced version of the module as outlined here: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields which requires Freesurfer 7.
We have successfully run the hippocampal segmentation using freesurfer_v7.0.0_dev_20200405 (7.1 was not available at the time).
My questions:
1. Given the recall of v7.0.0, does this mean that we should re-do the hippocampal segmentation that used v7.0.0 with v7.1.0? In other words, are all functions within v7.0.0 to be avoided, or just the recon-all stream?
2. Given that the recon-all was processed with v6, is it ok to perform the hippocampal subfield segmentation with v7? I understand that it is fine to perform post-processing functions outside the recon-all stream with newer versions (provided recon-all was done with the same version). Is my understanding correct?
Thank you for your assistance.
- Vanessa
External Email - Use Caution
Dear Eugenio,
Thank you very much for your prompt reply. This has clarified things for us.
Best wishes, Vanessa
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 20 May 2020 at 10:44 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer version 7.0.0 and hippocampal segmentation
Dear Vanessa,
1. No changes were made in the hippocampal module between 7.0 and 7.1, so you don’t need to rerun (as the subjects were reconned-all with 6.0, which doesn’t have any problems). 2. Yeah it may not be as easy to reproduce as running everything with the same version, but it’s perfectly fine to write in your paper that you reconned the brains with 6.0 and then processed the hippo and amygdala with 7.1. People (even reviewers!) understand that some labs don’t have the CPU cycles to quickly rerun all their data with FS every time a new version comes out. Cheers, /Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.comhttp://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Vanessa Cropley vcropley@unimelb.edu.au Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, May 20, 2020 at 01:35 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer version 7.0.0 and hippocampal segmentation
External Email - Use Caution Hello Freesurfer team,
I have just become aware of the release notes concerning v7.0.0 being recalled and not to be used, with the recommendation to use v7.1.0 instead: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNoteshttps://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
I have a couple of questions about the implications of this recall.
We have processed a large dataset using freesurfer version 6, with all subjects being processed (recon-all) with the same version/platform.
We would now like to segment the hippocampal subfields using the enhanced version of the module as outlined here: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldshttps://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields which requires Freesurfer 7.
We have successfully run the hippocampal segmentation using freesurfer_v7.0.0_dev_20200405 (7.1 was not available at the time).
My questions:
1. Given the recall of v7.0.0, does this mean that we should re-do the hippocampal segmentation that used v7.0.0 with v7.1.0? In other words, are all functions within v7.0.0 to be avoided, or just the recon-all stream?
2. Given that the recon-all was processed with v6, is it ok to perform the hippocampal subfield segmentation with v7? I understand that it is fine to perform post-processing functions outside the recon-all stream with newer versions (provided recon-all was done with the same version). Is my understanding correct?
Thank you for your assistance.
- Vanessa
freesurfer@nmr.mgh.harvard.edu
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Iglesias Gonzalez, Juan E. -
Vanessa Cropley