Not yet. We are hoping FreeSurfer 6.1 will work nicely with the HCP Pipelines. For now version 6.0 has some regressions as far as surface placement goes and there are also some adaptations we need to make to the pipelines.
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of CAGNA Bastien bastien.CAGNA@univ-amu.fr Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, March 13, 2017 at 7:21 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?
Dear freesurfer experts,
I'm wondering if it's possible to run the human connetome project's minimal processing pipeline using freesurfer 6 ?
Does it require some update of the pipeline or is there anybody that have already enjoyed the new freesurfer version with this pipeline ?
Thank you for your attention and your help,
Bastien Cagna
_______________________________________________ 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.
To augment Matt's comment, the v6.0 T1-only stream is more accurate and sensitive to than 5.3 according to our tests (both cortically and subcortically). I think Matt has found some examples where the T1+T2 stream has some inaccurate placement. Matt, weren't you going to send me examples?
doug
On 3/13/17 5:09 PM, Matt Glasser wrote:
Not yet. We are hoping FreeSurfer 6.1 will work nicely with the HCP Pipelines. For now version 6.0 has some regressions as far as surface placement goes and there are also some adaptations we need to make to the pipelines.
Peace,
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of CAGNA Bastien <bastien.CAGNA@univ-amu.fr mailto:bastien.CAGNA@univ-amu.fr> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, March 13, 2017 at 7:21 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?
Dear freesurfer experts,
I'm wondering if it's possible to run the human connetome project's minimal processing pipeline using freesurfer 6 ?
Does it require some update of the pipeline or is there anybody that have already enjoyed the new freesurfer version with this pipeline ?
Thank you for your attention and your help,
Bastien Cagna
_______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Matt
To state without qualification that "6.0 has some regressions as far as surface placement" is incorrect. We quantified its test-retest reliability, accuracy and power to detect disease effects and all were improved relative to 5.3. We tested V6 on hundreds of datasets across an array of pathologies and different MR sequences, field strengths and scanners. We visually inspected dozens of brains multiple times in the process of improving accuracy and robustness. I can believe that on Wash U HCP data there could be some specific issues, but to imply that V6 is generally less accurate is simply incorrect.
cheers Bruce
On Mon, 13 Mar 2017, Matt Glasser wrote:
Not yet. We are hoping FreeSurfer 6.1 will work nicely with the HCP Pipelines. For now version 6.0 has some regressions as far as surface placement goes and there are also some adaptations we need to make to the pipelines.
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of CAGNA Bastien bastien.CAGNA@univ-amu.fr Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, March 13, 2017 at 7:21 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?
Dear freesurfer experts,
I'm wondering if it's possible to run the human connetome project's minimal processing pipeline using freesurfer 6 ?
Does it require some update of the pipeline or is there anybody that have already enjoyed the new freesurfer version with this pipeline ?
Thank you for your attention and your help,
Bastien Cagna
_______________________________________________ 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.
Hi Bruce,
I don¹t think the hires T1w and T2w stuff are as accurate as 5.3 in the HCP 0.7mm data that I have looked at (and as I recall at least one other user had some similar issues, as did one of my collaborators), but that was all I meant to refer to. Sorry if my reply came across more general than that, as of course we want to move to using FreeSurfer V6+ in the future. It is the highres T1w and T2w stuff that my pipelines are designed to exploit, however. Also there are some changes I have to make to the HCP Pipelines for FreeSurfer V6+ because of differing file names, etc.
Best,
Matt.
On 3/13/17, 9:40 PM, "Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Matt
To state without qualification that "6.0 has some regressions as far as surface placement" is incorrect. We quantified its test-retest reliability, accuracy and power to detect disease effects and all were improved relative to 5.3. We tested V6 on hundreds of datasets across an array of pathologies and different MR sequences, field strengths and scanners. We visually inspected dozens of brains multiple times in the process of improving accuracy and robustness. I can believe that on Wash U HCP data there could be some specific issues, but to imply that V6 is generally less accurate is simply incorrect.
cheers Bruce
On Mon, 13 Mar 2017, Matt Glasser wrote:
Not yet. We are hoping FreeSurfer 6.1 will work nicely with the HCP Pipelines. For now version 6.0 has some regressions as far as surface placement goes and there are also some adaptations we need to make to the pipelines.
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of CAGNA Bastien bastien.CAGNA@univ-amu.fr Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, March 13, 2017 at 7:21 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?
Dear freesurfer experts,
I'm wondering if it's possible to run the human connetome project's minimal processing pipeline using freesurfer 6 ?
Does it require some update of the pipeline or is there anybody that have already enjoyed the new freesurfer version with this pipeline ?
Thank you for your attention and your help,
Bastien Cagna
_______________________________________________ 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. _______________________________________________
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.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Matt Glasser