Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much more externally in comparison to v5.3

2017-02-07 Thread Antonin Skoch 
Dear Matt,

I do not use HCP pipeline scripts for this project.

This is standard 1x1x1 mm3 data so I thought standard freeSurfer pipeline could 
work well here. 
I also thought that standard recon-all version 6.0 with this data should work 
better than v5.3 which, I expect, solved some issues with v5.3 (some of them I 
was discussing in the forum previously):

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41880.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42312.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41375.html

But anyway, thank you for your feedback.

Antonin



Since I believe you said you are using my code, I would recommend to stick
with 5.3 at this time.Peace,

Matt.

From:   on behalf of Antonin Skoch

Reply-To:  Freesurfer support list 
Date:  Tuesday, February 7, 2017 at 2:59 PM
To:  
Subject:  Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much
more externally in comparison to v5.3

Dear Bruce,

thank you for the feedback. I would definitely be interested in 6.1 beta.
What is the approximate timeline of release?
We are working on quite large project (involving -FLAIRpial) and I have to
decide whether to go to v6.0 or to stick with v5.3.
Do you think that so far the 5.3 version is better for T2/FLAIR? Why this is
the case?

Antonin

Hi Antonin

yes, V6 was not meant for T2/FLAIR and we didn't test it extensively. We
have been optimizing things in the past week for T2/FLAIR and I expect 6.1
will be better for them. We can give you a beta soon if you like.
cheers
Bruce
  On Tue, 7 
Feb 2017, Antonin Skoch wrote:

> Dear experts,
> 
> I have reprocessed my groups of subjects (originally processed by v5.3) by
> v6.0. I am using -FLAIRpial for pial surface refinement.
> 
> I have noticed that the pial surfaces in v6.0 after -FLAIRpial are positioned
> much more externally in comparison to -FLAIRpial in v5.3. The v6.0 version
> includes to pial sheet much more partial volume voxels in
> comparison to v5.3.
> 
> In contrast to v5.3, where the surfaces after -FLAIRpial were mostly
> internally with respect to pial surfaces determined by T1, in v6.0 there are
> many regions where the pial surfaces after -FLAIRpial are placed
> much externally with respect to pial surfaces determined by T1.
> 
> See the screenshot (red surfaces are pial surfaces after -FLAIRpial with
> v6.0, yellow are surfaces after -FLAIRpial with v.5.3).
> 
> I have used -nsigma_above 8 in mris_make_surfaces to prevent excluding some
> cortical regions with high signal intensity but this I used consistently in
> both versions so it should not be the reason of difference.
> 
> I have uploaded the subject processed both by 5.3 and 6.0 version to your
> server, files FLAIRpial_v5.3.tar.gz and FLAIRpial_v6.0.tar.gz.
> 
> Could you please look at my data and check whether the pial surfaces after
> -FLAIRpial in v6.0 look OK from your perspective?
> 
> Regards,
> 
> Antonin Skoch___
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Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much more externally in comparison to v5.3

2017-02-07 Thread Matt Glasser 
Since I believe you said you are using my code, I would recommend to stick
with 5.3 at this time.

Peace,

Matt.

From:   on behalf of Antonin Skoch

Reply-To:  Freesurfer support list 
Date:  Tuesday, February 7, 2017 at 2:59 PM
To:  
Subject:  Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much
more externally in comparison to v5.3

Dear Bruce,

thank you for the feedback. I would definitely be interested in 6.1 beta.
What is the approximate timeline of release?
We are working on quite large project (involving -FLAIRpial) and I have to
decide whether to go to v6.0 or to stick with v5.3.
Do you think that so far the 5.3 version is better for T2/FLAIR? Why this is
the case?

Antonin

Hi Antonin

yes, V6 was not meant for T2/FLAIR and we didn't test it extensively. We
have been optimizing things in the past week for T2/FLAIR and I expect 6.1
will be better for them. We can give you a beta soon if you like.
cheers
Bruce
  On Tue, 7 
Feb 2017, Antonin Skoch wrote:

> Dear experts,
> 
> I have reprocessed my groups of subjects (originally processed by v5.3) by
> v6.0. I am using -FLAIRpial for pial surface refinement.
> 
> I have noticed that the pial surfaces in v6.0 after -FLAIRpial are positioned
> much more externally in comparison to -FLAIRpial in v5.3. The v6.0 version
> includes to pial sheet much more partial volume voxels in
> comparison to v5.3.
> 
> In contrast to v5.3, where the surfaces after -FLAIRpial were mostly
> internally with respect to pial surfaces determined by T1, in v6.0 there are
> many regions where the pial surfaces after -FLAIRpial are placed
> much externally with respect to pial surfaces determined by T1.
> 
> See the screenshot (red surfaces are pial surfaces after -FLAIRpial with
> v6.0, yellow are surfaces after -FLAIRpial with v.5.3).
> 
> I have used -nsigma_above 8 in mris_make_surfaces to prevent excluding some
> cortical regions with high signal intensity but this I used consistently in
> both versions so it should not be the reason of difference.
> 
> I have uploaded the subject processed both by 5.3 and 6.0 version to your
> server, files FLAIRpial_v5.3.tar.gz and FLAIRpial_v6.0.tar.gz.
> 
> Could you please look at my data and check whether the pial surfaces after
> -FLAIRpial in v6.0 look OK from your perspective?
> 
> Regards,
> 
> Antonin Skoch
___ Freesurfer mailing list
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___
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much more externally in comparison to v5.3

2017-02-07 Thread Antonin Skoch 
Dear Bruce,

thank you for the feedback. I would definitely be interested in 6.1 beta. What 
is the approximate timeline of release? 
We are working on quite large project (involving -FLAIRpial) and I have to 
decide whether to go to v6.0 or to stick with v5.3.
Do you think that so far the 5.3 version is better for T2/FLAIR? Why this is 
the case?

Antonin

Hi Antonin

yes, V6 was not meant for T2/FLAIR and we didn't test it extensively. We 
have been optimizing things in the past week for T2/FLAIR and I expect 6.1 
will be better for them. We can give you a beta soon if you like.cheers
Bruce
  On Tue, 7 
Feb 2017, Antonin Skoch wrote:

> Dear experts,
> 
> I have reprocessed my groups of subjects (originally processed by v5.3) by 
> v6.0. I am using -FLAIRpial for pial surface refinement.
> 
> I have noticed that the pial surfaces in v6.0 after -FLAIRpial are positioned 
> much more externally in comparison to -FLAIRpial in v5.3. The v6.0 version 
> includes to pial sheet much more partial volume voxels in
> comparison to v5.3.
> 
> In contrast to v5.3, where the surfaces after -FLAIRpial were mostly 
> internally with respect to pial surfaces determined by T1, in v6.0 there are 
> many regions where the pial surfaces after -FLAIRpial are placed
> much externally with respect to pial surfaces determined by T1.
> 
> See the screenshot (red surfaces are pial surfaces after -FLAIRpial with 
> v6.0, yellow are surfaces after -FLAIRpial with v.5.3).
> 
> I have used -nsigma_above 8 in mris_make_surfaces to prevent excluding some 
> cortical regions with high signal intensity but this I used consistently in 
> both versions so it should not be the reason of difference.
> 
> I have uploaded the subject processed both by 5.3 and 6.0 version to your 
> server, files FLAIRpial_v5.3.tar.gz and FLAIRpial_v6.0.tar.gz.
> 
> Could you please look at my data and check whether the pial surfaces after 
> -FLAIRpial in v6.0 look OK from your perspective?
> 
> Regards,
> 
> Antonin Skoch___
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] -FLAIRpial in v6.0 positions pial surfaces much more externally in comparison to v5.3

2017-02-07 Thread Bruce Fischl 
Hi Antonin

yes, V6 was not meant for T2/FLAIR and we didn't test it extensively. We 
have been optimizing things in the past week for T2/FLAIR and I expect 6.1 
will be better for them. We can give you a beta soon if you like.

cheers
Bruce
  On Tue, 7 
Feb 2017, Antonin Skoch wrote:

> Dear experts,
> 
> I have reprocessed my groups of subjects (originally processed by v5.3) by 
> v6.0. I am using -FLAIRpial for pial surface refinement.
> 
> I have noticed that the pial surfaces in v6.0 after -FLAIRpial are positioned 
> much more externally in comparison to -FLAIRpial in v5.3. The v6.0 version 
> includes to pial sheet much more partial volume voxels in
> comparison to v5.3.
> 
> In contrast to v5.3, where the surfaces after -FLAIRpial were mostly 
> internally with respect to pial surfaces determined by T1, in v6.0 there are 
> many regions where the pial surfaces after -FLAIRpial are placed
> much externally with respect to pial surfaces determined by T1.
> 
> See the screenshot (red surfaces are pial surfaces after -FLAIRpial with 
> v6.0, yellow are surfaces after -FLAIRpial with v.5.3).
> 
> I have used -nsigma_above 8 in mris_make_surfaces to prevent excluding some 
> cortical regions with high signal intensity but this I used consistently in 
> both versions so it should not be the reason of difference.
> 
> I have uploaded the subject processed both by 5.3 and 6.0 version to your 
> server, files FLAIRpial_v5.3.tar.gz and FLAIRpial_v6.0.tar.gz.
> 
> Could you please look at my data and check whether the pial surfaces after 
> -FLAIRpial in v6.0 look OK from your perspective?
> 
> Regards,
> 
> Antonin Skoch
> 
>
___
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.