Segmentation comparison between FS5.3 and FS6beta

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R: Re: recon-all base error

Matthieu Vanhoutte

15 Dec 2015 15 Dec '15

5:22 a.m.

Dear FS's experts,

I have tried the recon-all process on one subject with both FS v5.3 and v6_beta.

Although subcortical structures seems to be better segmented in v6_beta, I find that v6_beta over-segmented some other structures as cerebellum, hippocampus, ...

I will attached in the FileDrop my T1.mgz, and aparc.a2009s+aseg.mgz files for both freesurfer versions.

Could you please look at it and tell me what do you think about and advise me ?

Thank you !

Best regards, Matthieu

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Bruce Fischl

15 Dec 15 Dec

11:38 a.m.

Hi Matthieu

I think 6.0 looks better overall, even in the beta that you have. The 5.3 segmentation looks like it is underestimating cerebellum and hippocampus to me.

cheers Bruce

On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

...

Dear FS's experts,

I have tried the recon-all process on one subject with both FS v5.3 and v6_beta.

Although subcortical structures seems to be better segmented in v6_beta, I find that v6_beta over-segmented some other structures as cerebellum, hippocampus, ...

I will attached in the FileDrop my T1.mgz, and aparc.a2009s+aseg.mgz files for both freesurfer versions.

Could you please look at it and tell me what do you think about and advise me ?

Thank you !

Best regards, Matthieu

Matthieu Vanhoutte

12:13 p.m.

Hi Bruce,

Is it better to overestimate than underestimate ? Please find joined this two saggital images (FS v5.3 and FS v6_beta) of brain segmentation. Cerebellum in v6_beta really seems to go outside of its borderlines even if cerebellum in v5.3 is indeed lightly underestimated.

Looking at the cerebral cortex I found the segmentation less "smoothed" in v6_beta (with more irregularities near pial surface) than in v5.3 according to coronal views of segmentations joined.

What do you think about it ? Would you advise me to go on with the v6_beta anyway ?

Would it be better and coherent to use a more recent "nightly dev builds" of FreeSurfer for future publication ?

Thanks in advance for helping !

Best regards,

Matthieu

2015-12-15 17:38 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:

...

Hi Matthieu

I think 6.0 looks better overall, even in the beta that you have. The 5.3 segmentation looks like it is underestimating cerebellum and hippocampus to me.

cheers Bruce

On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

...
Dear FS's experts,

I have tried the recon-all process on one subject with both FS v5.3 and

v6_beta.

...
Although subcortical structures seems to be better segmented in v6_beta,

I find that v6_beta over-segmented some other

...
structures as cerebellum, hippocampus, ...

I will attached in the FileDrop my T1.mgz, and aparc.a2009s+aseg.mgz

files for both freesurfer versions.

...
Could you please look at it and tell me what do you think about and

advise me ?

...
Thank you !

Best regards, Matthieu

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.

Harms, Michael

12:22 p.m.

Bruce Fischl

12:26 p.m.

me too On Tue, 15 Dec 2015, Harms, Michael wrote:

...

It seems problematic to me to use a nightly dev build for publication.

cheers, -MH

-- Michael Harms, Ph.D.

Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu

From: Matthieu Vanhoutte matthieuvanhoutte@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, December 15, 2015 11:13 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation comparison between FS5.3 and FS6beta

Hi Bruce,

Is it better to overestimate than underestimate ? Please find joined this two saggital images (FS v5.3 and FS v6_beta) of brain segmentation. Cerebellum in v6_beta really seems to go outside of its borderlines even if cerebellum in v5.3 is indeed lightly underestimated.

Looking at the cerebral cortex I found the segmentation less "smoothed" in v6_beta (with more irregularities near pial surface) than in v5.3 according to coronal views of segmentations joined.

What do you think about it ? Would you advise me to go on with the v6_beta anyway ?

Would it be better and coherent to use a more recent "nightly dev builds" of FreeSurfer for future publication ?

Thanks in advance for helping !

Best regards,

Matthieu

2015-12-15 17:38 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Matthieu
  I think 6.0 looks better overall, even in the beta that you have. The 5.3
  segmentation looks like it is underestimating cerebellum and hippocampus to
  me.

  cheers
  Bruce


  On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

  > Dear FS's experts,
  >
  > I have tried the recon-all process on one subject with both FS v5.3 and v6_beta.
  >
  > Although subcortical structures seems to be better segmented in v6_beta, I find that v6_beta over-segmented some
  other
  > structures as cerebellum, hippocampus, ...
  >
  > I will attached in the FileDrop my T1.mgz, and aparc.a2009s+aseg.mgz files for both freesurfer versions.
  >
  > Could you please look at it and tell me what do you think about and advise me ?
  >
  > Thank you !
  >
  > Best regards,
  > Matthieu
  >
  >
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.

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Bruce Fischl

12:22 p.m.

Hi Matthiew

we are still hoping to get an official v6 release out in the next month or two, so it would be best to use that which I think will outperform whatever beta you have and 5.3. If you can't wait you are probably better off using 5.3 (although I think the v6 you have is more accurate) so that people can at least replicate the software version you are using

cheers Bruce

On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

...

Hi Bruce,

Is it better to overestimate than underestimate ? Please find joined this two saggital images (FS v5.3 and FS v6_beta) of brain segmentation. Cerebellum in v6_beta really seems to go outside of its borderlines even if cerebellum in v5.3 is indeed lightly underestimated.

Looking at the cerebral cortex I found the segmentation less "smoothed" in v6_beta (with more irregularities near pial surface) than in v5.3 according to coronal views of segmentations joined.

What do you think about it ? Would you advise me to go on with the v6_beta anyway ?

Would it be better and coherent to use a more recent "nightly dev builds" of FreeSurfer for future publication ?

Thanks in advance for helping !

Best regards,

Matthieu

2015-12-15 17:38 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Matthieu
  I think 6.0 looks better overall, even in the beta that you have. The 5.3
  segmentation looks like it is underestimating cerebellum and hippocampus to
  me.

  cheers
  Bruce


  On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

  > Dear FS's experts,
  >
  > I have tried the recon-all process on one subject with both FS v5.3 and v6_beta.
  >
  > Although subcortical structures seems to be better segmented in v6_beta, I find that v6_beta over-segmented some
  other
  > structures as cerebellum, hippocampus, ...
  >
  > I will attached in the FileDrop my T1.mgz, and aparc.a2009s+aseg.mgz files for both freesurfer versions.
  >
  > Could you please look at it and tell me what do you think about and advise me ?
  >
  > Thank you !
  >
  > Best regards,
  > Matthieu
  >
  >
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.

Matthieu Vanhoutte

12:33 p.m.

Hi Bruce,

All right then it's only a question of time ofr the new v6 release !

Meanwhile, is it possible and coherent : 1) to use the partial volume correction provided in the v6 beta version of FreeSurfer despite the fact that recon-all have been done for all subjects with the v5.3 ? 2) to use sub-segmentations of brainstem and hippocampus provided by v6 beta version of FreeSurfer despite the fact that recon-all have been done for all subjects with the v5.3 ?

Thanks !

Best regards, Matthieu

2015-12-15 18:22 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:

...

Hi Matthiew

we are still hoping to get an official v6 release out in the next month or two, so it would be best to use that which I think will outperform whatever beta you have and 5.3. If you can't wait you are probably better off using 5.3 (although I think the v6 you have is more accurate) so that people can at least replicate the software version you are using

cheers Bruce

On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

Hi Bruce,

...
Is it better to overestimate than underestimate ? Please find joined this two saggital images (FS v5.3 and FS v6_beta) of brain segmentation. Cerebellum in v6_beta really seems to go outside of its borderlines even if cerebellum in v5.3 is indeed lightly underestimated.

Looking at the cerebral cortex I found the segmentation less "smoothed" in v6_beta (with more irregularities near pial surface) than in v5.3 according to coronal views of segmentations joined.

What do you think about it ? Would you advise me to go on with the v6_beta anyway ?

Would it be better and coherent to use a more recent "nightly dev builds" of FreeSurfer for future publication ?

Thanks in advance for helping !

Best regards,

Matthieu

2015-12-15 17:38 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Matthieu
  I think 6.0 looks better overall, even in the beta that you have.
The 5.3 segmentation looks like it is underestimating cerebellum and hippocampus to me.
  cheers
  Bruce


  On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

  > Dear FS's experts,
  >
  > I have tried the recon-all process on one subject with both FS
v5.3 and v6_beta. > > Although subcortical structures seems to be better segmented in v6_beta, I find that v6_beta over-segmented some other > structures as cerebellum, hippocampus, ... > > I will attached in the FileDrop my T1.mgz, and aparc.a2009s+aseg.mgz files for both freesurfer versions. > > Could you please look at it and tell me what do you think about and advise me ? > > Thank you ! > > Best regards, > Matthieu > > _______________________________________________ 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.

Bruce Fischl

1 p.m.

1) what partial volume correction do you mean? 2) I'll leave this for Eugenio and Koen.

Bruce

On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

...

Hi Bruce,

All right then it's only a question of time ofr the new v6 release !

Meanwhile, is it possible and coherent :

to use the partial volume correction provided in the v6 beta version of FreeSurfer despite the fact that recon-all have been

done for all subjects with the v5.3 ? 2) to use sub-segmentations of brainstem and hippocampus provided by v6 beta version of FreeSurfer despite the fact that recon-all have been done for all subjects with the v5.3 ?

Thanks !

Best regards, Matthieu

2015-12-15 18:22 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Matthiew

  we are still hoping to get an official v6 release out in the next month or two, so it would be best to use that
  which I think will outperform whatever beta you have and 5.3. If you can't wait you are probably better off using
  5.3 (although I think the v6 you have is more  accurate) so that people can at least replicate the software version
  you are using

  cheers
  Bruce

  On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

        Hi Bruce,

        Is it better to overestimate than underestimate ? Please find joined this two saggital images (FS v5.3
        and FS v6_beta) of brain
        segmentation. Cerebellum in v6_beta really seems to go outside of its borderlines even if cerebellum in
        v5.3 is indeed lightly
        underestimated.

        Looking at the cerebral cortex I found the segmentation less "smoothed" in v6_beta (with more
        irregularities near pial surface)
        than in v5.3 according to coronal views of segmentations joined.

        What do you think about it ?  Would you advise me to go on with the v6_beta anyway ?

        Would it be better and coherent to use a more recent "nightly dev builds" of FreeSurfer for future
        publication ?

        Thanks in advance for helping !

        Best regards,

        Matthieu

        2015-12-15 17:38 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
              Hi Matthieu

              I think 6.0 looks better overall, even in the beta that you have. The 5.3
              segmentation looks like it is underestimating cerebellum and hippocampus to
              me.

              cheers
              Bruce


              On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

              > Dear FS's experts,
              >
              > I have tried the recon-all process on one subject with both FS v5.3 and v6_beta.
              >
              > Although subcortical structures seems to be better segmented in v6_beta, I find that v6_beta
        over-segmented some
              other
              > structures as cerebellum, hippocampus, ...
              >
              > I will attached in the FileDrop my T1.mgz, and aparc.a2009s+aseg.mgz files for both freesurfer
        versions.
              >
              > Could you please look at it and tell me what do you think about and advise me ?
              >
              > Thank you !
              >
              > Best regards,
              > Matthieu
              >
              >
        _______________________________________________
        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.

Douglas N Greve

1:21 p.m.

btw, we are still making changes to version 6 so don't assume that the results from the beta will be consistent with the current beta distribution.

On 12/15/2015 12:22 PM, Bruce Fischl wrote:

...

Hi Matthiew

we are still hoping to get an official v6 release out in the next month or two, so it would be best to use that which I think will outperform whatever beta you have and 5.3. If you can't wait you are probably better off using 5.3 (although I think the v6 you have is more accurate) so that people can at least replicate the software version you are using

cheers Bruce

On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

...
Hi Bruce,

Is it better to overestimate than underestimate ? Please find joined this two saggital images (FS v5.3 and FS v6_beta) of brain segmentation. Cerebellum in v6_beta really seems to go outside of its borderlines even if cerebellum in v5.3 is indeed lightly underestimated.

Looking at the cerebral cortex I found the segmentation less "smoothed" in v6_beta (with more irregularities near pial surface) than in v5.3 according to coronal views of segmentations joined.

What do you think about it ? Would you advise me to go on with the v6_beta anyway ?

Would it be better and coherent to use a more recent "nightly dev builds" of FreeSurfer for future publication ?

Thanks in advance for helping !

Best regards,

Matthieu

2015-12-15 17:38 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Matthieu
  I think 6.0 looks better overall, even in the beta that you 
have. The 5.3 segmentation looks like it is underestimating cerebellum and hippocampus to me.
  cheers
  Bruce


  On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

  > Dear FS's experts,
  >
  > I have tried the recon-all process on one subject with both 
FS v5.3 and v6_beta. > > Although subcortical structures seems to be better segmented in v6_beta, I find that v6_beta over-segmented some other > structures as cerebellum, hippocampus, ... > > I will attached in the FileDrop my T1.mgz, and aparc.a2009s+aseg.mgz files for both freesurfer versions. > > Could you please look at it and tell me what do you think about and advise me ? > > Thank you ! > > Best regards, > Matthieu > > _______________________________________________ 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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Matthieu Vanhoutte

2:51 p.m.

Sorry Douglas I didn't well understand what you mean. Did you mean that results from beta distribution aren't valuable ?

Best regards,

Matthieu Le 15 déc. 2015 19:24, "Douglas N Greve" greve@nmr.mgh.harvard.edu a écrit :

...

btw, we are still making changes to version 6 so don't assume that the results from the beta will be consistent with the current beta distribution.

On 12/15/2015 12:22 PM, Bruce Fischl wrote:

...
Hi Matthiew

we are still hoping to get an official v6 release out in the next month or two, so it would be best to use that which I think will outperform whatever beta you have and 5.3. If you can't wait you are probably better off using 5.3 (although I think the v6 you have is more accurate) so that people can at least replicate the software version you are using

cheers Bruce

On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

...
Hi Bruce,

Is it better to overestimate than underestimate ? Please find joined this two saggital images (FS v5.3 and FS v6_beta) of brain segmentation. Cerebellum in v6_beta really seems to go outside of its borderlines even if cerebellum in v5.3 is indeed lightly underestimated.

Looking at the cerebral cortex I found the segmentation less "smoothed" in v6_beta (with more irregularities near pial surface) than in v5.3 according to coronal views of segmentations joined.

What do you think about it ? Would you advise me to go on with the v6_beta anyway ?

Would it be better and coherent to use a more recent "nightly dev builds" of FreeSurfer for future publication ?

Thanks in advance for helping !

Best regards,

Matthieu

2015-12-15 17:38 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Matthieu
  I think 6.0 looks better overall, even in the beta that you
have. The 5.3 segmentation looks like it is underestimating cerebellum and hippocampus to me.
  cheers
  Bruce


  On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

  > Dear FS's experts,
  >
  > I have tried the recon-all process on one subject with both
FS v5.3 and v6_beta. > > Although subcortical structures seems to be better segmented in v6_beta, I find that v6_beta over-segmented some other > structures as cerebellum, hippocampus, ... > > I will attached in the FileDrop my T1.mgz, and aparc.a2009s+aseg.mgz files for both freesurfer versions. > > Could you please look at it and tell me what do you think about and advise me ? > > Thank you ! > > Best regards, > Matthieu > > _______________________________________________ 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Douglas N Greve

3:08 p.m.

I mean that they may/will change between the current beta release and the final release.

On 12/15/2015 02:51 PM, Matthieu Vanhoutte wrote:

...

Sorry Douglas I didn't well understand what you mean. Did you mean that results from beta distribution aren't valuable ?

Best regards,

Matthieu

Le 15 déc. 2015 19:24, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> a écrit :

btw, we are still making changes to version 6 so don't assume that the
results from the beta will be consistent with the current beta
distribution.

On 12/15/2015 12:22 PM, Bruce Fischl wrote:
> Hi Matthiew
>
> we are still hoping to get an official v6 release out in the next
> month or two, so it would be best to use that which I think will
> outperform whatever beta you have and 5.3. If you can't wait you are
> probably better off using 5.3 (although I think the v6 you have is
> more  accurate) so that people can at least replicate the software
> version you are using
>
> cheers
> Bruce
>
> On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:
>
>> Hi Bruce,
>>
>> Is it better to overestimate than underestimate ? Please find
joined
>> this two saggital images (FS v5.3 and FS v6_beta) of brain
>> segmentation. Cerebellum in v6_beta really seems to go outside
of its
>> borderlines even if cerebellum in v5.3 is indeed lightly
>> underestimated.
>>
>> Looking at the cerebral cortex I found the segmentation less
>> "smoothed" in v6_beta (with more irregularities near pial surface)
>> than in v5.3 according to coronal views of segmentations joined.
>>
>> What do you think about it ?  Would you advise me to go on with the
>> v6_beta anyway ?
>>
>> Would it be better and coherent to use a more recent "nightly dev
>> builds" of FreeSurfer for future publication ?
>>
>> Thanks in advance for helping !
>>
>> Best regards,
>>
>> Matthieu
>>
>> 2015-12-15 17:38 GMT+01:00 Bruce Fischl
<fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>:
>>       Hi Matthieu
>>
>>       I think 6.0 looks better overall, even in the beta that you
>> have. The 5.3
>>       segmentation looks like it is underestimating cerebellum and
>> hippocampus to
>>       me.
>>
>>       cheers
>>       Bruce
>>
>>
>>       On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:
>>
>>       > Dear FS's experts,
>>       >
>>       > I have tried the recon-all process on one subject with both
>> FS v5.3 and v6_beta.
>>       >
>>       > Although subcortical structures seems to be better
segmented
>> in v6_beta, I find that v6_beta over-segmented some
>>       other
>>       > structures as cerebellum, hippocampus, ...
>>       >
>>       > I will attached in the FileDrop my T1.mgz, and
>> aparc.a2009s+aseg.mgz files for both freesurfer versions.
>>       >
>>       > Could you please look at it and tell me what do you think
>> about and advise me ?
>>       >
>>       > Thank you !
>>       >
>>       > Best regards,
>>       > Matthieu
>>       >
>>       >
>> _______________________________________________
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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
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>> contains patient information, please contact the Partners
Compliance
>> HelpLine at
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>>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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freesurfer@nmr.mgh.harvard.edu

10 comments

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participants (4)

Bruce Fischl
Douglas N Greve
Harms, Michael
Matthieu Vanhoutte