mri_label2label results

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Monte Carlo correction

Problem with freeview

Yang, Daniel

19 Jun 2014 19 Jun '14

7:50 p.m.

Dear all,

I found that mri_label2label generates different results, depending on whether the software’s platform is MacOS Lion or CentOS 6.

Is this possible?

Thanks! Daniel

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Bruce Fischl

19 Jun 19 Jun

7:55 p.m.

what version are you using? I think this is a bug we fixed a few months ago. Or another one....

Bruce

On Thu, 19 Jun 2014, Yang, Daniel wrote:

...

Dear all,

I found that mri_label2label generates different results, depending on whether the software’s platform is MacOS Lion or CentOS 6.

Is this possible?

Thanks! Daniel

Yang, Daniel

8:13 p.m.

Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013.

Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013?

Thanks, Daniel

On 6/19/14, 7:55 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

...

what version are you using? I think this is a bug we fixed a few months ago. Or another one....

Bruce

On Thu, 19 Jun 2014, Yang, Daniel wrote:

...
Dear all,

I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6.

Is this possible?

Thanks! Daniel

Yang, Daniel

8:48 p.m.

I just tried a few different versions of FreeSurfer. Here are the results:

1. FreeSurfer-5.3 (Linux, CentOS 6, Release: 05/15/2013) 2. FreeSurfer-5.3 (Darwin, Lion, Release: 05/15/2013) 3. FreeSurfer-dev (Linux, CentOS 6, 06/19/2014) 4. FreeSurfer-dev (Darwin, Lion, 06/19/2014)

I am comparing the results of mri_label2label and then mris_anatomical_stats here.

The results of 3 and 4 are the same The results of 1 and 2 are different The results of 1 and 3 are different The results or 2 and 4 are different

In my testing, I used an arbitrary label file and here is detail information of area, volume, thickness, thicknessstd, meancurv, gauscurv, foldind, and curvind

1: 1261.0,4900.0,2.763,0.818,0.145,0.048,28.0,3.7 2: 1109.0,4343.0,2.761,0.798,0.15,0.046,23.0,2.8 3: 1261.0,4900.0,2.763,0.818,0.132,0.032,22.0,2.3 4: 1261.0,4900.0,2.763,0.818,0.132,0.032,22.0,2.3

What should we do here? Is the difference between 1 and 3 trivial?

Thanks! Daniel

On 6/19/14, 8:13 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:

Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013.

Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013?

Thanks, Daniel

On 6/19/14, 7:55 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

what version are you using? I think this is a bug we fixed a few months ago. Or another one....

Bruce

On Thu, 19 Jun 2014, Yang, Daniel wrote:

Dear all, I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel

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

9:08 p.m.

I think it was a bug we fixed after the release. We can send you new versions on those operating systems and you can try them out.

Zeke: can you get Daniel new versions of mri_label2label?

thanks Bruce

On Fri, 20 Jun 2014, Yang, Daniel wrote:

...

Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013.

Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013?

Thanks, Daniel

On 6/19/14, 7:55 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

...
what version are you using? I think this is a bug we fixed a few months ago. Or another one....

Bruce

On Thu, 19 Jun 2014, Yang, Daniel wrote:

...
Dear all,

I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6.

Is this possible?

Thanks! Daniel

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

Yang, Daniel

10:14 p.m.

Thanks! Is there a list of bug fixed (after release) somewhere? Should we use the development version instead?

Please tell me that it is only mri_label2label that has a bug …

On 6/19/14, 9:08 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

I think it was a bug we fixed after the release. We can send you new versions on those operating systems and you can try them out.

Zeke: can you get Daniel new versions of mri_label2label?

thanks Bruce

On Fri, 20 Jun 2014, Yang, Daniel wrote:

Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013.

Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013?

Thanks, Daniel

On 6/19/14, 7:55 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

what version are you using? I think this is a bug we fixed a few months ago. Or another one....

Bruce

On Thu, 19 Jun 2014, Yang, Daniel wrote:

Dear all,

I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6.

Is this possible?

Thanks! Daniel

Bruce Fischl

10:17 p.m.

Yes, it was only mri_label2label has that bug

...

On Jun 19, 2014, at 10:14 PM, "Yang, Daniel" yung-jui.yang@yale.edu wrote:

Thanks! Is there a list of bug fixed (after release) somewhere? Should we use the development version instead?

Please tell me that it is only mri_label2label that has a bug …

On 6/19/14, 9:08 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

I think it was a bug we fixed after the release. We can send you new versions on those operating systems and you can try them out.

Zeke: can you get Daniel new versions of mri_label2label?

thanks Bruce

On Fri, 20 Jun 2014, Yang, Daniel wrote:

Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013.

Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013?

Thanks, Daniel

On 6/19/14, 7:55 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

what version are you using? I think this is a bug we fixed a few months ago. Or another one....

Bruce

On Thu, 19 Jun 2014, Yang, Daniel wrote:

Dear all,

I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6.

Is this possible?

Thanks! Daniel

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

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

Yang, Daniel

10:53 p.m.

That is great to know!

I personally feel that there should be some sort of autoupdate function or patch file list in FreeSurfer so that when a bug like this is fixed, FreeSurfer can be updated automatically or we can apply the patch from the website. I think the one currently released should be FreeSurfer 5.3.1, with this bug fixed. This bug could have invalidated the research results to some extent if one is retrieving ROI-based stats manually, I feel. Many major software tend to have bugs after release, like SPSS, so this should be a routine... These are just my two cents.

Daniel

On Jun 19, 2014, at 10:20 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

Yes, it was only mri_label2label has that bug

On Jun 19, 2014, at 10:14 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:

Thanks! Is there a list of bug fixed (after release) somewhere? Should we use the development version instead?

Please tell me that it is only mri_label2label that has a bug …

On 6/19/14, 9:08 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

I think it was a bug we fixed after the release. We can send you new versions on those operating systems and you can try them out.

Zeke: can you get Daniel new versions of mri_label2label?

thanks Bruce

On Fri, 20 Jun 2014, Yang, Daniel wrote:

Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013.

Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013?

Thanks, Daniel

On 6/19/14, 7:55 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

what version are you using? I think this is a bug we fixed a few months ago. Or another one....

Bruce

On Thu, 19 Jun 2014, Yang, Daniel wrote:

Dear all,

I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6.

Is this possible?

Thanks! Daniel

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

Bruce Fischl

20 Jun 20 Jun

11:04 a.m.

yes, that's a lovely idea, but it is very, very difficult to get NIH funding to support such a thing.

cheers Bruce On Fri, 20 Jun 2014, Yang, Daniel wrote:

...

That is great to know!

I personally feel that there should be some sort of autoupdate function or patch file list in FreeSurfer so that when a bug like this is fixed, FreeSurfer can be updated automatically or we can apply the patch from the website. I think the one currently released should be FreeSurfer 5.3.1, with this bug fixed. This bug could have invalidated the research results to some extent if one is retrieving ROI-based stats manually, I feel. Many major software tend to have bugs after release, like SPSS, so this should be a routine... These are just my two cents.

Daniel

On Jun 19, 2014, at 10:20 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
  Yes, it was only mri_label2label has that bug
On Jun 19, 2014, at 10:14 PM, "Yang, Daniel" yung-jui.yang@yale.edu wrote:
  Thanks! Is there a list of bug fixed (after release)
  somewhere? Should we use the development version instead?
Please tell me that it is only mri_label2label that has a bug …

On 6/19/14, 9:08 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
  I think it was a bug we fixed after the release. We
  can send you new
versions on those operating systems and you can try them out.

Zeke: can you get Daniel new versions of mri_label2label?

thanks Bruce

On Fri, 20 Jun 2014, Yang, Daniel wrote:
  Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May
  2013.
Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013?

Thanks, Daniel

On 6/19/14, 7:55 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
  what version are you using? I think this
  is a bug we fixed a few months
ago. Or another one....

Bruce

On Thu, 19 Jun 2014, Yang, Daniel wrote:
  Dear all,
I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6.

Is this possible?

Thanks! Daniel

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

  _______________________________________________
  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
Yang, Daniel