Freesurfer tutorial

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Esteban, Eva(GE Healthcare)

22 Aug 2017 22 Aug '17

noon

Good afternoon, I am new to Freesurfer and following the instructions to find out the Cortical Thickness of a Volume-defined ROI(http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness), everything goes well until step 4. Even if I try to use -reshape-factor 7 as suggested, it reshapes it to 6 and so the next step gives an error because the segmentation is shaped to 7. Would anyone mind giving me some guidance on how to do it? Many thanks, Eva

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Douglas Greve

22 Aug 22 Aug

12:32 p.m.

try it without doing any reshaping. If that works, then I'll edit the wiki

On 8/22/17 12:00 PM, Esteban, Eva(GE Healthcare) wrote:

...

Good afternoon,

  I am new to Freesurfer and following the instructions to find
  out the Cortical Thickness of a Volume-defined
  ROI(http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness),
  everything goes well until step 4. Even if I try to use
  –reshape-factor 7 as suggested, it reshapes it to 6 and so the
  next step gives an error because the segmentation is shaped to
  7. Would anyone mind giving me some guidance on how to do it?


  Many thanks,


  Eva

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

Esteban, Eva(GE Healthcare)

24 Aug 24 Aug

2:09 p.m.

Hello,

That worked! Thank you very much. Also, I am trying to understand the information given by mri_segstats and I can find info on the different arguments for the command but not on how to interpret the output. Any recommendations?

Thank you!

Eva

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: 22 August 2017 17:33 To: freesurfer@nmr.mgh.harvard.edu Subject: EXT: Re: [Freesurfer] Freesurfer tutorial

try it without doing any reshaping. If that works, then I'll edit the wiki

On 8/22/17 12:00 PM, Esteban, Eva(GE Healthcare) wrote: Good afternoon, I am new to Freesurfer and following the instructions to find out the Cortical Thickness of a Volume-defined ROI(http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness), everything goes well until step 4. Even if I try to use -reshape-factor 7 as suggested, it reshapes it to 6 and so the next step gives an error because the segmentation is shaped to 7. Would anyone mind giving me some guidance on how to do it? Many thanks, Eva

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Boyd, Emma

2:51 p.m.

Hi Eva,

Have you taken a look at the help text for mri_segstats (mri_segstats --help)? The information under 'summary file format' and 'examples' may be helpful.

Also, this page might have some helpful information for you on working with FreeSurfer stats files: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROIV6.0

Please let us know if there's anything you'd like us to clarify.

Best,

Emma

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Esteban, Eva(GE Healthcare) Eva.Esteban@ge.com Sent: Thursday, August 24, 2017 2:09 PM To: Freesurfer support list Subject: [Freesurfer] Freesurfer tutorial

Hello,

Thank you!

Eva

try it without doing any reshaping. If that works, then I'll edit the wiki

On 8/22/17 12:00 PM, Esteban, Eva(GE Healthcare) wrote:

Good afternoon,

I am new to Freesurfer and following the instructions to find out the Cortical Thickness of a Volume-defined ROI(http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness), everything goes well until step 4. Even if I try to use –reshape-factor 7 as suggested, it reshapes it to 6 and so the next step gives an error because the segmentation is shaped to 7. Would anyone mind giving me some guidance on how to do it? Many thanks, Eva

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Douglas Greve

3 Sep 3 Sep

6:59 p.m.

Thanks, I've changed the wiki. Can you be more specific about your mri_segstats question?

On 8/24/17 2:09 PM, Esteban, Eva(GE Healthcare) wrote:

...

Hello,

That worked! Thank you very much. Also, I am trying to understand the information given by mri_segstats and I can find info on the different arguments for the command but not on how to interpret the output. Any recommendations?

Thank you!

Eva

*From:*freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Douglas Greve *Sent:* 22 August 2017 17:33 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* EXT: Re: [Freesurfer] Freesurfer tutorial

try it without doing any reshaping. If that works, then I'll edit the wiki

On 8/22/17 12:00 PM, Esteban, Eva(GE Healthcare) wrote:
Good afternoon,


      I am new to Freesurfer and following the instructions to
      find out the Cortical Thickness of a Volume-defined
      ROI(http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness),
      everything goes well until step 4. Even if I try to use
      –reshape-factor 7 as suggested, it reshapes it to 6 and so
      the next step gives an error because the segmentation is
      shaped to 7. Would anyone mind giving me some guidance on
      how to do it?


      Many thanks,


      Eva




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