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
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
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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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,
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
Hi,
That worked, thank you!
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu