Can you upload an example dataset? It looked like an intensity normalization failure that probably caused a topological defect
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Elana Sarabin Sent: Friday, August 7, 2020 11:08 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all Soft Errors
External Email - Use Caution More so that the brainmask.mgz is missing a lot of both grey and white matter. For some the area cut out in brainmask is much smaller and for others it is large just like the photo I sent. I am wondering if there is a way to fix this since 50% of my participants scans look like this.
Thanks, Elana
Get Outlook for iOShttps://aka.ms/o0ukef ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Sent: Friday, August 7, 2020 8:17:42 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all Soft Errors
[△EXTERNAL]
This error shows a massive failure. Is this what you are describing as:
includes areas to the white matter, even though visual inspection concludes that the area should be grey matter.
On 8/6/2020 9:00 PM, Elana Sarabin wrote:
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Here is one photo. Seems this is the most I can send at once. Most errors look just like this however sometimes larger and sometimes smaller.
Best,
Elana
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, August 4, 2020 at 8:01 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all Soft Errors
[△EXTERNAL]
Can you send a picture of the type of errors you are seeing?
On 7/31/2020 9:03 AM, Elana Sarabin wrote:
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Here is the recon-all.log file.
Thanks,
Elana
-----Original Message-----
From: Elana Sarabin
Sent: July 30, 2020 10:21 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: Recon-all Soft Errors
Here is the recon-all.log file.
Thanks,
Elana
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu
Sent: July 30, 2020 10:00 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 197, Issue 59
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Today's Topics:
1. FS 7.1.0 - Editing intensity values for WM (Nils B?er)
2. Re: FS 7.1.0 - Editing intensity values for WM (Fischl, Bruce)
3. Creating .annot file for a mri_decimate downsampeld version
of pial surface (Donelson Berger)
4. GONE: -make to recon-all (Johnson, Hans J)
5. Re: fsgd file - glmfit error
(Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience)
6. Re: Recon-all Soft Errors (Zollei, Lilla,Ph.D.)
7. bad interpreter: No such file or directory error
(Hengameh Marzbani)
8. Re: overlapping/ superimposing regions of one analysis over
another (Douglas N. Greve)
9. Re: Creating .annot file for a mri_decimate downsampeld
version of pial surface (Douglas N. Greve)
10. Re: Recon-all Soft Errors (Douglas N. Greve)
11. Re: Coregistration to MNI (Douglas N. Greve)
12. mri_aparc2aseg: how to remove redundant output labels? (Ellen Ji)
13. Re: bad interpreter: No such file or directory error (fsbuild)
----------------------------------------------------------------------
Message: 1
Date: Wed, 29 Jul 2020 21:27:03 +0200
From: Nils B?er nils.tobias94@gmail.commailto:nils.tobias94@gmail.com
Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM
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Hello everyone,
I just have a short question, because I can't find anything helpful in the tutorials.
In my MRI scans freesurfer includes areas to the white matter, even though visual inspection concludes that the area should be grey matter. Is there a possibility to change the value at which freesurfer includes areas to the WM, which i can just change? For example freesurfer includes areas to the WM with intensity values below 85 and i want to change that.
I'd be thankful for any feedback/links to guides.
Best regards,
Nils
--
Nils B?er
Research Assistant with Bachelor Degree (WHB) *Psychology and Movement* University of Paderborn Department of Sports and Health Warburger Str. 100
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Email: nils.tobias94@gmail.commailto:nils.tobias94@gmail.com / nboeer@mail.uni-paderborn.demailto:nboeer@mail.uni-paderborn.de nils.tobias94@gmail.commailto:nils.tobias94@gmail.com
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