Re: [Freesurfer] Recon-all Soft Errors

Can you send a picture of the type of errors you are seeing?

On 7/31/2020 9:03 AM, Elana Sarabin wrote:

     External Email - Use Caution

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.edu Subject: Re: Recon-all Soft Errors

Here is the recon-all.log file.

Thanks, Elana

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of freesurfer-request@nmr.mgh.harvard.edu Sent: July 30, 2020 10:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 197, Issue 59

[△EXTERNAL]

Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu

You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."

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.com Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM To: freesurfer@nmr.mgh.harvard.edu Message-ID: CALZW1G2=-OvWkL81sZxTBiMCKBwiOn6EwSfd2xP0NzEWQYBSTw@mail.gmail.com Content-Type: text/plain; charset="utf-8"

     External Email - Use Caution

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 33098 Paderborn Room: Sp 1.401

Email: nils.tobias94@gmail.com / nboeer@mail.uni-paderborn.de nils.tobias94@gmail.com Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ https://sug.uni-paderborn.de/department/it/ https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/

https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail Virenfrei. www.avast.com https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>