New subject: Using SPM segmentations in FreeSurfer

24 Jan 2022


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Oh, sorry... Following the steps from the previous mail you should run this command:
mri_mask brain.mgz new_segmentation.mgz wm.seg.mgz
Best,
Falk
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Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von falk.luesebrink@med.ovgu.de falk.luesebrink@med.ovgu.de
Gesendet: Montag, 24. Januar 2022 08:41:15
An: Freesurfer support list
Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
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Hi Nathan,
well, once again, I can't be much of help with regards to your error message. Have you had a look at the data and does it looks reasonable up to that point? Which FreeSurfer version are you running?
FreeSurfer needs to have the data in a very specific form. In case of the white matter segmentation the resulting volume should have a value of 110 where white matter is located. The SPM segmentation has values of 0 to 1. Therefore, if you would simply try to use that, it wouldn't work. The given command should do that while using the SPM segmentation to mask the brain.mgz. Afterwards, the ventricles and subcortical structures will be filled based on the aseg.presurf.mgz and set to values of 250. The other commands changes the WM segmentation so that the neighbors of all voxels labeled as WM have a face in common - no edges or corners allowed.
Best,
Falk
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Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Nathan Kindred (PGR) N.Kindred1@newcastle.ac.uk
Gesendet: Freitag, 21. Januar 2022 18:18:14
An: Freesurfer support list
Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
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Hi Falk,
Thank you, I appreciate your help. By using the convert and mask steps you used I can get through to the -pial stage of autorecon3 before hitting an error (command terminated by signal 11).
I was wondering about the mri_edit_wm_with_aseg and mri_pretess steps you take though as won’t these essentially overwrite the wm.mgz file so that the SPM segmentation is no longer incorporated? Apologies if I am miss understanding, that is just what appears to happen when I try to replicate those steps (with those included I hit no errors but the outputs are unchanged from before I incorporated the SPM file).
Best,
Nathan
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of falk.luesebrink@med.ovgu.de falk.luesebrink@med.ovgu.de
Date: Thursday, 20 January 2022 at 07:57
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
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Hi Nathan,
well, I never encountered that error. Therefore, I probably can't be of much help. Anyways, if you provide more details, e.g. which FreeSurfer version you are using, the recon-all.log, and what commands you are running exactly to incorporate the SPM segmentation someone else probably can help.
When I was using different WM segmentations in v6, I did the following:
*   Convert the segmentation (e.g. mri_convert -rl wm.mgz new_segmentation.nii new_segmentation.mgz)
  *   Mask brain.mgz using the segmentation (e.g. mri_mask brain.mgz new_segmentation.mgz wm.mgz)
  *   Then continuing with the remaining steps of the segmentation stage accoring to the recon-all table (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1RWkD9q9eCja6mIMMwKBpTWWFQ5PbuMZrYDBZdgbIW7YokG...<https://secure-web.cisco.com/1reDdF1_RCvW1SGMg5MMY-wNwDhAcqYlMuRhT7puZZazh6c...
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     *   mri_edit_wm_with_aseg wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz
     *   mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
  *   Then continuing with the remaining stages of autorecon2 of recon-all by running
     *   recon-all -s <your_ID> -fill -tessellate -smooth1 -inflate1 -qsphere -fix -white -smooth2 -inflate2 -curvHK -curvstats -autorecon3
This will work for FreeSurfer v6. For v7 the stages of recon-all have changed and you might miss something. However, there is no such table like for v6 and I haven't been using v7 much, so I can't provide a guide like above for v7.
Best,
Falk
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Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Nathan Kindred (PGR) N.Kindred1@newcastle.ac.uk
Gesendet: Mittwoch, 19. Januar 2022 14:00:23
An: Freesurfer support list
Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
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Hi Falk,
Thank you for the response!
I have given your suggestion a try and I am still getting the following error:
free(): double free detected in tcache 2
Command terminated by signal 6
Best,
Nathan
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of falk.luesebrink@med.ovgu.de falk.luesebrink@med.ovgu.de
Date: Wednesday, 19 January 2022 at 12:52
To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
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Hi Nathan,
are you sure that the SPM segmentation and the wm.mgz share the same space? You could try e.g. mri_convert -rl wm.mgz your_spm_segmentation.nii spm_wm.mgz
Best,
Falk
________________________________
Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Nathan Kindred (PGR) N.Kindred1@newcastle.ac.uk
Gesendet: Mittwoch, 19. Januar 2022 13:29:46
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Using SPM segmentations in FreeSurfer
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Hi,
I have been trying to incorporate segmentation files from SPM into FreeSurfer to improve the surfaces, but I am not sure if I am going about it in the right way. I have been replacing the wm.mgz file with a file from SPM and then running ‘recon-all -s ${subject} -autorecon2-wm -autorecon3’, but I keep getting errors. I have tried using both conform and conform_min as part of mri_convert when replacing the wm.mgz file with an SPM file but in both cases I still get errors.
Are there other steps I should be taking or a different line of code I should run to get this to work?
Thanks,
Nathan
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