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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 External Email - Use Caution
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 (https://secure-web.cisco.com/1dyRROYKDNJGarNKmjCVc1Mu8ZTZROVHZf9v1uzAx0R8RhM...) by running * 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
________________________________ 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
External Email - Use Caution 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 ⚠ External sender. Take care when opening links or attachments. Do not provide your login details.
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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
External Email - Use Caution 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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