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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
falk.luesebr...@med.ovgu.de <falk.luesebr...@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/1dyRROYKDNJGarNKmjCVc1Mu8ZTZROVHZf9v1uzAx0R8RhMHBLp-Xwwnu5IcbXdOimmuEd35Mf_UeaX7DDcG18FOk3cc5Nj5kgG_-isHhABzKvwWNs7DMSAh2kmaGQkix13yiUy2QRIzMxBywFd-OUzrensggjAS9vAu0cuTjr-Ob3qKoBPTNgaUIc7Tw2GnIATB0P66MODoz4pd_10hyn73MO0x4hSizx9QhMDR1IUEOyFbACkpynswiwklPBcZ8hBi2s7Ht5eTTAtJfjg3nttNUwt_IOsiBjmLz7jTQLHkb_UivAtJ5e6CD-fNW-Kg0QPlniFOw52FNXh_py0bHgELxnS0Pr2QBHD0nFI5bOFA/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F14Ybbj5o3PlY7rPb2i6Je_DtLBE_kvAlsgXuobTS7kuy-VQ4H0H0u_O6ON675Adm7LBJkPN_vbKMesdE-BPOlb6c9cWE6diVILr-eiEfuVnxEsFGJ_BDbWV5Vvhp8DXYvq0pbAMZpoReB6ERBzfAEp6u_T9joWGQX5b3F0vTAEGUh6bY3vcO8F70NmZCAhvzqxSzA6oJmHKlXuqoe4p1MDlDt20A8EyV3oESStmEgvCMc8O2DPvuiRBqjOM9d5JZSZ2ZakNr6H_llRM8aJh8XDUJmv1aFfE3T0a2UMJ2bz43xy_jEZSLjJo8a6MwlIgeVGD0UsPQhYLCsK4ff9qaZ6Q%252Fhttps%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Ffswiki%25252FReconAllTableStableV6.0%26data%3D04%257C01%257CN.Kindred1%2540newcastle.ac.uk%257C162fbeaa1c654f80909008d9dbea65b5%257C9c5012c9b61644c2a91766814fbe3e87%257C1%257C0%257C637782622499068823%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C2000%26sdata%3DdzLH8xPfzoOZHO5Gmlew9NBRmGfH3nDb6AfWcqoKS70%253D%26reserved%3D0)
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Nathan Kindred (PGR)
<n.kindr...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
falk.luesebr...@med.ovgu.de <falk.luesebr...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Nathan Kindred (PGR)
<n.kindr...@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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