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/14Ybbj5o3PlY7rPb2i6Je_DtLBE_kvAlsgXuobTS7kuy-VQ4H0H0u_O6ON675Adm7LBJkPN_vbKMesdE-BPOlb6c9cWE6diVILr-eiEfuVnxEsFGJ_BDbWV5Vvhp8DXYvq0pbAMZpoReB6ERBzfAEp6u_T9joWGQX5b3F0vTAEGUh6bY3vcO8F70NmZCAhvzqxSzA6oJmHKlXuqoe4p1MDlDt20A8EyV3oESStmEgvCMc8O2DPvuiRBqjOM9d5JZSZ2ZakNr6H_llRM8aJh8XDUJmv1aFfE3T0a2UMJ2bz43xy_jEZSLjJo8a6MwlIgeVGD0UsPQhYLCsK4ff9qaZ6Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllTableStableV6.0) 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 ⚠ External sender. Take care when opening links or attachments. Do not provide your login details. External Email - Use Caution 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? 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