Dear Emma, Thank you for your response!
Since I got this message I added the -cw256 flag: The physical sizes are (512.00 mm, 512.00 mm, 110.00 mm), which cannot fit in 256^3 mm^3 volume. ERROR! FOV=512.000 > 256 Include the flag -cw256 with recon-all! However, when inspecting the orig.mgz file the head is still not entirely visible any more (with -cw256 flag) ... Is is possible to link (-ln) the orig.mgz to the rawavg.mgz file to work around this problem? Or are there other options? I added screenshots for visualisation purposes. Kind regards, Aicha Dijkshoorn ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Boyd, Emma [ebo...@mgh.harvard.edu] Sent: Friday, February 02, 2018 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mpr2mni305 talaraich transformation error Hi Aicha, Have you visually inspected your input image, rawavg.mgz or orig.mgz to make sure they look ok? Emma ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Dijkshoorn, A.B.C. (Aicha) <a.b.c.dijksho...@uu.nl> Sent: Friday, February 2, 2018 7:37:25 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mpr2mni305 talaraich transformation error Hello free surfer developers, I am attempting to compute cortical thickness for anatomical ROIs in neonates, but for some of my subjects I get the following error when I run the auto-recon1 command: \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin leia.ds.umcutrecht.nl 14.5.0 Darwin Kernel Version 14.5.0: Sun Jun 4 21:40:08 PDT 2017; root:xnu-2782.70.3~1/RELEASE_X86_64 x86_64 recon-all -s N192_con_recon exited with ERRORS at Fri Feb 2 12:32:02 CET 2018 Is there any way I can work around this error? I've also attached the recon-all.log and the talaraich_avi.log in case it's of any use. Kind regards, Aicha Dijkshoorn
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