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Hi all,

I encountered a problem about the T2.mgz in subject/mri.

I ran my data using recon-all -all -i T1path -s name -T2 T2path -T2pial(7.1.1 or 7.1.0), but the results were inconsistent, sometimes the mri/T2.mgz had skull sometimes it didn't.

That is weird. I read the recon-all.log

T2.mgz with skull, the code is:

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writing normalized volume to /xx/subject/mri/T2.norm.mgz #VMPC# mri_normalize VmPeak 978796 mri_normalize done @#@FSTIME 2021:01:31:21:55:47 mri_normalize N 18 e 42.55 S 2.36 U 40.16 P 99% M 723884 F 0 R 925502 W 0 c 78 w 4 I 0 O 78480 L 62.01 61.65 61.48 @#@FSLOADPOST 2021:01:31:21:56:29 mri_normalize N 18 61.84 61.65 61.49 mri_mask -transfer 255 -keep_mask_deletion_edits /xx/subject/mri/T2.norm.mgz /xx/subject/mri/brain.finalsurfs.mgz /xx/subject/mri/T2.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Writing masked volume to /xx/subject/mri/T2.mgz...done.

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when it comes to no skull, the code is:

writing normalized volume to /xx/subject/mri/T2.norm.mgz mri_mask /xx/subject/mri/T2.norm.mgz /xx/subject/mri/brainmask.mgz /xx/subject/mri/T2.mgz DoAbs = 0 Writing masked volume to /xx/subject/mri/T2.mgz...done.

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it seems that the pial is not refined by the T2 image if the T2.mgz is with-skull.

anybody know what's going on here?

Thanks,

Yijun.