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:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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.