Also, are you running it with a T1 input or a T2? The file name looks
like it might be a T2.
On 4/10/2020 10:12 AM, Bruce Fischl wrote:
Hi David
did you check the skull stripping as suggested? Seems like the input
volume given to the CC finder was empty. Work backwards and find the
earliest volume where something is wrong
cheers
Bruce
On Fri, 10 Apr 2020, David Schwantner wrote:
External Email - Use Caution
Thank you in advance for the assistance!
I am running the following command:
recon-all -i 1131_T2_raw.nii.gz -s DS_T2 -all
The log
isat https://github.com/dschwant/mri_to_3d/blob/master/202004090853_error_rec
on-all.log, and the nii file
isat https://github.com/dschwant/mri_to_3d/blob/master/202004_DS_Brain_MRI/11
31_T2_raw.nii.gz.
Here is the tail of the log. As you can see, I am running it in Ubuntu
18.04.4 under the Windows Subsystem for Linux.
...
searching rotation angles z=[-9 5], y=[-22 -8]
searching scale 1 Z rot 5.3 global minimum found at slice 139.0,
rotations (-14.14, -1.42)
final transformation (x=139.0, yr=-14.141, zr=-1.420):
0.96940 0.02478 -0.24423 8.04082;
-0.02403 0.99969 0.00605 -41.07934;
0.24430 0.00000 0.96970 18.40543;
0.00000 0.00000 0.00000 1.00000;
mri_cc: no WM voxels found with norm > 40 -- check skull stripping
No such file or directory
Linux LT499318 4.4.0-17763-Microsoft #864-Microsoft Thu Nov 07
15:22:00 PST 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s DS_T2 exited with ERRORS at Thu Apr 9 11:19:24 DST 2020
...
Is it just not enough "details" in the nifti file? I am trying the next
larger one now.
---------------------------- David - dschw...@gmail.com
----------------------------
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