I uploaded the datasets to the ftp site, does anyone have further advice regarding this issue?
Both datasets are for the same subject for a longitudinal concussion study and fail for different reasons.
matt1 - has "ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 errors" and fails with "CORRECTING DEFECT 51 (vertices=28380, convex hull=5261, v0=32826)
XL defect detected..." never completing.
matt2 - is leaving out large sections of brain despite various wsthresh adjustments (see thread below)
I appreciate any assistance you can provide.
All the best,
-Matt
Hi Matt
no idea what that would happen. If you upload the dataset we will take a lookcheers
Bruce
On Mon, 5 Mar 2018, Matthew Grecsek wrote:
Following your advice below, it was clearly apparent that the output from the
skull stripping step
was missing a lot. I tried adjusting the -wsthresh flag from 50 -> 200 and it
still left major parts
of the brain out.
I have a good quality mri and subject with no known anatomical abnormalities.
The log file indicates "surface validation has detected possible Error"
Does this suggest a more meaningful defect in the base image or something that
can be corrected via
other parameters or manual editing?
Log file attached.
Thanks,
-Matt
Bruce Fischl Fri, 02 Mar 2018 08:00:11 -0800
Hi Matt
check the output of the skull stripping. This error usually means that too much
(everything?) has
been erased and no plausible cc could be found
cheers
Bruce
On Thu, 1 Mar 2018, Matthew Grecsek wrote:
My recon-all ended prematurely with the following message:
final transformation (x=136.0, yr=-10.054, zr=-0.114):
0.98464 0.00200 -0.17457 15.51372;
-0.00197 1.00000 0.00035 17.22442;
0.17457 0.00000 0.98464 -17.83761;
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 centos-7-1 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018
x86_64 x86_64 x86_64 GNU/Linux
recon-all -s matt2 exited with ERRORS at Thu Mar 1 04:35:09 UTC 2018
I am running: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
My full log file is attached.
Please let me know suggestions for correcting and continuing the process.
Thanks,
-Matt