Hi guys,

The problem was garbage in - garbage out:

1. The issue manifested in the skull stripping step but was caused by bad input

2. I am a data science guy (not neurology), new to freesurfer, and followed the instructions at https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide

3. When I issued recon-all, I gave it a -i of an image file from my mri data. I assumed that it would find the T1- weighted data from my collection automatically as in dcmunpack. 

4. It seems that the -i requires specifically the T1-weighted data, because when I looked at the tkmedit brainmask images they were inverted (maybe from T2 or something else).

5. I re-ran the recon-all on the proper T1 data and it ran to completion with no errors.

I recommend making the requirement for input of T1-weighted data more explicit in the wiki page. 

As a feature request, it seems pretty easy to use dcmunpack to find the correct data from a collection and make it part of initial recon-all.

I had uploaded my original data to the ftp site per reply below, but feel free to delete and close the issue as solved.

Cheers,

-Matt

------------

Hi Matt

no idea what that would happen. If you upload the dataset we will take a look

cheers
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