I added some text to clarify in that wiki page. See if you think it is
sufficient (and suggest some wording if you don't:).
On 3/22/18 4:22 PM, Bruce Fischl wrote:
Hi Matt
it's not that trivial. There are frequently multiple T1-weighted
protocols, and the naming is hardly standardized. We would need to run
some type of MR simulator to decide if something was T1-weighted in
the most general sense, and even then it could be mag-trans or with
contrast or something.
cheers
Bruce
On Thu, 22 Mar 2018, Matthew Grecsek wrote:
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
recon-all \
-i <one slice in the anatomical dicom series> \
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 received several offline requests from other users, so it seems
like this may be a common mistake.
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
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