Hi Bryan,
Re: 1a) Did you run the case all the way through recon-all? Even if the
skullstripping looks poor, it's possible that the surfaces will turn out
ok and might only require some pial edits. Otherwise, this site has some
helpful info on rerunning the skullstripping step:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview
Re: 1b) If you are referring to voxels located in dura being labelled as
cerebral cortex in the aseg then this can be ignored. The cerebral cortex
labeled voxels are not used to calculate the morphometry stats.
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
Re: 3) You probably just need to adjust the contrast and brightness, using
the window and level sliders on the left in freeview.
Re: 4) Could you send a snapshot (or two) of that?
-Louis
On Thu, 26 Jun 2014, Martin Reuter wrote:
Hi Bryan,
I can answer the longitudinal question (2), the rest is about cross sectional
editing and can probably better
be answered by someone else.
So yes, I would run the base and check brainmask and surfaces there before
going too deep into editing the
cross.
Best Martin
Sent via my smartphone, please excuse brevity.
-------- Original message --------
From: "Chiu, Bryan (PHTH)"
Date:06/26/2014 8:06 PM (GMT+01:00)
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal preprocessing troubleshooting
Hi all,
I have a set of data with ~75 subjects with up to 4 timepoints of scans. The
structure of the data indicates
that it would be best processed using a longitudinal design.
I have recon-all most of the scans. There are a few scans that I am worried
about and wondering how to treat
each case. I do one sanity check with freeview using a modified version of
bert's command:
"freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v
$SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2
-f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f
$SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f
$SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f
$SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red"
1a) Skull strip or underanalysis errors: I have attached one screenshot of a
very severe case of an
underanalysis. How should I treat this case? I have recently read about Editing
a Recon in Freeview, but I'm
not sure how to proceed with this.
b) Skull strip errors -- Some scans have a very small amount of cerebral cortex
labelling into the dura mater/
skull. Does this warrant the manual removal via freeview of the skull?
2) Since I am running this through the longitudinal processing, could I be able
to skip #1 hoping that the
averaging of the timepoints into a 'base' will remove these issues?
3) I have 2 brains that are completely whited out in Freeview (see attached).
However the analysis went through
and it looks good to me. Opening the raw Nifti file in mricroGL does not show
this at all. What is going on and
should I be concerned?
4) I have 2 other brains that failed the recon-all. One of them is a Talairach
fail and the other one failed
mri_watershed. Looking at these brains in mricroGL shows a dark shadow being
cast over the brain running
diagonally from the front of the head to the back. I think this is the root of
the problem. Is there a way to
fix this or should I consider these scans problematic and exclude them?
Regards,
- Bryan
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