Dear FreeSurfur Gurus,
It appears that the using -use-mritotal worked to get past the talairach
error.
Thank you for all your help. We really appreciate it.
Joshua
On Wed, Nov 2, 2011 at 7:01 PM, Bruce Fischl wrote:
> Hi Michael
>
> we found that the conversion to unsigned character sometim
Hi Michael
we found that the conversion to unsigned character sometimes compressed
the brain into only a couple of bits of the dynamic range. We know use
the talairach xform to locate the center of the brain and make sure that
a ball centered at the tal origin occupies a lot of the histogram.
Hi,
What was the reason for this switch? Intuitively it seems that a
bias-corrected image is likely to get a better registration (since I assume
the target has essentially uniform intensities).
Michael
On Wed, Nov 2, 2011 at 1:15 PM, Nick Schmansky wrote:
> no, v5.0 uses nu.mgz as input to the
it should not change the quality of the subcortical or cortical streams
at all. the talairach.xfm is used for reporting purposes in the gui
tools, and for group averaging (in some instances, qdec not being one of
them). so i would not worry about introducing a bias. if you are
concerned about a
OK, now I understand better.
One further question: Would the use of MRI-total degrade quality of the
Freesurfer segmentations substantively, and would using it only on a
portion of my data introduce a systematic bias to the data set?
Josh
On Wed, Nov 2, 2011 at 4:15 PM, Nick Schmansky wrote:
>
no, v5.0 uses nu.mgz as input to the talairach_avi routine, whereas v5.1
uses orig.mgz.
its hard to say why it would fail for some subjects but not others,
other than head positioning and to some degree ventricle size makes a
difference.
n.
On Wed, 2011-11-02 at 16:10 -0400, Joshua Lee wrote:
>
Thanks Nick,
Is use-mritotal equivalent to what version 5.0 does by default?
Also, any suggestions on why this talairach error would occur only on a
portion of my data, despite all being collected with the same imaging
protocol, same conversions from dicom, etc?
-
Joshua Lee
Graduate Student
Cen
joshua,
try adding -use-mritotal to the end of your recon-all command. it will
use an alternate way to compute the talairach.xfm which works better on
some data.
the change from v5.0 to v5.1 in the talairach stage was that in v5.1,
the talairach.xfm is needed to compute nu.mgz, so the talairach
can you send us an example that works in 5.0 and fails in 5.1?
thanks
Bruce
On Wed, 2 Nov
2011, Joshua Lee wrote:
Small Update: Error Disappears if Using Freesurfer version 5.0 instead of
5.1. However, since I am keenly interested in the hippocampal-subfield
segmentation capabilities of the m
Small Update: Error Disappears if Using Freesurfer version 5.0 instead of
5.1. However, since I am keenly interested in the hippocampal-subfield
segmentation capabilities of the most recent version, I am loathe to
regress to an earlier version of FreeSurfer
-
Joshua Lee
Graduate Student
Center for
#@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011
/home/virtualuser/freesurfer/subjects/test005/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
I am receiving the error (pasted below) on about half of my scans, despite
all cans using same protocol. I detect no obvious issue w
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