Folks:
It would be *really* great if there was a page somewhere (or just a file)
giving some info on the various measures that are captured in the aseg and
aparc files.
For each measure (in the table or the "comments" above the table):
-- Description of what it includes -- some are obvious f
Hi Darren,
we are you still using parcellate)_subject? It's old, old old. What version
are you running?
Bruce
On Mon, 24 Jul 2006, Darren
Weber wrote:
--[PinePGP]--[begin]--
--[PinePGP]---
(...and now to the list, for closure...)
Jenni:
Ah-ha, got it -- "hidden" in the comments :-)
Thanks,
Graham
At 7/24/2006 02:44 PM, Jenni Pacheco wrote:
The ICV is calculated during the -segstats step with all of the other
volume measures that use the aseg. They are all found within the
ase
Hi Graham,
the ICV (or eTIV) we use is from a clever idea that Denise Head and Randy
Buckner had. They showed that the total intracranial volume could be
accurately estimated from the jacobian of the talairach transform (to an
atlas with a skull), so the eTIV is just linearly related to the de
Hi Neel,
the .annot files should have the color table embedded in them precisely
to avoid this type of confusion. I think Doug has a tool for extracting the
color table from the .annot file, don't you Doug?
cheers,
Bruce
On Mon, 24 Jul 2006, Neel Kishan wrote:
surface_labels.txt has 94 ROI
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
What is this error:
endorphin.16> parcellate_subject ucsf_wa
could not open translation file
/home/dweber/freesurfer/home/Simple_surface_labels2002.txt
mris_ca_label: could not read annotation file
/home/dweber/freesurfer/home/Simple_surface_labels2
The ICV is calculated during the -segstats step with all of the other
volume measures that use the aseg. They are all found within the
aseg.stats file in the stats subdir.
Jenni
On Mon, 24 Jul 2006, Graham Wideman wrote:
Folks:
A couple of weeks ago, Bruce noted that:
EM Registration wit
Folks:
A couple of weeks ago, Bruce noted that:
> EM Registration with Skull is for generating ICV measures
... so I just got around to investigating where the ICV measures might be
getting saved.
Bottom line is I don't see what file that ICV measure is getting saved into.
Details:
I tried
surface_labels.txt has 94 ROIs in contrast to the 81 in
Simple_surface_labels2005.txt, and it does not seem to match the
numbering system I find in SUMA. Does this file indicate that there is
another parcellating method to identify 94 ROIs?
Nick Schmansky wrote:
Simple_surface_labels2005.txt
Simple_surface_labels2005.txt was the older name. It is now called:
surface_labels.txt
and is found in $FREESURFER_HOME. Sorry!
On Mon, 2006-07-24 at 15:47 -0500, Neel Kishan wrote:
> Thanks for the information. Please note that
> Simple_surface_labels2005.txt was not distributed in v3.0.3
Thanks for the information. Please note that
Simple_surface_labels2005.txt was not distributed in v3.0.3 for Mac OS X
Tiger.
To convert an annot file to roi file for SUMA the following lines can be
used for each hemisphere:
FSread_annot -input $SUBJECTS_DIR/subject/label/rh.aparc.a2005s.ann
I've just modified the way the DEV version of mri_convert reads in
generic (ie, non-siemens) dicom files. This change makes it so that it
can convert multi-frame GE (and possibly other) dicom files. Thanks to
Adam Thomas at NIH for supplying the GE data.
I've also fixed a slight bug in the w
Neel,
In the aparc.annot files, the ROIs are ordered alphabetically (except
for the first one, 'unknown'; and 'frontal pole', which is next to
'temporal pole' in the .stats file).
Nick
On Mon, 2006-07-24 at 14:02 -0500, Neel Kishan wrote:
> Hi List,
>
> Thanks for providing the mris_ca_label pr
Hi Neel,
there's not really an internal order to the annotations (they are coded
by the RGB value). I would suggest posting to the afni list.
Alternatively, you can use tksurfer in combo with suma to reverse
engineer what they've done.
doug
Jenni Pacheco wrote:
Hi Neel,
You could refer
Hi Neel,
You could refer to the surface label files that should be in your
$FREESURFER_HOME directory. I believe that the
$FREESURFER_HOME/Simple_surface_labels2005.txt corresponds with
aparc.a2005s.annot parcellations and the
$FREESURFER_HOME/average/colortable_desikan_killiany.txt correspo
Hi List,
Thanks for providing the mris_ca_label program and the two papers from
2004 and 2006. I'm using AFNI's FSread_annot to read the aparc.annot and
aparc.a2005s.annot files into SUMA. The ROIs are imported numbered 0 to
34 for the aparc.annot files and 0 to 81 for the aparc.a2005s.annot
Thomas,
What you are seeing is a bug that will be fixed in the next release,
within the next couple weeks (the next version will be v3.0.4).
To see your version, type:
cat $FREESURFER_HOME/build-stamp.txt
And for notes on known bugs (issues) in current and past releases, see
this page:
htt
Dear List,
when I press the button to display the colorbar in tksurfer I receive
the following error
message, followed by a crash:
freeglut ERROR: Function called without first
calling 'glutInit'.
There has been recent discussion about a 'glutinit-bug', but I could not
find the solutio
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