Dear FreeSurfers
I have a problem editing pial surfaces. My pial "borders" do not include
Some important brain parts i.e. amygdala.
Can anybody help me?
Tnx
Sharon
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Hi Graham,
Another way is to generate your TCL on the fly, see below for a simple
example:
- snip -
#!/bin/sh
outdir=/usr/people/johannes/scratch/fssubjects/pictures
mkdir -p $outdir
cd $SUBJECTS_DIR
# put your subjects here
for f in CONTROL*; do
for hemi in lh rh; do
echo "scale_brain 1.05
Hi Sharon,
the surfaces shouldn't include non-neocortical structures like amygdala.
They are modeled separately (in the aseg.mgz file).
cheers,
Bruce
On
Mon, 16 Apr 2007, Sharon Ruso wrote:
Dear FreeSurfers
I have a problem editing pial surfaces. My pial "borders" do not include
Some imp
There are is nothing that simple, as it does all the threshold
calculating in the tcl code. You can use:
set gaLinkedVars(fopaqueflag) <1 or 0>
SendLinkedVarGroup overlay
to turn on and off the opaque flag, and:
set gaLinkedVars(fthresh)
set gaLinkedVars(fmid)
set gaLinkedVars(fslope)
SendLi
> 1. When you launch FS from command line and provide a -tcl command to
> invoke a tcl script, how do you supply arguments to that script (or is that
> even possible)?
There's no way to pass arguments along on the command line, so Bruce's
suggestion works best.
> 3. What assumptions, if any, c
Newer (dev) versions will use $FREESURFER_HOME/FreeSurferColorLUT.txt
as the default.
On Thu, 12 Apr 2007, Nick Schmansky wrote:
This should work:
tkmedit good_output brainmask.mgz \
lh.white -aux T1.mgz \
-aux-surface rh.white \
-segmentation mri/aseg.mgz \
$F
Hi,
I just want to clear up some confusion about this topic. There is a
difference currently between the dev (and stable) versions within the
Martinos Center and versions that have been posted for download.
Some versions will require you to specify a color table, and also to use the
mri/ designa
Hi,
Can mri_convert work with slice orientation other than axial? My input is
sagittal (slices collected from right to left), but when I create files from
mri_convert the header reads axial. This is particularly problematic when
converting to analyze format from dicoms or another file type because
To more fully explain the road block, this is the output of 'mri_info
analyzefile --slicedirection'
MatlabRead: readHeader returned NULL
WARNING: analyzeRead(): matfile
analyzefile.mat exists but could not read ...
may not be matlab4 mat file ... proceeding without it.
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