the control points are stored in $SUBJECTS_DIR/$subject/tmp/control.dat
does this file exist? If not can you create it (e.g. with touch)?
cheers,
Bruce
On Thu, 9 Oct 2008, Kellen Mobilia wrote:
Help-
As a relatively new user to Freesurfer, I have encountered some problems
none that more exper
QDEC transform your data into a common spherical space.
So this file y.mgh is already in a common space.
Running that script into your y.mgh (from QDEC directory) will retrieve the
values of the surface stat in fsaverage space.
>> mri_convert --frame $i y.mgh ../../fsaverage/surf/lh.$i.m
Mishkin,
Try appending .asc to your file (ie, lh.mystats.asc) and try again.
freesurfer interprets .asc as an ascii file (otherwise it tries to read
it as binary).
Nick
On Thu, 2008-10-09 at 17:23 -0400, Mishkin Derakhshan wrote:
> Hi,
> I have my own stats files that I would like to incorporat
Hi,
I have my own stats files that I would like to incorporate into the
freesurfer stream, if possible. Ie. after running FreeSurfer, I create
a ?h.mystats (containing something like image intensities for
example), where the format of ?h.mystats is just an ascii file, where
each line is the value a
Hello Kellen
Can you create a directory named tmp/ inside your subjects directory.
Suppose you had a subject named 'kellen'
cd $SUBJECTS_DIR
cd kellen/
mkdir tmp
and try again ?
If 'tmp/' already exists, make sure it's write-able.
Krish
On Oct 9, 2008, at 4:37 PM, Kellen Mobilia wrote:
Kellen,
I think you could send us the system you use (Linux/Mac) and the FreeSurfer
version.
PPJ
2008/10/9 Kellen Mobilia <[EMAIL PROTECTED]>
> Help-
> As a relatively new user to Freesurfer, I have encountered some problems
> none that more experienced users have been able to solve until now. E
Derin,
Can you do this:
source $FREESURFER_HOME/bin/tcl_setup
then send me the output of:
ldd `which tkmedit.bin`
and
ldd `which tksurfer.bin`
I will be looking to see if the proper tcl/tk/tix/blt libs are being
used (those in freesurfer/lib/tcltktixblt).
Nick
On Thu, 2008-10-09 at
Help-
As a relatively new user to Freesurfer, I have encountered some problems
none that more experienced users have been able to solve until now. Every
time I try to add a control point, the message "MRIwriteColtrolPoints( ): could not write file Permission denied" This may have to do with
our ser
Help-
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Hi Derin,
with regard to #2, we haven't setup any official procedure although it is
a good idea. You could use the tools Xiao developed for that paper to do
so.
cheers,
Bruce
On Thu, 9 Oct 2008, Derin Cobia wrote:
Nick,
Yes, our tcltktixblt directory was intact and set correctly. The reas
At some point in early 2008, Doug had created a version of tkregister2
that he graciously provided us, which had --gca-skull and --gca flags,
which greatly simplified the process of confirming the accuracy of
either the talairach_with_skull.lta and talairach.lta transforms
(respectively). However
I just added those changes to stable, so it should be in our next stable
release.
Michael Harms wrote:
At some point in early 2008, Doug had created a version of tkregister2
that he graciously provided us, which had --gca-skull and --gca flags,
which greatly simplified the process of confirmin
One method that leaps to mind is to have new RAs analyze a relatively
small set of data (say 10), then do a vertex-wise paired t-test between
your gold standard set and the new RA's set.
doug
Derin Cobia wrote:
Nick,
Yes, our tcltktixblt directory was intact and set correctly. The reason I
Nick,
Yes, our tcltktixblt directory was intact and set correctly. The reason I
thought it was a BLT lib was it came up missing when I ran fs_lib check.
At any rate, the DefaultDepth is already at 24 in our xorg.conf file and
the problem persists. Any other thoughts what might be occurring? Wo
Hi Joost, can you look at the original sig map thresholded at 1.3 to see
if there is a cluster of that size?
Hi,
version 4.0.5
after:
mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf
fsaverage lh --C qdec/diff-1-2.txt --sim perm 1000 1.3 stats/newperm_lh
--glmdir st
Hi Juergen,
yes, the tp2 subject should have a transform in the mri/transforms dir that
registers it to tp1 that you can load in tkmedit. Note that we are
releasing a new rev in the next week or so that fixes a serious inaccuracy
in the longitudinal stream, so we would recommend rerunning your
Hi Juergen,
we do have tools for this but have never really formalized it since we've
always found this analysis to be too fraught with ambiguity to pursue.
If you feel like messing around with it you can use mri_extract_label to
copy (and smooth/transform) a label from the aseg (e.g. 17=Left
Dear FS experts
I am wondering whether it is possible to do an voxel-wise analysis on the
subcortical segmentations similar to a voxel-based morphometry (VBM) in SPM
or FSL.
Because there is no .mgz file that encodes the probability that a particular
voxel belongs to a particular tissue type (GM
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