Dear FreeSurfer developers,
We are planning to rerun previously processed data (3 waves) with the newest FS
version from scratch. We have some questions before starting the pipeline.
1) to keep white matter edits is it enough to copy tmp/control.dat file or we
need to copy the complete FS tree
Dear FS experts,
I would like to downsample a subject's white surface to arrive with a smaller
number of vertices in order to feed the surface into FSL's surface tracking.
I tried to map the fsaverage6 onto the single subject:
mri_surf2surf --hemi lh --srcsubject fsaverage6 --sval-xyz white --t
Hi Daniel
what was your original data format? Did you start with dicoms?
Bruce
On Thu, 18
Oct 2012, Daniel Ferreira wrote:
Thanks Nick very much for your suggestion.
Unfortunately it did not fix the error.
I run the mri_nu_correct command trying several -n values (1, 5, 20), then I
-talaira
There were recently a few messages on the list regarding this.
What you should do is include "set reinit=1" in your config file, and then run
trac-all -priors -c $CONFIG
trac-all -path -c $CONFIG
Make sure you only include the pathway of interest in the config file;
otherwise, it will re-run the
It is possible to visualize topological defects in tksurfer by loading the
curvature from surf/?h.defect_labels. Is there any way to visualize these
defects in tkmedit? I am having trouble seeing how the defects are related to
wm.mgz, etc., in tksurfer, and it would be very helpful if there were
Hi Fernando - Thank you for your kind words. You can indeed try the reinit
option as Christofer suggested when one of the pathways looks like a
single curve and not like a volume.
However, because some of your other pathways in the screenshots look a bit
funky too, I would also check that th
Hi Franz, try mapping the xyz coordinates of the individual into
fsaverage6 (or fsaverage5 or lower) space. This should solve both of
your problems (I think).
doug
On 10/18/2012 07:53 AM, Franz Liem wrote:
> Dear FS experts,
>
> I would like to downsample a subject's white surface to arrive wit
Is training a within subject factor or between? If between, then you can
do it as a two group design as I described in a post yesterday.
doug
On 10/17/2012 08:04 PM, Harry Hallock [hhal5...@uni.sydney.edu.au] wrote:
> Hi Doug,
>
> Is it possible to add an extra factor to this repeated measures fs
Try using the defect-seg script. It will create labels and segmentations
of defects that you can visualize. Run it with --help to see how to run
it and call tkmedit and tksurfer to visualize the defects.
doug
On 10/18/2012 10:41 AM, Benjamin Kay wrote:
> It is possible to visualize topological d
Hi Knut, if you have a glm analysis, set up a contrast for group1 vs 0
and group2 vs 0. This will create gamma.mgh files that are the mean
thicknesses for each group. You can then compute the mean:
fscalc group1/gamma.mgh add group2/gamma.mgh div 2 -o group.mean.mgh
Then compute the percent diffe
It is too hard to tell what is going on here from just this image. I
would not immediately conclude that it is a vessel. Does the activation
otherwise look ok? What about other contrasts? Is the registration
accurate? When trying to debug these things, it often makes sense to
analyze the data i
Hi Gabriel, don't use the ASegStatsLUT.txt ctab file. It will only
report the volumes of structure in the ctab, and that ctab does not have
the WM parcellations. You can use FreeSurferColotLUT.txt instead. When
you use --empty, this will report on *everything* in the ctab, which
will probably b
Hi,
I did recon-all -i -s
and then what Nick posted.
2012/10/18 Bruce Fischl
> Hi Daniel
>
> what was your original data format? Did you start with dicoms?
> Bruce
>
> On Thu, 18 Oct 2012, Daniel Ferreira wrote:
>
> Thanks Nick very much for your suggestion.
>> Unfortunately it did not fix
Hi Doug,
thanks for the answer. This works great.
Franz
Am 18.10.2012 um 17:37 schrieb Douglas N Greve:
> Hi Franz, try mapping the xyz coordinates of the individual into
> fsaverage6 (or fsaverage5 or lower) space. This should solve both of
> your problems (I think).
> doug
>
>
> On 10/18/2
Dear Freesurfer expert
I have produce a script to make percent difference in cortical thickens using
information from the mailing list.
Could you please take look if this script is correct, or if there is a better
way to do it?
function [ out ] = diff_map( difference, average )
%percent differ
how about this instead?
out = difference;
out.vol = 100*difference.vol./average.vol;
On 10/18/2012 04:00 PM, Knut J Bjuland wrote:
> Dear Freesurfer expert
>
> I have produce a script to make percent difference in cortical thickens using
> information from the mailing list.
> Could you please
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