Dear FS team,
I used read_annotation(lh.aparca.annot) for obtaining [vertexs, label,
colortable]. After that, I have modified these variables and would
like to write a new annotation file. Is there the function
"write_annotation" (or something similar)?
Thanks in advance.
Best,
Rafa
Dear FS-Team,
I have mapped some PET-data on the corresponding subject's cortical
surface. Is it possible to get some statistics from the resulting
curv-file using the FS-parcellation as ROIs?
Thanks in advance,
Florian
begin:vcard
fn:Florian Gerstl
n:Gerstl;Florian
org:Medical University of V
sure, once you have it sampled on the surface you can treat it like a
thickness study (unless you have a timecourse, in which case it would be
like an fMRI study).
cheers,
Bruce
On Mon,
2 Mar 2009, Florian Gerstl wrote:
Dear FS-Team,
I have mapped some PET-data on the corresponding subj
Thanks for your quick reply!
However, when I cast the mris_anatomical_stats command with the "-log"
flag the program seems to crash. That's not really a concern for me as I
can still use the -f flag to obtain a results-file (no problems there)
and I'm not sure whether this is a problem only with o
what version of freesurfer is being used?
type freesurfer --version and send us the last line. we may have
fixed this in an earlier version.
On Mon, 2009-03-02 at 16:43 +0100, Florian Gerstl wrote:
> Thanks for your quick reply!
> However, when I cast the mris_anatomical_stats command with th
Florian Gerstl wrote:
Thanks for your quick reply!
However, when I cast the mris_anatomical_stats command with the "-log"
You might also try 'mris_curvature_stats'. It gives mostly the same
stats that 'mris_anatomical_stats' (and some additional ones geared to
curvature-type files):
freesurfer --version produces the following output (last 2 lines):
You are running this version of FreeSurfer:
freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0
Actually, I thought I had a pretty recent version...
Kind regards
Florian
Nick Schmansky wrote:
> what version of freesurfer
Thank you for your help. As regards to the display, I am using the command
that is found in the mri_glmfit-sim documentation. Even with that command I
don't see the display as it is shown in the documentation. In addition to
showing the clusters (all of them), the display also shows what looks l
Hi Jose,
this looks pretty much correct. We have another utility, called
mris_make_face_parcellation that can be used to generate parcellation units
of mostly uniform area over the surface of the cortex. If you tell us your
hardware/software environment we can give you a beta.
cheers,
Bruce
Dear Freesurfers,
I was wondering whether it would be possible to run recon-all with MT
images? My final aim is to compare cortical thickness between two groups.
I've done this with T1 weighted images, but was wondering whether i could
also do with MT images. Segmentation in SPM worked really well
Jose,
mris_make_face_parcellation is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc
for three of the supported platforms.
Nick
On Mon, 2009-03-02 at 13:23 -0500, Bruce Fischl wrote:
> Hi Jose,
>
> this looks pretty much correct. We have another utility, called
> mris_make_fa
Hi Lucia,
we've never tried, but certainly give it a shot. You would want to apply
an MT subtraction that enhances gray/white contrast though.
cheers,
Bruce
On Mon, 2 Mar
2009, Lucia Garrido wrote:
Dear Freesurfers,
I was wondering whether it would be possible to run recon-all with MT
ima
Many thanks for your e-mail, Bruce.
I've tried and it gives an out of memory error. Perhaps it's because
there's not enough contrast. I'll try that.
Many thanks,
Lucia
> Hi Lucia,
>
> we've never tried, but certainly give it a shot. You would want to apply
> an MT subtraction that enhances gray
Hello Surfers,
I have an overlay file with values ranging from -4.63 (n=138477) to 1.34
(n=25365). I would like to display this data with more than the two colors of
the Green/Red, Heat, Blue/Red, or complex Color Scales in the Configure Overlay
dialog. So far, no luck, even with toying with
Hi Jeff,
have you tried setting the offset in the configure functional overlay
panel to be around the middle of your range (-1.5 or so I guess)?
cheers,
Bruce
On Mon, 2
Mar 2009, Jeff Sadino wrote:
Hello Surfers,
I have an overlay file with values ranging from -4.63 (n=138477) to 1.34
(n
Hello FS Team,
I had a question recently regarding an error encountered in the
freesurfer recon-all. I believe error is the result of:
mris_fix_topology -mgz -sphere qsphere.nofix -ga FirstOrderPoly lh
CORRECTING DEFECT 3 (vertices=10731, convex hull=2557)
normal vector of length zero at vertex 9
Hi Pradeep,
sounds like a bug. Can you overlay the surface defect segmentations and
see what defect #3 is? If you edit it a bit this will probably go away.
If you tar and gzip the subject dir and send it to us we'll take a look You
can also try the alternative (newer) topology correction and s
Hi Bruce,
Thanks for your quick reply. I tried fine-tuning the offset and the midpoint.
I guess what I would like to have happen is to have a couple more colors come
out beyond the blue-to-light blue range for the thinning. If I could get some
greens in there too, that would make the pictur
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