Hi Pedro,
Have a look at this article:
http://brainder.org/2011/07/05/freesurfer-brains-in-arbitrary-colours
I think this is the same you'd like to do (or you can change some steps
easily).
Hope it helps!
All the best,
Anderson
On 05/07/12 20:44, Pedro Paulo de Magalhães Oliveira Junior wr
Hi freesurfers,
Can a .annot file include labels with overlapping vertices? If not, then when
using mris_label2annot, how does freesurfer decide which label to assign the
vertices to?
Thanks,
David
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Hi Pedro Paulo, it is not quite the right procedure, but I'm surprised
that it gave unknown for all labels. Try
modifying the colortable.txt such that the first entry is the name and
color for your first label, etc.
doug
On 07/05/2012 03:44 PM, Pedro Paulo de Magalhães Oliveira Junior wrote:
> D
Hi Carolina
I don't know anyone who has ever tried. It will depend a lot on the CNR
of the data
Bruce
On Thu, 5 Jul 2012, carolina.mr wrote:
> Hello,
> I would like to know if it is possible to process T1 images with a slice
> tickness of 5mm / 0.5mm of gap in freesurfer and obtain reliable
Hello,
I would like to know if it is possible to process T1 images with a slice tickness of 5mm / 0.5mm of gap in freesurfer and obtain reliable cortical tickness measurements and parcelations?
Thank you,
Carolina Rimkus
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Doug,
I did
mri_annotation2label --subject bert --hemi lh --outdir
$SUBJECTS_DIR/bert/label
mri_annotation2label --subject bert --hemi rh --outdir $SUBJECTS_DIR
/bert/label
And then
mris_label2annot --s bert --hemi lh --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --l lh.bankssts.label --l
lh.c
You can also break up the annot into labels ( mri_annotation2label) then
recombine them with a new color table with mris_label2annot.
doug
On 07/05/2012 02:57 PM, Bruce Fischl wrote:
> Hi PPJ,
>
> I think the color lut is embedded in the aparc.annot. If you want to
> change it you have to change
Hi PPJ,
I think the color lut is embedded in the aparc.annot. If you want to
change it you have to change the one that's in the .annot. I would do it in
matlab.
cheers
Bruce
On Thu, 5 Jul 2012, Pedro Paulo de Magalhães Oliveira
Junior wrote:
I'm trying to generate an image to a paper and
I'm trying to generate an image to a paper and I have to colorize some
areas of the cortex with specific colors.
I have edited the FreeSurferColorLUT.txt changing the following lines:
1001 ctx-lh-bankssts 255 42 0 0
1003 ctx-lh-caudalmiddlefrontal 255 14 0 0
1006 ctx-lh-entorhinal 255 17 0 0
1017
Hi Meng, if you are doing whole hemisphere correction, it will used
already computed values which should only take a few seconds to run.
doug
On 07/05/2012 11:03 AM, Meng Li wrote:
>
> Hi, all,
>
> I have some questions about the multiple correction in qdec.
>
> I performed group analysis using q
Hi, all,
I have some questions about the multiple correction in qdec.
I performed group analysis using qdec. There are 5 factors in the
qdec.table.dat file: 1 discrete, 4 continuous variables (covariates). When I
tried to perform the multiple correction, Whether I can choose one of two ways
(t
On Tue, Jul 3, 2012 at 5:56 PM, Akio Yamamoto
wrote:
> Yes, as Richard pointed out, I just wanted to know the numbers for input
> to Amdahl's law, if you have already something, to figure out the maximum
> expected speedup using multiple processors/cores.
>
> As for improvements of em_reg, I'll t
Of course, you are right...It fits perfectly now. Thank you so much!
Best,
Anders
2012/7/4 Douglas Greve
> Where did rh.v1.probl.label come from? The way you call mri_label2vol, it
> should be in fsaverage space. If it is in an individual space, then the
> registration is wrong. Try running mn
Thank you so much for your answer Koen,I understand, but now I'm having some trouble when running the command on one subject, hope you can help me.I have tried to perform the hippocampal subfields segmentation by running:recon-all -s MySubject -hippo-subfields and also:kvlSegmentHippocampalSubfield
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