The images are: 0.5 x 0.5 x 1.0
Can mri_convert fix it or should I edit the Nifti header?
2011/5/16 Nick Schmansky
> PPJ,
>
> Hi,
>
> mri_info /space/incoming/ga_2010.nii
>
> shows that the image is 0.5 x 0.5 x 0.5. but when viewing in freeview
> or tkmedit, the brain seems 'squashed', as if
You can try use the flood-fill tool to fill the ROI you outlined.
On 5/16/11 5:58 PM, Lynette Silva wrote:
> Thanks Ruopeng,
>
> I tried tracing the outline with the freehand tool, and I also tried
> setting waypoints around the surface area of my ROI. What tools would
> you recommend?
>
> Thanks
Thanks Ruopeng,
I tried tracing the outline with the freehand tool, and I also tried
setting waypoints around the surface area of my ROI. What tools would
you recommend?
Thanks again!
Lynette
On Mon, May 16, 2011 at 3:46 PM, Ruopeng wrote:
> When you say tracing an ROI by hand in freeview, did
PPJ,
Hi,
mri_info /space/incoming/ga_2010.nii
shows that the image is 0.5 x 0.5 x 0.5. but when viewing in freeview
or tkmedit, the brain seems 'squashed', as if there is a slice gap. do
you know the details of how this was acquired?
N.
On Mon, 2011-05-16 at 17:49 -0300, Pedro Paulo de Ma
When you say tracing an ROI by hand in freeview, did you fill it or just
traced the outline? In any case, you will need to do this on each slice
by hand. However, there're various options and tools in freeview that
may help speed up the process dramatically.
Ruopeng
On 5/16/11 5:12 PM, Lynette
Hello All,
I think I am missing a key step in creating an ROI in freeview. I have
been tracing an ROI by hand in freeview, and saving as a label. Then I
use mri_label2vol followed by mri_label_volume, and this works
GREAT... except the output has far too few voxels to be the whole
volume of my ROI
OK, I've verified and fixed this. It will be in dev in the next build
(probably overnight). Are you using dev?
doug
Marcus Belke wrote:
> Hi,
> I am experiencing the same problem. When I try to do the motion
> correction on fmri data it stops with a segmentation fault in
> mri_convert. This use
I'm having this error in the recon-all
#
#@# Talairach Mon May 16 16:38:01 EDT 2011
/usr/local/freesurfer/subjects/GAGRICOLA/mri
talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm
ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
Hi,
I am experiencing the same problem. When I try to do the motion
correction on fmri data it stops with a segmentation fault in
mri_convert. This used to work until this week.
Best
Marcus
On 13.05.2011 12:48, Chindhuri Selvadurai wrote:
> Hi all,
>
> We are trying to run individual analyses
yes, that is fine.
doug
Fernanda Palhano wrote:
> Doug,
>
> I have another question about doing a volumetric group analysis. I
> used the command:
> asegstats2table --subjects V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13
> V14 V15 V16 V17 V18 V19 V20 V21 V22 V23 V24 V25 V26 V27 V28 V29 V30
> V31
Hi Ilana,
Normality isn't a requirement for FDR to work. However, if the
distribution of your statistic isn't normal **under the null
hypothesis**, neither follows t, F or any other well known
parametrizable distribution, then you have to obtain p-values in a
different way, not from the cdf/p
And do you have write permissions? Can you
touch stats/aseg.stats
doug
Fernanda Palhano wrote:
> Yes.
>
> [Fernanda-Palhanos-Mac-Pro:group_analysis_tutorial/004/stats]
> fernandapalhano% ls
> aseg.statslh.aparc.a2009s.statslh.supramarg.stats
> rh.aparc.a2009s.statswmparc.stat
does the stats directory exist?
doug
Fernanda Palhano wrote:
> Hello,
>
> I'm trying to use mri_segstats to obtain some subcortical volume
> stats. When running the command line both in the tutorial data or in
> my own data, I have the follow error: ERROR: could not open
> stats/aseg.stats for
Hello,
I'm trying to use mri_segstats to obtain some subcortical volume stats. When
running the command line both in the tutorial data or in my own data, I have
the follow error: ERROR: could not open stats/aseg.stats for writing
[Fernanda-Palhanos-Mac-Pro:buckner_data/tutorial_subjs/group_analys
Hi Ilana,
I'll let the first question to the FS experts to answer. For the second:
> 1. Is it legitimate toconclude from this that the regressor's overall effect
> is that it's associated with a thinner cortex (e.g., older subjects have a
> thinner cortex), eventhough most of the cortex does no
Today it was released the version 3.0.0 of iSurf Brainview, it's a major
version release for IPad, IPhone and IPod Touch.
Major New Features
- Quiz for Brain structures (you can take a Quiz with 10 random questions
about structure locations. The current database has more than 40 questions)
- Selec
Hi all,
I am experiencing the infamous sliver problem in tksurfer over VNC. I tried
solving it by installing VirtualGL, but it doesn't work, I get the following
error message:
[VGL] WARNING: VirtualGL attempted and failed to obtain a Pbuffer-enabled
[VGL]24-bit visual on the 3D X server :
Hi Chinduri, is this still happening? I can't replicate.
doug
Chindhuri Selvadurai wrote:
> Hi all,
>
> We are trying to run individual analyses on several subjects, and we keep
> getting a 'Segmentation Fault.' We have run other subjects with the same
> command a while ago, and the command work
Hi Rene, you can load these with MRIread.m
doug
René Besseling wrote:
> Dear all,
>
> I'd like to analyse some Freesurfer outputs in Matlab. I know it is
> possible to load ./surf/lh.thickness into Matlab using read_curv, but
> is it also possible to load normalized (and smoothed) thickness maps,
Those residuals are actually whitened, but there is still a problem in
that you need to include the whitening matrix in the equation for the t
ratio below. I don't know any easy way to do it from there. You can save
the unwhitened residuals with -svres-unwhitenen, then compute the
average of t
Hi Elisa, how was the slt file created? Can you send it and the summary
file to me (don't send to the group).
doug
Elisa Golfinopoulos wrote:
> Hi all,
>
> I wanted to follow-up on my previous e-mail, which may have been a bit
> too vague.
>
> I am using the command:
>
> mri_surfcluster --in ./o
Hi Heidi, I think this is what you need:
csdbase.sig.cluster.mgh - the sig volume corrected for multiple
comparisons on a cluster-wise basis. The value at each voxel
is the -log10(p), where p is the pvalue of the cluster at
that voxel. If that voxel does not belong to a cluster, its
value will be
Hi there,
First the simple question - is there a way to run mris_anatomical_stats on all
my subjects at once generating a single output file?
Second - actually comprised from several questions: when looking a the
unthresholded group analysis on cortical thickness (in the averaged space), the
Hi Ri,
I think you can use mri_cor2label with flag --id set to 1.
Sita.
On Mon, 16 May 2011, Ritobrato Datta wrote:
> Hello All,
>
> How do I convert an .mgh file (my .mgh file is a binary mask) onto a label ?
> Is there an automated way other than drawing ?
>
> Thanks
>
> Ri
>
Hello All,
How do I convert an .mgh file (my .mgh file is a binary mask) onto a label ? Is
there an automated way other than drawing ?
Thanks
Ri
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