Hi Nikita
you need to give us more information if we are to help you. What was thec
command line? What was the output of the command other than the error
message? What version of FS and what version of Linux?
cheers
Bruce
On Tue, 23 Sep 2014, Nikita Zhitkevich wrote:
Hi,
I am currently r
Hi Emma,
yes, LME is Matlab, but the wiki page describe the use step-by-step.
LME makes sense in your case because some subjects have less time points
than others.
The alternative (if only a very small minority of subjects differs from
the rest) would be the 2-stage approach, where you first
Dear experts,
I had a question concerning the output of the Monte Carlo Z-simulation
(abs) in Qdec. When I run the analysis, Qdec prints out a table including
the max vertex, p-values, and coordinates of significant clusters. However,
when I hit the button 'Find clusters go to max', qdec provides
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Hello,
I have some unexpected results from the mne_watershed_bem script that
uses Freesurfer mri_watershed program.
For one of my subject's the inner scull surface (
_inner_scull_surface in bem/watershed/) partially excludes
cerebellum (the left screen shot). All my other subjects have c
You can run mri_glmfit-sim using the same voxel-wise threshold and
setting the clusterwise threshold to .5. This will create several files.
One will be called something like {csdbase}.y.ocn.annot. Load this in
tksurfer or freeview to find which cluster corresponds to your cluster.
Then look in
When I run your commands, the pial is correctly oriented and placed.
What is your freeview command? This is what I use
freeview -v rawavg.mgz --surface ../surf/lh.pial.native:edgecolor=yellow
On 09/23/2014 06:11 PM, Zachary Greenberg wrote:
> Hi Doug,
>
> Thanks for getting back to me and sorry
X and C have different numbers of columns. What was your mri_glmfit
command line? If you used a --pvr, then the pcc script will not work.
doug
On 09/22/2014 01:21 PM, Celine Louapre wrote:
> Thanks for pointing me to the file and the help. I found the info I needed
> there fro the cache.th13.abs
On 09/23/2014 04:05 AM, Salil Soman wrote:
> Dear Doug,
>
> Thank you for your email. You were correct, there are values in the
> output file from running mri_segstats.
>
> I was hoping for your advice on the following:
>
> 1) as I used FreeSurferColorLUT.txt and the aparc+aseg.mgz files, are
>
See if this page gives you the answer you need
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 09/23/2014 10:39 AM, Michael WOODMAN wrote:
> Hello freesurfers,
>
> I would like to identify, in surface/vertex coordinates, certain points
> in a volume. Is there a straightforward way
Hi Emma
As Martin said not having a control group (or placebo group in which subjects
don't receive any treatment) is not a good study design.
In your case you will need to use LME because it looks like you are expecting
some sort of non-linear change for the mean response over time (pre-trea
Use this command
surfreg --s sub001 --t fsaverage_sym --lh --xhemi
On 09/18/2014 07:59 PM, ting xu wrote:
> Dear FreeSurfers,
>
> I have data has been recon-all analyzed. I would like to compare the
> symmetry of function/structure property between LH and RH, such as
> cortical thickness. I al
Dear All,
Is there any way I can get the Desikan-Killiany cortical and subcortical
labels on MNI152 template. I know I can get a rough estimate using the
linear transformation matrix "mni152.register.dat". I also find that the
subject cvs_avg35 is non-linearly registered to MNI152 and given in the
Thanks, indeed we used --pvr.
The command line was:
mri_glmfit \
--y ${PATH_DIR}/{surf}.mgh \
--pvr CT_surf.mgh \
--fsgd myfsgd.fsgd \
--C cont.mat \
--surf fsaverage $hemi \
--glmdir outputdir \
--mask mask_minimum_of_subjects.mgh \
--frame-mask mask_for_0_values.mgh \
--no-prune
Would there be a
No, there is not an easy way to work around this.
On 09/24/2014 03:01 PM, Celine Louapre wrote:
> Thanks, indeed we used --pvr.
> The command line was:
> mri_glmfit \
> --y ${PATH_DIR}/{surf}.mgh \
> --pvr CT_surf.mgh \
> --fsgd myfsgd.fsgd \
> --C cont.mat \
> --surf fsaverage $hemi \
> --glmdir
Hi Barbara - You can just insert the command that does your correction
right after that dtifit command line. As long as your command produces
the same set of outputs with the same naming convention (dtifit_FA.nii.gz,
dtifit_V1.nii.gz, ...), all subsequent steps will work the same.
Hope this
Hi Ben - There is a "E-10" in the gradient vector table, and it could be
what it's choking on. Can you try changing that and retrying?
a.y
On Fri, 12 Sep 2014, bigben2...@web.de wrote:
Hey everyone,
i have tried to run the trac-all command (Tracula), but it returned an error
(bvecs and b
Hi Barbara - The bbregister step registers from DWI to T1. This is a
necessary step because tracula needs to use the anatomical segmentation
derived from the T1. It cannot be replaced with DWI to T2 registration.
The anatomical segmentation is used to calculate the anatomical priors
that tracu
Hi Peggy - Yes, this error has been encountered before, and it should be
fixed in the latest tracula update. Can you please try it with this
version?
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates
a.y
On Fri, 12 Sep 2014, Peggy Skelly wrote:
Hi,
I'm processing 3T data wi
Hi Barbara - It means that, depending on the peculiarities of a specific
data set, one tract may be trickier than others and the algorithm may need
to retry multiple initializations to get it right. It would be nice if it
figured that out by itself and reinitialized without you having to do it
Hi Gabriel - The eddy-current correction method that's appropriate depends
on the b-value. For a moderate b-value, the DWIs have enough features to
be registered to the b=0 image. If you have something like b=2000, this
won't work so well.
The reorientation of tensors is just applied to the gr
Hi Michele - It seems like it's failing in the right uncinate again. From
the error, I would guess that part of that tract is getting left out of
the brain mask or something of that sort. Can you please check how that
area looks in the aparc+aseg and in the diffusion data?
a.y
On Thu, 18 Se
Hi Philip - Can you send your trac-all.log file and your configuration
file? Thanks!
a.y
On Mon, 22 Sep 2014, Philip Lindner wrote:
> Hi Freesurfers,
>
> I am having some trouble running TRACULA on the tutorial data that I
> downloaded from the site ("diffusion_recons" and "diffusion_tutoria
Hi Freesurfers,
I am curious about why in QDEC, when you correct for multiple comparisons
and
it spits out significant clusters with their cluster-wise p-values and
annotations and then click on find clusters and go to max, it changes the
annotation and coordinates of the previous output? I guess
Hi Gabriel - The standard pre-processing in tracula is likely to work for
all these cases. To make sure that the standard registration-based
eddy-current correction worked for all cases, you should look at the final
correct images (dmri/dwi.nii.gz) and make sure that all images in the
series a
Dear experts
I run mri_glmfit-sim with the following command : mri_glmfit-sim --glmdir
autistic.rh.volume.20 --cache 1.3 ${corr} --cwp 0.5 --2spaces did it right?
In the creating files, I found cache.th13.pos.sig.ocn.annot. But I don't know
how to load it in to freeview or tksurfer. Could y
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