Hi,all:
As we have too many controls and patients to run the "recon-all",and it
is really time-suming,so,how can I reduce the time of recon-all in a group of
patients?
After read the statistic info on the website
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllRunTimes
It seems the mac
Hello All,
I get the following error while trying to run mri_glmfit. I am running a
2.93
ghz imac with 8gb of ram. I am also running freesurfer version 5.0.0 on Snow
Leopard OS version 10.6.
/Applications/freesurfer/subjects/qdec$ mri_glmfit --glmdir
lh.paired-diff
--fsgd paired-diff.fsgd --C
Hi Michael,
I doubt that the loss of 1 DOF is causing the disappearance. In both
models, the test for the difference between groups occurs at a
particular age (age=0). This is not a factor in the DOSS model because
the lines for the two groups are forced to be parallel (so the
difference is
two row contrast matrix
[1 1 -1 -1 0 0]
[1 1 0 0 -1 -1]/2
1st row test for a difference bet G1 and G2
2nd row tests for a difference bet G1 and G3
Note that you don't need to test G2 vs G3 (that is implied by the other
two tests).
doug
On 3/9/11 7:33 PM, Gabriel Go.Es. wrote:
Thank
The native resolution of the other subjects is (1,1,1)mm voxel size and
(256,256,160) voxels, whereas this subject is (0.7,0.7,0.8) mm voxel size and
(288,288,165) voxels. Sorry that wasn't clear in my previous email. I'd
appreciate any insight that anyone might be able to share.
Thanks,
Tric
What is the resolution of your other subjects?
On Mar 9, 2011, at 5:21 PM, Tricia Merkley wrote:
> Hello,
>
> One of our subjects was scanned with (0.7,0.7,0.8) mm voxel size, although
> all other acquisition parameters were the same as the other subjects. I'm
> wondering to what extent th
Hi Marie,
Thank you for the information.
The routine fspecial() is used in four M-files, 'make_outer_surface.m' where it
is used to setup a 2-D Gaussian filter; 'read_eccen_patch.m',
'read_freq_patch.m' and 'read_patch.m', where in all 3 cases it's used to setup
a simple averaging filter.
Michael,
Thanks for your response. It was helpful. As you suggested the
"thickness-age correlation group difference" under DOSS is meaningless, so I
have ignored that output.
I am currently left with a situation where under the DOSS model I see a
large ageXthickness effect (controlling for group)
hi, not sure what you are trying to do, as the commands below seem to do
what i expect them to do, which is to create a masked (skull-stripped)
version of rawavg.mgz. what do you mean by 'manual segmentation
changes'?, and what exactly is going wrong?
if you deleted voxels in brainmask.mgz, then
Gabriel Go.Es. wrote:
>
> Thank you so much, Doug
>
> I've check at your update and saw that this contrast has to be /2,
> wich I guess means 0.5 instead of one to keep the scale right?
Yes.
>
> and the contrast for me, would be something like:
> Let's suppose
> group1_males
> group1_females
> g
That is the file created by registering your orig.mgz to the mni152
brain (assuming you are using the 152). You can create this registration
file with the mni152reg script.
doug
Seok Lew wrote:
> Thanks, first of all.
>
> I tried with the following scripts, but ended up with an error. I am
>
Hello everybody,Sorry for the insistance, but I need to solve this...
I'm making some manual segmentation changes in the brainmask.mgz and using
mri_vol2vol and mri_mask commands to apply these changes to the rawavg.mgz, the
output from the mri_vol2vol looks perfectly normal,and retains all c
Hello,
One of our subjects was scanned with (0.7,0.7,0.8) mm voxel size, although all
other acquisition parameters were the same as the other subjects. I'm
wondering to what extent this might affect the results of the subcortical
segmentation, cortical thickness measurements, etc., as compared
Thanks, first of all.
I tried with the following scripts, but ended up with an error. I am
not sure which format or file is required for the --volreg.
#
mri_surf2surf --s FS --hemi lh --sval-nxyz pial --tval ./ttt.mgz
#
mri_surf2vol --surfval ttt.mgz --hemi lh --volreg mri/transforms/
talaira
Hi Chris,
Regarding your question on lGI, I am sure that imclose is one of the required
function belonging to the Image Processing Toolbox. I may be wrong but I think
that it is the only one. More specifically I don't remember that I used
fspecial, where did you see it? (Apart from imclose, if
Hi Everyone Again,
I thought I'd re-state my question more clearly:
I managed to make an annotation with 2 parts: one, of interest, and the
other, not. On the color table file, the "not of interest" part has 0 0 0 0
for Red, Green, Blue, and Opacity.
However, when I load the annotation in TkSurf
Research Assistant Position in Cognitive Neuroscience
Department of Neurology, School of Medicine, New York University
We are seeking a full-time Research Assistant to assist with cognitive
neuroscience experiments involving human intracranial EEG. Main topics of
investigation are language, mem
Hi,
I made a label for the rest of the brain. In the colour table, I put 0 0 0
and 0 for opacity. This may make the desired annotation transparent, but the
rest of the original brain is still grey. Is there a way to not view the
original brain surface? Or to change the colour?
Thanks,
Allie
O
For mni152 space, you'll need to register your anatomical to the 152
brain. You can do this with the freesurfer mni152reg program (might only
be in the new version). Then use mri_vol2vol specifying this reg and
also making sure that you use nearest neighbor interpolation. One
problem is that this d
That contrast is wrong. I've updated this page with the correct contrast
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf6G0V
which is:
|+1 -1 0 -1 +1 0|
|+1 0 -1 -1 0 +1|
This is an F-contrast (two rows). The first row looks for a difference
between L and R for M and F (ie, a simple interact
Hi Freesurfer users,
I have been working from the list posting below for vertex comparison of
longitudinal thickness data, although there are a couple issues I was hoping
someone could help with.
Using FS v5.0 with the fixed binaries, I have put together the following
steps for data comparison f
?? wrote:
Hi,all:
I have several problems about the qdec in freesurfer 5.0.
Firstly,can somebody explain the function of the buttons in the qdec's
third step (display),such as Set using FDR in the False Discovery Rate
,Monte Carlo Null-Z simulation.If I just let these buttons as the
defa
Well, .3mm is still 30%, which means that your brains will show up 30%
smaller/larger. This could mess up any number of things. Unfortunately,
the right answer is to fix your data then re-run everything. Try using
FreeSurfer's mri_convert to convert from dicom. You can also just pass
the dicom
Hi Doug,
I used --help. I loaded the annotation but the other regions were still all
present. This makes me think that I need to have ALL areas of the brain
included in the colour table, with values of 0 for the colours, or values of
100 for opacity. I'll give this a shot.
Thanks,
Allie
On We
The idea is that you copy it into one location (no need to make multiple
copies), then modify it to match what you want. You'll need to change
the names at least. Try running it with --help to get more info. And,
yes, you can make your own label!
doug
Allie Rosen wrote:
> Hi Again,
>
> I ma
Hi,
Please ignore the previous question. I seem to have figured it out... for
now.
Thanks,
Allie
On Wed, Mar 9, 2011 at 2:29 PM, Allie Rosen wrote:
> Hi Again,
>
> I made a label on my own instead of using annotation2label. First, is this
> even allowed?
>
> Now I am trying to use label2anno
Hi Katie, sorry for the delay. This is actually a pretty complicated
question. It probably does mean that you are getting a better fit,
though you have to be careful if you attempt to keep playing with your
model and only keep the one that gives you the most activation.
Eventually, you will pi
Hi Nathan
does it match the underlying MRI (e.g. the orig.mgz)?
Bruce
On Wed, 9 Mar 2011,
Nathan Dankner wrote:
> Hi all,
>
> After running a surface through autorecon2 and checking it I noticed that it
> is tilted up at approximately a 45 degree angle. Is this a problem? If so,
> how should
Hi Again,
I made a label on my own instead of using annotation2label. First, is this
even allowed?
Now I am trying to use label2annot. I'm not sure how to specify the colour
table. I typed in: "--ctab FreeSurferColourLUT.txt but it can't find the
file. I found it in the freesurfer home file, and
Hi all,
After running a surface through autorecon2 and checking it I noticed that it
is tilted up at approximately a 45 degree angle. Is this a problem? If so,
how should I go about fixing it?
Nathan
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My lab doesn't have matlab... I'll work on the label2annot and
annotation2label programs.
Thanks,
Allie
On Wed, Mar 9, 2011 at 2:02 PM, Bruce Fischl wrote:
> we don't have any tools for doing so, but you could do it in matlab
> On Wed,
> 9 Mar 2011, Allie Rosen wrote:
>
> > Hi,
> >
> > Can I m
we don't have any tools for doing so, but you could do it in matlab
On Wed,
9 Mar 2011, Allie Rosen wrote:
> Hi,
>
> Can I modify the colour table of an annotation file? Apparently there is an
> embedded colour table in annotation files.
>
> Allie
>
>
>
> On Wed, Mar 9, 2011 at 1:07 PM, Douglas N
You can break the annots into labels, then recombine them with
mris_label2annot and spec a color table. Not sure if you can edit it
directly in the annot.
doug
Allie Rosen wrote:
> Hi,
>
> Can I modify the colour table of an annotation file? Apparently there
> is an embedded colour table in an
Hi,
Can I modify the colour table of an annotation file? Apparently there is an
embedded colour table in annotation files.
Allie
On Wed, Mar 9, 2011 at 1:07 PM, Douglas N Greve
wrote:
> It will eliminate them from the annotation which should mean that those
> areas should be transparent.
> do
Try using mri_surf2surf with the --sval-nxyz. The output have 3-frame,
one for each component in the normal. Then use mri_surf2vol to stuff
this back into a volume.
doug
Seok Lew wrote:
> Hello users,
>
> My colleagues and I are trying to create a gray matter electric
> conduction model where
Hello users,
My colleagues and I are trying to create a gray matter electric
conduction model where a preferable conduction direction is aligned
with the normal direction induced from the pial and white surface
normals.
Freesurfer reconstruction already gives pial and white matter surface
It will eliminate them from the annotation which should mean that those
areas should be transparent.
doug
Allie Rosen wrote:
> Hi Doug,
>
> Thanks for the response. Do those commands make the annotations/labels
> transparent?
>
> Allie
>
>
>
> On Tue, Mar 8, 2011 at 10:58 PM, Douglas Greve
> ma
Hi Brian
you should be able to compute this with mri_distance_transform and a bit
of matlab code
cheers
Bruce
On Wed, 9 Mar 2011, Weisinger, Brian (NIH/NIMH) [F] wrote:
> Hello,
>
> Is there any chance that there is a general table of Euclidean distances for
> each freesurfer segmented brain r
Hi Doug,
Thanks for the response. Do those commands make the annotations/labels
transparent?
Allie
On Tue, Mar 8, 2011 at 10:58 PM, Douglas Greve wrote:
> I've never used that, but you can use mris_annotation2label to break the
> annotation in to individual labels,then use mris_label2annot t
Hi Alan,
yes, we are hoping by the end of the month. We are in our 2nd or 3rd round
of testing and bug fixing, so hopefully it is converging.
Bruce
On Wed, 9 Mar
2011, Alan Francis wrote:
> Hi Bruce, Nick & Doug:
>
> Any chance of FS 5.1 coming out in the near future? We have 2 longitudinal
>
Hello,
Is there any chance that there is a general table of Euclidean distances for
each freesurfer segmented brain region relative to each other. So something
like a matrix table for each side of the brain
Brain region 1 Brain region 2
Brain region 1
Hi Bruce, Nick & Doug:
Any chance of FS 5.1 coming out in the near future? We have 2 longitudinal
data sets that we are holding back till we have this installed.
Thanks so much,
Alan
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https://ma
I had asked the Listserv a week or so ago if there was a way to get the Folding
Index measurement for each subject and ROI using aparcstats2table, similar to
area, thickness, gray volume etc.. The data are in the ?h.aparc.stats files for
each subject, along with thickness, thickness std, surface
Do you have permission to write to that directory?
Bruce
On Mar 9, 2011, at 7:45 AM, Tetiana Dadakova wrote:
> Dear FreeSurfer list,
>
> I try to open RB_all_2008-03-26.gca by typing
>
> mri_convert RB_all_2008-03-26.gca -nth 0 means.mgz
>
> and get an error:
>
> mri_convert RB_all_2008-0
Dear FreeSurfer list,
I try to open RB_all_2008-03-26.gca by typing
mri_convert RB_all_2008-03-26.gca -nth 0 means.mgz
and get an error:
mri_convert RB_all_2008-03-26.gca -nth 0 means.mgz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from RB_all_2008-03-26.gca...
readi
Dear Users,
Is there a way to process fixated brain (after autopsy) with Freesurfer?
I have read somewhere that I should just "invert" the image, but what does
it mean? And would it not increase the noise and the signal from the CSF?
Of course, the brain is without any skull, pia and dura mat
Hello,
I'm making some manual segmentation changes in the brainmask.mgz and using
mri_vol2vol and mri_mask commands to apply these changes to the rawavg.mgz, the
output from the mri_vol2vol looks perfectly normal,and retains all changed made
by me, but when I use the mri_mask command over th
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