Dear freesurfers,
I would like to obtain the cluster size (in mm3) and coordinates of the
maxima of a cortical volume comparison using mri_surfcluster.
mri_surfcluster --in
$PATH/control_cronic_dones_right_volume/rh-Diff-control-cronic-Intercept-volume/sig.mgh
--hemi rh --subject fsaverage --thmi
Hi Bruce,
Yes, it should be classified as a gray matter, if I save a point of an
heterotopia in the tkmedit and then open it in tksurfer the point showed at
the inflated surface correspond to that point or to the projection of the
heterotopia in the cortical surface?
what happen with these measure
Hi Natalia,
/TemplateSub1/surf/lh.thckness.fwhm10.fsaverage.mgh
there is an 'i' missing in thckness (but that might be just a typo).
also this is a regular thickness file. You cannot analyze the thickness
in the base. That is meaningless, you need to select one of the other
files in qdec, e.g. t
Hi Silvia,
it is never a good idea to mix versions and we did not test any such
combinations. Also because 5.1 is much better than 4.5 I would
definitely recommend to rerun.
However, I still believe that it should be possible to use the 5.1
post-processing scripts to e.g. create rate maps for ea
Hi Carolina,
the yellow line represents the gray/white boundary, and so presumably
should follow the bottom of the heterotopia. If it is large though, it
may be difficult to obtain an accurate boundary since it breaks many of
our assumptions (e.g. max thickness, sharp intensity gradient at gra
It won't give you talairach coords in the label file, it will give you
MNI305 coords. Use the View->Information in tkmedit to get MNI305 coords.
doug
Jed Singer wrote:
> That almost works; tkmedit is giving talairach coordinates of, for a few
> examples:
>
> 14.7 23.9 -22.3
> 24.8 21.9 -18.8
>
Hi Katie, it should not matter that they are across hemispheres. Are you
getting an error?
doug
Katie Bettencourt wrote:
> I'm still looking for an answer on this. If the answer is you can't
> do it, I'm ok with that, I just would like to know! Thanks!
>
> Hi all,
>
> I was wondering i
Hi Knut, why does the color bar need to change? It should be symmetric.
Do you mean that you want the color bar to flip?
doug
Knut J Bjuland wrote:
> HI
>
> I have reproduce the error by using the group data from
> buckner_tutorials. The files may be download
> from this link with the error
> htt
No errors, I hadn't actually tried it because everything else was so
hemispheric based, and I didn't want to just blindly try it and be unsure of
the data I got out. So I should be able to (in surface space) draw a LH and
RH ROI, combine them using labels_union and do an standard ROI analysis on
t
Hi Chris, mri_surfcluster should output coordinates in "Talairach" space
(The newer 5.1 version uses MNI305 space). Internally, we always use
MNI305 space. To report "Talairach" coordinates, we then apply a
transform (http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html) to give
particular values
yep, that should work
Katie Bettencourt wrote:
> No errors, I hadn't actually tried it because everything else was so
> hemispheric based, and I didn't want to just blindly try it and be
> unsure of the data I got out. So I should be able to (in surface
> space) draw a LH and RH ROI, combine t
Hi Yolanda, don't use thmax (it will exclude everything with a sig>7 --
not what you want I assume). That command otherwise looks right, but it
won't correct for multiple comparisons. You can run
mris_anatomical_stats on the output label to give you the stats you want.
doug
Yolanda Vives wrot
Hi Knut, why does it need to be reversed?
doug
Knut J Bjuland wrote:
> Hi
> When I click on reverse values in Qdec the color on the hemisphere will
> change, but the color bar at the bottom on the screen will stay the
> same. Is there anything I can do to force Qdec to change the color bar
> at th
Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School
Job Description
A postdoctoral position is available with the TRANSCEND Research Program
(www.transcendresearch.org) at the Martinos Center for Biomedical Imaging
in Charlestown, MA (www.martinos.org) which is affiliated
Hi Bruce,
I will graetly appreciate if you can help me with the following questiosn:
1).I am not sure what you mean by type of acquisition but going back to my last
question, the only thing I know is that my MRI data contains more
sequences/series (3DAx_T1, 3DSag_T1, Ax_Flair, Ax_PD, Ax_T2, BO
1. Yes, that's reasonable. You can use .nii.gz and the output extension
and it will automatically gzip compress it.
2. No, I don't think so.
3. The only real way to check is visual inspection.
cheers
Bruce
On Tue, 26 Jul 2011,
Antonella
Kis wrote:
Hi Bruce,
I will graetly appreciate if y
Hi Bruce,
I forgot to ask why my data does not include an unknown region in my
aparc.stats file? My stats data starts with bankssts region and continue with
caudalanteriorcingulate, etc. Do I need to have the unknown region if I use the
new version of the FS 5.1.0?
Thank you.
Antonella
_
Does anyone knows which command would exercise the GPUs using CUDA as benchmark?
Thanks,
Leo Souza
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, July 26, 2011 8:58 AM
To: Knut J
Hi,
I would like to check if my subcortical segmentation is correct so I was
running:
tkmedit SUBJECT1 brainmask.mgz \
-aux T1.mgz -surfs \
-segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
1). Pial (red line), and white (yellow line) surfaces are shown and I wonde
Hi Antonella
the atlas is not guaranteed to be correct. If it were we would just take
the labels from it :) The only way to tell if it is correct is to look at
the segmentations on top of the MR and see if they follow the visible
boundary
To get the surfaces you should do
tkmedit SUBJECT1 b
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