Hi surfers,
as of FreeSurfer version 5.3, i am missing the option to choose between DOSS
and DODS design in QDEC. The radiobuttons in the design tab are no longer
there. The default behaviour, judging from the results, seems to be DODS. Has
this option been removed?
regards,
Andreas
Hi All,
I am using freesurfer 5.1 for my analysis. In FS 5.1, does the Supratentorial
volume include the Optic chaism volume ?
Please let me know.
Thanks
Ri
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Andreas,
DOSS was removed from qdec because the contrast generation code in qdec
was not appropriate for it (and we didnt have time to add it). You will
have to use the command-line mri_glmfit and create your own contrasts to
use DOSS. There are examples on the wiki i think.
Nick
Hi
Akio,
You should just run -autorecon2 instead of -subcortseg in order to get the
subcortical segmentation.
Nick
Hi Freesurfer experts,
After installing v5.3.0 (CentOS 6 64bit), the command recon-all -s test
-i sample-001.mgz -i sample-002.mgz -autorecon1 finished without error.
Then,
Jamie,
Does running with the -all flag run all the way to complete without error?
We recommend running with -all and then inspect for defects afterwards
instead of running the first run in stages.
Nick
Hi Freesurfer List-
My group just recently installed 5.3.0 and I kept running into the
Hi All,
I am using freesurfer 5.1 and I want to compute the brain parenchymal fraction
(GM+WM/GM+WM+ventricularCSF).
In aseg.stats, I get the whole GM vol and I can also get the total ventricular
CSF by adding the vols of different ventricles.
But I am confused abt the terminology -
It excludes WM in cerebellum and brain stem.
doug
On 05/21/2013 10:31 AM, Ritobrato Datta wrote:
Hi All,
I am using freesurfer 5.1 and I want to compute the brain parenchymal
fraction (GM+WM/GM+WM+ventricularCSF).
In aseg.stats, I get the whole GM vol and I can also get the total
Hi Mingxia, if you have a binarized map, then just use --id 1 with
mri_cor2label (not need to for mri_binarize if it is already binary)
doug
On 05/21/2013 03:55 AM, zhang mingxia wrote:
Hi Doug,
Thanks very much. A few more question after I read the description of
mri_cor2label.
1.
you can use mris_fwhm with the mask option. Just give it a maks of the
places that are NOT NaNs
doug
On 05/21/2013 09:37 AM, Glen Lee wrote:
Inline image 1
Hi freesurfer experts,
I'm dealing with an issue with smoothing on surface data that
unfortunately contain 'NaN' in the
Dear Martin,
Thank you for your helpful information. You were right that something had
gone wrong with my preprocessing (for some unknown reasons). I re-run the
preprocessing and was able to get the long_mris_slopes command
up-and-running.
Keith
On Wed, May 8, 2013 at 4:28 PM, Martin Reuter
Hi Vincent, I don't think it is supposed to be. Is that a problem?
doug
On 05/21/2013 09:02 AM, Vincent Koppelmans wrote:
Dear FreeSurfer experts,
I have used dt_recon for tensor fitting of my diffusion data. I used
the following syntax:
dt_recon --i dwi.nii.gz --b data.bval data.bvec --s
Hi!
I am trying to work around this now using more control points.
However, I was wondering whether the fixed version of mri_segment for
v4.5 that accepts the -p parameter is still available? Just in case I
need to use a different threshold at some point.
Thanks, Caspar
2013/5/17 Caspar M.
Hello list!
Is there a way to display the thickness of individual Bordmann areas
in the inflated surface using tksurfer?
I'm able to show surface area with File- Label - Load label and
choosing the thresholded label. Now, I qould like to do the same but
with cortical thickness, is this
Hi Andreia, do you mean that you want to display a constant value in
each BA on the surface? We don't haveanything explicit to do that, but
you could do it in matlab. Let me know if you need more info.
doug
On 05/21/2013 11:46 AM, _andre...@sapo.pt wrote:
Hello list!
Is there a way to
Hello list!
Can I use the command mri_segstats to calculate the statistics across
multiple subjects? If yes, how to do it? Thank you in advance,
Fang
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Hi Doug,
I would like to have the thickness map restricted to the BAs where the
group differences showed up. Could it be possible to overlay the
thickness map of an individual and then restrict it to the chosen BA,
for example?
The ideia is to have two subjects with the thickness overlayed
1) BEST FITNESS (M) is 984.24263
mri =0.000 curv = 4.318 unmri = -1001.515
( f=0.00 , v=0.00 , c=4.32 , q= 8.64 )
( f=0.00 , v=0.00 , c=4.32 , q= 8.64 )
63 patches have been generated - 38 self-intersected
max face = 36973(40653) - loop = 46 (73) - ntries
Hi Fang,
mri_segstats can only be run on individual subjects, but you could easily
write a script to run it on all your subjects, then use asegstats2table to
merge all the individual subject stats into a spreadsheet ready table.
-Louis
On Tue, 21 May 2013, Fang CAO wrote:
Hello list!
Can I
Hi Martin,
Now I move onto the mri_glmfit step (still within the two stage method).
The on-line tutorial for doing this is not very clear.
The output of the first stage is stored in the subject-template (base),
already in fsaverage space. Simply replace the thickness file with your
Perhaps the problem has already been solved but I just ran into the same issue
(on OS X 10.8.2). After poking around, what I found was that while the current
AFNI distribution does not have a file named 3dvolreg.afni, it does have one
named 3dvolreg. I'm guessing the problem is that it has
Hi Keith,
you are right, the lh.long.thickness-spc.fwhm5.fsaverage.mgh in each
base folder is only for that subject. You process this the same way as
you'd usually do thickness in a cross sectional analysis. Except you can
skip the mris_prepoc step (as everyting is mapped to fsaverage and
Hello
I am interested in downloading the FreeSurfer v5.3.0. I will be running
it on a virtual machine platform in Windows (xubuntu). Are there any
specific instructions for this on the FreeSurfer website because I noticed
it runs on CentOS 6 x86_64 (64b). Or does the download come with the
Kristina,
We havent created a Windows Virtual Machine freesurfer bundle yet, but
if you already have, or know how to create, an xubuntu vm instance on
windows, then all you have to do is download and install the centos
distribution from within that xubunbtu instance. if your xubuntu is 32,
then
You can create a binary mask from the labels (see mri_label2label with
the --outmask option), then run mri_glmfit with the --mask option to
only analyze data inside the mask.
doug
On 05/21/2013 12:19 PM, _andre...@sapo.pt wrote:
Hi Doug,
I would like to have the thickness map restricted to
Hello All,
I havent used dt-recon yet but I have a question abt it.
When the dt-recon computes the FA maps, whats the dimensions of these FA maps ?
Are they resampled to the freesurfer anatomical voxel size (1x1x1) or are they
in their native voxel size (in which they were collected) ?
If I
The native DTI space.
doug
On 05/21/2013 04:41 PM, Ritobrato Datta wrote:
Hello All,
I havent used dt-recon yet but I have a question abt it.
When the dt-recon computes the FA maps, whats the dimensions of these FA maps
? Are they resampled to the freesurfer anatomical voxel size (1x1x1)
It should be in $FREESURFER_HOME/bin/3dvolreg.afni
On 05/21/2013 02:49 PM, Joseph Dien wrote:
Perhaps the problem has already been solved but I just ran into the
same issue (on OS X 10.8.2). After poking around, what I found was
that while the current AFNI distribution does not have a
Hi Skyler - When you say it's been working fine, have you checked that the
orientations are correct by viewing dtifit_V1.nii.gz and dtifit_FA.nii.gz,
like in the snapshot that I sent you? If those orientations aren't
correct, the gradient table isn't correct either.
a.y
On Tue, 21 May 2013,
Kristina,
I do not know what virtual machine manager you intend to use. If you
will use Oracle's VirtualBox I would like to share my recent experience
with you. I tried a updated CentOS6 virtual machine with Freesurfer 5.2
running under Fedora 18 as host but I had problems during recon-all
tests.
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