Nope, bbregister is extremely good at this
Cheers
Bruce
On Sep 20, 2011, at 9:21 PM, SHAHIN NASR wrote:
> Hi
> I want to know if there is any limit for the automatic registration of
> functional scans on structural ones when we are scanning activity just in a
> specific part of the b
Hi,
I was wondering if it is possible to use optseq2 to get null events (e.g.
fixation) between each event type. I would like to see the optimal sequence of
trials for a design that involves two event types (each 0.5 sec), 60 TRs for
one event, 26 TRs for the other, and a 2sec TR. I would like
Hi
I want to know if there is any limit for the automatic registration of
functional scans on structural ones when we are scanning activity just in
a specific part of the brain (e.g. occipital cortex).
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Hi Michael,
the vertices in the patch file won't necessarily be in order (in general
they won't be), so we couldn't just get rid of the vno lines. I guess we
could have come up with a format that had all the indices, then all the
coords, but it's not the way I wrote it (sorry).
Not sure I un
Hi,
Two issues related to patch files.
Issue number 1:
If I generate an ascii flat patch file like so:
$ bin_patch=fsaverage/surf/lh.cortex.patch.flat
$ mris_convert -p $bin_patch lh.cortex.patch.flat.asc
And then inspect the file that gets created:
$ head lh.cortex.patch.flat.asc
#!ascii ver
you can select age, IQ and mean thickness as 'nuisance' variables, and
then your group can be the main discrete variable.
as for mean thickness causing a failure, it it probably the case that
the values are too close to each other. treating mean thickness as a
covariate is probably not necessary
Hello Freesurfer's,
I am using QDEC and I have created and FSGD descriptor file with 2 groups (pts
and ctrls) and three continuous variables: age, IQ and mean thickness. I have 2
questions:
1. I can only choose 2 covariates at one time? How can I choose all three
covariates in one model in
Can you tar up that subject and drop it to me at our file drop (url at
the end of this email).
doug
Ilana Hairston wrote:
> from my research assistant -
>
> On XXX the coordinates on the right side of the screen in tkmedit
> always start with a negative number.
>
> So that part is correct.
>
> O
from my research assistant -
On XXX the coordinates on the right side of the screen in tkmedit always
start with a negative number.
So that part is correct.
Our problem is that the brain is not flipped - if freesurfer displays
radiological and SPM8zero displays neurological, then when you compar
Hi all,
Trying to get mri_watershed to give me a good inner_skull_surface, which I want
to combine with the pial surface to estimate sulcal CSF, as I don't see any
other way. Unfortunately the data I have tested on all generate unreliable
inner_skull surfaces. Can anyone provide a tip for optimizi
You should map the fmri volume to the surface with mri_vol2surf. Then
run mri_segstats with --vox vertexno 0 0 and use the --avgwf output option.
doug
YUMI MAEDA wrote:
> when I want to get the timecourse from vertex number, what is the option
> name can I use?
>
> YUMI
>
>
>
>> Yes, that is c
Hi Greg, I think I've found and fixed the problem. I've but a new linux
version of mri_convert here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
Can you test it out to see if it works?
doug
Gregory Kirk wrote:
> i am trying to run tracula on a large number of subjec
What are the talairach coords for the left hemi? The first coordinate
(x) should always be negative.
doug
Ilana Hairston wrote:
> Hi Doug,
> No, we had the lh loaded in tksurfer, and when saving a point it
> showed up on the _left_ in tkmedit (i.e., the right side).
> thanks
> ilana
>
>
> On Tue
Hi Clark, have you looked at this documentation yet?
http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.ppt
doug
Clark Fisher wrote:
> Hello,
>
> I was wondering what orientation conventions are used when calculating the
> affine transformation matrix
i am trying to run tracula on a large number of subjects, tracula dies
quicklyin -prep stage when mri_convert tries to copy/rename the diffusion data,
the
error actually comes from the data read function. the data is already in .nii
format
the error is 'unsupported slice timing pattern 5' t
Hi Doug,
No, we had the lh loaded in tksurfer, and when saving a point it showed up
on the *left* in tkmedit (i.e., the right side).
thanks
ilana
On Tue, Sep 20, 2011 at 11:34 AM, weiland, Barbara
wrote:
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> fre
what other information would you like? Can you remind me: are you running
on a cluster? Does this happen if you run on your local workstation? Do you
have limits on # of open files?
On Tue, 20 Sep 2011, Lauge Emil Borch
Laurs S0rensen wrote:
> On Mon, Sep 19, 2011 at 15:20, R Edgar wrote:
>
>
On Mon, Sep 19, 2011 at 15:20, R Edgar wrote:
> Are you sure that there aren't per process limits which are set lower
> than those?
>
> Richard
I just checked, and no, there is no per process memory limit.
Is there any way to get more information out from mri_ca_register than
what is written i
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