Hi Sophy,
According to Qdec wiki page, you should also run
recon-all -s -qcache
This will create the pre-smoothed surfaces in surf/ directory.
Best wishes,
Tanja.
On Wed, Jun 29, 2011 at 3:16 AM, Sophy Zhu wrote:
>
> Hi Freesurfers,
>
> There existed an error "Error in Analyze: Couldn't open
LinkedIn
Paula Diniz souhaite se connecter à vous sur LinkedIn :
--
Je vous invite à faire partie de mon réseau professionnel en ligne sur le site
LinkedIn.
Accepter l'invitation de Paula Diniz
http://www.linkedin.com/e/-wptfe6-gpl2
Hi Tanja,
If it doesn't affect the surfaces or the aseg then you should be all set.
It doesn't look like there's a lot of skull left in your image anyway.
But if you have time and want it to look cleaner/prettier - you can try
running the skullstrip step again and then rerunning -autorecon2 -au
you should be fine.
cheers
Bruce
On Fri, 1 Jul 2011, Tetiana Dadakova wrote:
> Dear list,
>
> For one of my subjects the skull strip is bad, but it doesn't
> (visually) affect neither surfaces nor segmentation (see the image in
> the attachment).
> In this case, do I have to edit the skull strip?
Hi there,
I just installed freesurfer onto a mac os x. My computer seems to default
to bash, so I created a .bashrc file in my home directory and added the
lines:
export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
but just in case I also created a .cshrc
I'm trying to draw an ROI by selecting the center of activation for a
particular contrast and then selecting nearby voxels within a certain range
(for example. say 20 voxels). Ideally I'd like to select only the voxels
within this range that are activated by my contrast. However, I can't see
how
Hi forum
Is it possible to get statistical maps of cortical thickness differences in
the same subject? I.e. to know what areas differ most from the median
--
Ignacio
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Hi Katie,
you can use the custom fill tool in tksurfer for this. Display your
activation map at whatever threshold you want, then click in the middle of
the blob you want to create an ROI for and do custom fill with "up to
functional threshold". This will floodfill from that point outwards
st
Hi Ignacio
you mean different from the median in that subject? Easy enough to do in
matlab, but we don't have anything out of the box to do it
cheers
Bruce
On Fri, 1 Jul
2011, Ignacio Letelier wrote:
Hi forum
Is it possible to get statistical maps of cortical thickness differences in
th
Hi Bruce,
That's how I normally make my ROIs, but my boss is concerned that we are
going from one area to a nearby area that is also activated by this
contrast, so she wants to restrict it by a certain number of voxels from the
center of activation.
Katie
On Fri, Jul 1, 2011 at 1:55 PM, Bruce Fi
you can draw a boundary between them and also click "up to boundaries" or
something like that. Or just click the center and dilate it a few times
or some combination of thresholding and dilation. It's quite flexible
cheers
Bruce
On
Fri, 1 Jul 2011, Katie Bettencourt wrote:
Hi Bruce,
That'
What do you mean by dilate it?
Katie
On Fri, Jul 1, 2011 at 2:28 PM, Bruce Fischl wrote:
> you can draw a boundary between them and also click "up to boundaries" or
> something like that. Or just click the center and dilate it a few times or
> some combination of thresholding and dilation. It's
Sorry I didn't realize since you have the same domain.
Ok, Let's say I do know the mean cortical thickness value of a subject. Then
is it possible know what brain areas differ more from that mean value by
using a color map visualization (I.e. for example: red = higher deviations,
deep blue = low
under tools->label in tksurfer (I think) there's an option to dilate or
erode the boundary (expand or contract)
cheers
Bruce
On Fri, 1 Jul 2011, Katie
Bettencourt wrote:
What do you mean by dilate it?
Katie
On Fri, Jul 1, 2011 at 2:28 PM, Bruce Fischl wrote:
you can draw a boundary b
Ok, I see it. I'll see what I can do with this, but I guess that means
there's no way to do it and enter an explicit number of voxels to select
from that central point?
Katie
On Fri, Jul 1, 2011 at 2:39 PM, Bruce Fischl wrote:
> under tools->label in tksurfer (I think) there's an option to dila
not really
On Fri, 1 Jul 2011, Katie Bettencourt wrote:
Ok, I see it. I'll see what I can do with this, but I guess that means there's
no way to do it and enter an explicit number of voxels to select from that
central point?
Katie
On Fri, Jul 1, 2011 at 2:39 PM, Bruce Fischl wrote:
un
Ok, thanks!
Katie
On Fri, Jul 1, 2011 at 2:54 PM, Bruce Fischl wrote:
> not really
>
> On Fri, 1 Jul 2011, Katie Bettencourt wrote:
>
> Ok, I see it. I'll see what I can do with this, but I guess that means
>> there's no way to do it and enter an explicit number of voxels to select
>> from tha
Hi Anastasia,
That did the trick! Thanks so much!
Cheers,
Jared
On Jun 30, 2011, at 12:28 PM, Anastasia Yendiki wrote:
>
> Hi Jared - We haven't reproduced this error on our end. So if I understand it
> correctly, replacing "bedpostx_seychelles" with "bedpostx" in trac-all would
> solve the
Glad it worked. We'll have to make sure this agrees better with non-MGH
installations in the next release.
On Fri, 1 Jul 2011, Jared Saletin wrote:
> Hi Anastasia,
>
> That did the trick! Thanks so much!
>
> Cheers,
> Jared
> On Jun 30, 2011, at 12:28 PM, Anastasia Yendiki wrote:
>
>>
>> Hi Jar
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