So when viewing with tksurfer I am assuming that -map angle shows the
polar data. It looks ok. There's a lot of yellow and red, which I am
assuming is the overall significance and not significance by position
yes?
tksurfer-sess -a rtopy.self.lh -s sj09 -map angle
To view eccen data, is it
sorry, ignore my previous post. I thought it was mri_segstats.
doug
Bruce Fischl wrote:
> oops, I just fixed that. If you let us know what software/hardware env you
> are using we'll give you an updated binary.
>
> Bruce
>
>
> On Thu, 4 Aug 2011, Christopher Luna
> wrote:
>
>
>> Hello,
>> I'm
You need to place the -i flag before the input and the -seg flag before
the seg.
doug
Christopher Luna wrote:
> Hello,
>
> I'm trying to run mri_segment with some custom values in the optional
> flags, such as -p for setting the percentage threshold with a float value.
>
> When I run the command
oops, I just fixed that. If you let us know what software/hardware env you
are using we'll give you an updated binary.
Bruce
On Thu, 4 Aug 2011, Christopher Luna
wrote:
> Hello,
> I'm trying to run mri_segment with some custom values in the optional flags,
> such as -p for setting the percen
Hello,
I'm trying to run mri_segment with some custom values in the optional flags,
such as -p for setting the percentage threshold with a float value.
When I run the command though,
"mri_segment -p 0.6 brain.mgz wm.seg.mgz"
The command properly sets the threshold to 60%, but also takes the "0.6
Hi John
I doubt it will work. We incororporate a *ton* of information about human
neuroanatomy that will not be present in your phantom.
cheers
Bruce
On Thu, 4 Aug 2011, John Jan Drozd
wrote:
> Hi,
>
> I have MRI scans of a plastic polycarbonate ventricle that is an actual shape
> of a vent
try this
mri_segstats --annot bert lh aparc --i lh.thickness --sum
lh.aparc.thickness.stats
Antonella Kis wrote:
> Dear Doug,
>
> I was running the mri_segstats as you suggested but I got an error:
>
> Constructing seg from annotation
> reading colortable from annotation file...
> colortable with
Hi,
I have MRI scans of a plastic polycarbonate ventricle that is an actual shape
of a ventricle. It is in a brain mold of agar gel solution. I segmented the
ventricle successfully using multiple seeds fuzzy connectedness in ITK. My
segmentation was 97.2 % accurate. In ITK it had only single se
Or look at the x-coordinate (neg means left side)
Bruce Fischl wrote:
> you could overlay the surface I guess, or the aseg, or use the 3
> orthogonal views.
> On Thu, 4 Aug 2011, Antonella Kis wrote:
>
>> Hi,
>>
>> When visualizing the wm.mgz in the coronal view we can see both
>> hemispheres:
>
you could overlay the surface I guess, or the aseg, or use the 3
orthogonal views.
On Thu, 4 Aug 2011, Antonella Kis wrote:
Hi,
When visualizing the wm.mgz in the coronal view we can see both hemispheres:
lh and rh. How do I know which hemisphere I am visualising in a sagittal
view? Do I have
Hi,
When visualizing the wm.mgz in the coronal view we can see both hemispheres: lh
and rh. How do I know which hemisphere I am visualising in a sagittal view? Do
I have a transition from lh to the rh while passing through the slices?
Thank you,
Antonella
_
Hi Ammar - At which point does the allocation error occur? It'd help to
see your trac-all.log.
Thanks,
a.y
On Thu, 4 Aug 2011, Moiyadi, Ammar wrote:
> Thanks Anastasia - I decided to made an entirely new txt file and the proper
> dmri/bvec file is now being created. Unfortunately now I'm runn
Thanks Anastasia - I decided to made an entirely new txt file and the proper
dmri/bvec file is now being created. Unfortunately now I'm running into a
memory allocation problem. Since I'm running on ubuntu I'm not sure its the
same problem that mac users are facing. Any suggestions for how to pr
I guess it is detecting the fact that gcuts failed. Nick: is there any way
to disable the failure detection so Jacquie can see what it did?
Bruce
On Thu, 4 Aug 2011,
Jacquelynn Nicosia Copeland wrote:
> Hi Khoa,
>
> Thanks for your response. The extra dura/skull is being included in some
> pa
So when viewing with tksurfer I am assuming that -map angle shows the
polar data. It looks ok. There's a lot of yellow and red, which I am
assuming is the overall significance and not significance by position
yes?
tksurfer-sess -a rtopy.self.lh -s sj09 -map angle
To view eccen data, is it
Hi Jacquie,
I'm not sure why gcut isn't working. If you want, you can compress one of
the subject dirs and upload it. I can take a look and also see which other
ways you can fix the problem.
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-Khoa
On Thu, 4 Aug 2011, Jacquelynn Nico
Hi Khoa,
Thanks for your response. The extra dura/skull is being included in some parts
of the pial surface, particularly around the superior surfaces of the brain
(gray matter and cortical regions that we are interested in are being
affected). Thus, manual editing by erasing dura/skull has bee
How do the eccen and polar look by themselves? You can look at them with
tksurfer-sess
doug
Michelle Umali wrote:
> Hi Freesurfers,
> I'm troubleshooting my retinotopy data and am still having issues with
> wonky fieldsign data. The registration looked ok, so now I am trying
> to look at the
Hi Freesurfers,
I'm troubleshooting my retinotopy data and am still having issues with
wonky fieldsign data. The registration looked ok, so now I am trying
to look at the retinotopy results using rtview. I got an error
message saying it can't find the register.dof6.dat file. So, now I am
Hi Antonella,
try running things all the way through, then the only stuff you need to
fix is if the surfaces are not visually in the right place.
cheers
Bruce
On Thu, 4 Aug
2011, Antonella Kis wrote:
Sorry I forgot to attach the manual so you can compare the image on the page
57 with my s
You can use mri_segstats with the --annot option. The output summary
table will have a column with the number of "voxels". In this case, it
will actually be number of vertices.
doug
Antonella Kis wrote:
> Hi Doug,
>
> Thank you for your help. Based on your answer my questions is: Do I
> have t
what does the surface look like? It's probably not a problem
On Thu, 4 Aug
2011, Antonella Kis wrote:
> Hi Bruce,
>
> Many thanks for your answer and for your valuable help. I was just following
> the the examples from the Free Surfer manual on the page 57 (please see the
> attachment). I believ
Hi Bruce,
Many thanks for your answer and for your valuable help. I was just following
the the examples from the Free Surfer manual on the page 57 (please see the
attachment). I believe my image (the slice I sent you on yesterday) is similar
or closed looking with the one on the page 57.
Since
you can load the annotation into matlab with read_annotation.m
doug
Antonella Kis wrote:
> Hi Doug,
>
> Thank you very much for your answer. I need to prepare a table here
> to include the number of vertex and the cortical thickness, for some
> further studies. Is there a way to do it in MATLAB
Hi,
How much dura/skull is left on your subjects that you want to remove?
Sometimes gcut takes away more than just dura, especially in the
cerebellum region so that might be why it is much smaller.
If the surfaces are not including the extra dura/skull, then it is not
necessary that you remove
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