using it as a gold-standard to interpret the T1. I would
> need more information to say for sure
>
>
>
> On Thu, 20 Oct 2016, Dorsa Haji Ghaffari wrote:
>
> So basically we have two types of images. One has a better contrast for
>> seeing the STN to that we can target it f
using it as a gold-standard to interpret the T1. I would
> need more information to say for sure
>
>
>
> On Thu, 20 Oct 2016, Dorsa Haji Ghaffari wrote:
>
> So basically we have two types of images. One has a better contrast for
>> seeing the STN to that we can target it f
Hi,
I have done the sub-cortical segmentation in Freesurfer and have extracted
the left thalamus, when I put it on top of the original MRI, it seems like
it is getting out of the border of thalamus, also it is not smooth. I
wanted to ask if anyone knows how to limit the computation only to
thalamu
Hi all,
I have done segmentation with Freesurfer but when I create a mask for the
left thalamus and import it to CAD software it doesn't seem to be at the
right coordinates. This may be due to the change in the mask
volume(256x256x256) from the original MRI volume(512x512x288).
I did re-slice the
by processing the upsampled
> data and it will waste lots of time
>
>
> cheers
> Bruce
>
> On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:
>
> Yes I created it using the higher resolution and I think it looks fine. I
>> attached the aseg.mgz. Is there any way to c
Thank you I'll try that.
On Thursday, July 21, 2016, Bruce Fischl wrote:
> try using the -rl switch in mri_convert. It will "reslice
> like" the you give. Give it the 512 volume as
>
> cheers
> Bruce
> On Thu,
> 21 Jul 2016, Dorsa Haji Ghaffari wrote
Hi,
I have segmented 288 slices of 512x512 dicom MRIs but when I create a mask
of the left thalamus I get 256 slices of 256x256 images. Is there any way
to get the same number of slices with the same size as I had before?
Thank you
Dorsa
___
Freesurfer
#x27;t good enough to say how accurate it was in some
> places
>
> On Wed, 20 Jul 2016, Dorsa Haji Ghaffari wrote:
>
> Yes it is taken at 3T. I have asked our team to provide these information
>> about the
>> MRIs and will let you know when I hear back. I also wanted to ask
, Bruce Fischl
wrote:
> what is a "3TS" image? Do you mean it was acquired at 3T? What sequence
> and what parameters (TE/TR/TI/TD/flip angle)?
>
> cheers
> Bruce
> On Tue, 19 Jul 2016, Dorsa
> Haji Ghaffari wrote:
>
> > Hi Bruce,
> > that is a 3TS T1
, Bruce Fischl
wrote:
> also, please post to the list so that others can answer!
> thanks
> Bruce
> On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote:
>
> Here it is. Also can you explain why the algorithm works best with 1mm^3
>> voxel size?
>>
>> Thank you!
>>
pushing the resolution and if
> they are really that high res they will be either very noisy or very long
> scans (or both)
>
> cheers
> Bruce
>
>
> On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote:
>
> Hi,
>> I have a T1 weighted MRI which I want to segment using Free
Hi,
I have a T1 weighted MRI which I want to segment using Freesurfer. The
voxel sizes are 0.48*0.48*0.48. I read that the ideal voxel size for
freesurfer is 1mm^3. Is there any manual adjustments that I can make to get
good results with my 0.48 voxel size images?
Thank you
Dorsa Ghaffari
__
Hi,
I want to refine the surface of my segmented subcortical structures such as
thalamus. I know -fix is used for refining the cortex surface, but is there
any function that refines the subcortical structures?
Thank you
Dorsa
___
Freesurfer mailing lis
you mean isolate? what do you mean export? You can create a
> binary mask in nifti format with mri_binarize --i aseg.mgz --match 10 49
> --o thalamus.mask.nii.gz
>
>
> On 07/06/2016 04:46 PM, Dorsa Haji Ghaffari wrote:
> >
> >
> >
> > Hi,
> >
> > I was
Hi,
I am trying to segment the thalamus into its nuclei such as VLA , VLP and
VIM. I see those labels available in the atlas but I do not get any of them
in my segmentation. Does anyone have any idea how to do that?
Thank you
Dorsa
___
Freesurfer maili
Hi,
I was able to segment the MRI successfully, now I am trying to isolate the
thalamus and export it out of FS as a volume. Is there a way to do that in
FS?
Thank you
Dorsa
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mg
ame>. It will figure out
>
> the rest of them
>
> On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote:
>
> > Hi,
> > I am a little confused about how should I save my files to execute
> recon-all on
> > them. I have 240 slices of dicom format and I put them in a folde
there are lots of tutorials and
> sample datasets and such
>
> cheers
> Bruce
>
> On Mon, 27 Jun 2016, Dorsa Haji
> Ghaffari wrote:
>
> > Hi,
> > I am graduate student at the University of Michigan and I am performing
> > research on deep brain stimu
hours is to process the data
> from a single subject at a single timepoint. If you check out our wiki
> (http://surfer.nmr.mgh.harvard.edu/fswiki) there are lots of tutorials and
> sample datasets and such
>
> cheers
> Bruce
>
> On Mon, 27 Jun 2016, Dorsa Haji
> Gh
Hi,
I am graduate student at the University of Michigan and I am performing
research on deep brain stimulation. I want to warp an anatomical brain
atlas to individual patient MRIs to get the patient specific brain models
out of it. I chose FreeSurfer to do this and I have installed it on my
comput
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