Hello Experts,
Can we do VBM in MNI template using the outputs from recon all? Which file
should I be using? And how do I smooth the volumes?
Thank you for the tips!
--
Shane S ___
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/09/2017 11:58 AM, Shane S wrote:
> Hi Doug,
>
> I want to derive a single averaged PET volume from the three
> reconstructed 5 min acquisitions, expressed in detected counts. Then
> we will divide the counts based on the cerebellum. Following that, I
> want to use Pet
Hi Freesurfer Users,
I am checking my data and there are many scans with a bit of dura being
captured as GM. I have attached some screenshots below. This happens in more
than 50% of my subjects. I am removing them manually them using Freeview, then
running the autorecon-pial. But this will
Hello Experts,
I am interested to do a segmentation of the thalamus subnuclei based on T1
data. Is there any atlas that I could use for this?
Best Wishes,
S
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Thank you very much!!
--
Shane S
On 9 March 2017 at 17:01:28, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote:
If the 3 volumes are in register (ie, no motion between them), then I
would just run the mri_concat command to create a single volume which is
the average of the 3, then proceed
the 3 images per subject?
Thank you.
--
Shane S
On 9 March 2017 at 16:18:33, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote:
How are you planning on analyzing the different time points?
On 03/08/2017 05:33 PM, Shane S wrote:
> Dear Doug,
>
> My PET data is 3 x 5 minute acq
) wrote:
No, the template is a within subject template used for registration. If your
pet data only has one frame (eg, FDG SUV), then you don't need to run
mri_convert or mri_concat, just use your pet image as the template
On 3/8/17 11:11 AM, Shane S wrote:
Hello Freesurfer,
I have 3 PET images
Hello Freesurfer,
I have 3 PET images per individual. I am learning PetSurfer based on the Greve
et al., 2014 paper.
On the PetSurfer link, there are 2 methods.
mri_convert pet.nii.gz —frame frameno template.nii.gz
or
mri_concat pet.nii.gz --mean —0 template.nii.gz
What are the differences?
Hi Bruce,
Where may I find more information about the differences in recon-all or
subcortical segmentations (aseg) between 5.3 and 6.0?
Is the 6.0 pipeline still based on this paper?
Fischl, B., Salat, D. H., Busa, E., Albert, M., Dieterich, M., Haselgrove, C.,
… Dale, A. M. (2002). Whole
Hi Antonin,
Thanks a lot. Those links are very helpful for me!
Cheers,
S
--
Shane Schofield
On 26 February 2017 at 12:51:23, Antonin Skoch (a...@ikem.cz) wrote:
Dear Shane,
the "topological defect" in FreeSurfer jargon means that the estimated surface
contains errors like "holes" or
Thanks Doug, I will give it try and update you on it.
S
--
Shane Schofield
On 26 February 2017 at 22:35:52, Douglas Greve (gr...@nmr.mgh.harvard.edu)
wrote:
Probably not. Probably you the cerebellum is still attached. You should check
the wm.mgz volume.
On 2/24/17 11:21 AM, Shane
for the hippocampus.
Sincerely,
Michel Hu
Van: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> namens Shane S
<shane.schofi...@yahoo.com>
Verzonden: maandag 27 februari 2017 11:00
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Overestimati
Hi Michel Hu,
Is that a summed value of left and right hippocampus? That seems normal to me
since averaged total hippocamppal volumes for MCI have been typically reported
at around 2500-3500mm3.
Thanks,
--
Shane S
On 27 February 2017 at 09:44:27, Michel Hu (a...@live.nl) wrote:
Dear
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