[Freesurfer] motioncor

2013-06-02 Thread Gabriel Obregon 
Hi,

Could someone please help me with the following concerns:

A. If I have multiple source volumes in mri/orig/ and run recon-all using the 
-nomotioncor option, how are these inputs processed compared to the case in 
which motion correction is employed, and what should I expect as my output?

B. If I want to process only one of the multiple source volumes, i.e., the 
"best", how should I proceed?

C. I've been encountering displaying issues of the raw volumes using tkmedit. 
What other interfaces are readily available for browsing through the source 
volumes in order to assess their quality?

D. Finally, if in one of my studies I could afford running only two MPRAGE 
sessions per subject, is motion correction advisable for segmenting the 
surfaces?

Thanks!

Gabriel
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Re: [Freesurfer] Segmentation of MR-PET structurals

2013-06-19 Thread Gabriel Obregon 
Hi Douglas,

The brainmask volumes are extremely grainy (similar to the raw structurals), 
i.e., dark voxels throughout the WM and high-intensity voxels across the gray 
matter. As far as I understood, all WM voxels (unless a lesion is present) 
should have a uniform intensity distribution after the normalization stages 
within the volume processing pipeline. Moreover, this makes the WM edits 
particularly challenging, for it's very difficult to trace the boundaries of 
some of the WM strands.

I don't know if this represents an issue but it's definitely something I hadn't 
encountered before. Any input would be really appreciated!

Thanks,

--G

On Jun 19, 2013, at 2:23 AM, Douglas Greve  wrote:

> Hi Gabriel, I don't have experience with the MR-PET yet. Why do you think 
> there is a problem? Try running wm-anat-snr on this subject. In general, you 
> don't want to be smoothing/denoising the anatomical
> doug
> 
> 
> 
> 
> 
> On 6/18/13 1:13 PM, obre...@nmr.mgh.harvard.edu wrote:
>> Hi,
>> 
>> I've started segmenting several structural scans from an MR-PET study
>> conducted in Bay 7, and was wondering if someone has previous experience
>> working with MPRAGE images acquired using the MR-PET coils?
>> 
>> The scans have a very low SNR and I am trying to figure out if this could
>> potentially affect the performance of the automated surface
>> reconstructions. I've scrolled through the volumes and even though the
>> surfaces seem normal, I am somewhat skeptical about their true quality
>> given that intermediate stages, such as the intensity normalization, seem
>> to be failing (please find an example from one of the brain masks
>> attached).
>> 
>> Is it essential to filter the raw structurals before segmenting them, and
>> if so, are there any readily available denoising tools? Furthermore, are
>> there any additional issues I should take into consideration?
>> 
>> Thanks for your help!
>> 
>> Gabriel
>> 
>> 
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[Freesurfer] Basic skullstrip Inquiry

2013-02-12 Thread Gabriel Obregon 
Hi,

I'm using the -gcut flag for the first time and I've noticed that the skull 
stripping process is still leaving small fragments of dura behind. Will this 
affect my surfaces? Should I manually edit the brainmask volume to remove as 
much of these fragments as I can? 

Also, should I only be concerned about the GM and cerebellum edges when 
checking for over-aggressive cutting, or are other brain structures important 
as well, e.g. optic chiasm?

Thanks,

--G

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