[caret-users] Mapping Paint areas from Surface to MRI

[Hamied Haroon]

Dear Donna, John and David,

Thanks so much for your kind replies.

Your invaluable instructions and advice worked a treat. I've got the
cortical partitioning schemes in exactly the format I needed.

Many thanks again.

Best wishes,
 
Hamied
 

-----Original Message-----
From: caret-users-bounces at brainvis.wustl.edu
[mailto:caret-users-bounces at brainvis.wustl.edu] On Behalf Of David Van
Essen
Sent: 07 January 2008 18:44
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] Mapping Paint areas from Surface to MRI

Hi again Hamied,

One minor clarification regarding the thickness.  Since the macaque  
cortex is only ~1.5 mm thick, you should modify the default settings  
to a smaller value.  Good results come from a choice of +/- 0.75 mm,  
though you can fine tune that if you are doing detailed quantitative  
studies that are sensitive to cortical thickness estimates.

Note that the macaque F99 atlas volume is 0.5 mm voxel size, but the  
paint to volume operates on mm not voxels if the volume file header  
has the appropriate metadata.

David VE

On Jan 7, 2008, at 11:28 AM, John Harwell wrote:

> Hamied,
>
> 1) Load the Macaque surface and paint file into Caret.
> 2) Select Attributes Menu->Paint->Convert Paint Column To Paint  
> Volume.
> 3) In the dialog that appears, use Surface Selection to choose the  
> fiducial surface in the Surface Selection section of the dialog.  In  
> the Volume Selection Dialog, press the Get Parameters Using a Volume  
> File and select the Macaque Anatomical volume which results in the  
> Volume Selection parameters matching the anatomical volume.  In the  
> Paint section of the dialog, choose the parcellation that you would  
> like to see in a volume.  Press the OK button to create a new paint  
> volume which may take several minutes.
> 4) Use the Display Control to view the new paint volume.
> 5) Use the File Menu->Save Data File dialog to save the new paint  
> volume.  Use the NIFTI  format (the AFNI and WUNIL formats can also  
> be used for paint volumes).
>
> In the Surface Selection section, the Inner Boundary and Outer  
> Boundary determine the estimated thickness of the cortical surface.   
> These default to -1.5mm and 1.5mm which approximates the typical 3mm  
> thick human cortex.
>
> Good Luck.
>
> -----------------------------------
> John Harwell
> john at brainmap.wustl.edu
>
> Department of Anatomy and Neurobiology
> Washington University School of Medicine
> 660 S. Euclid Ave   Box 8108
> Saint Louis, MO 63110
>
>
>
> On Jan 7, 2008, at 10:58 AM, Hamied Haroon wrote:
>
>> Dear Donna and David,
>>
>> There are about 12 different cortical parcellation paint files  
>> available in Caret for Macaque F99UA1 (right hemisphere). However,  
>> only LVE00 is mapped onto the anatomical MRI volume  
>> (Macaque.F99UA1.LR.03-11+orig.HEAD) as well as the surfaces. Is  
>> there anyway, in Caret, to map one of the other cortical  
>> parcellation paint files onto F99UA1's anatomical MRI volume, in  
>> the same way as was done for LVE00? I would be grateful if you  
>> could please let me know.
>>
>> I look forward to hearing from you.
>>
>> Many thanks in anticipation.
>>
>> Hamied
>>
>> ________________________________________________
>>
>> Hamied Ahmad Haroon   PhD  AMInstP
>> Research Associate in MR Neuroimaging
>> Imaging Science and Biomedical Engineering Research Group
>> School of Medicine
>> Faculty of Medical and Human Sciences
>> The University of Manchester
>> Room G.603 Stopford Building, Oxford Road,
>> Manchester   M13 9PT
>> England, United Kingdom
>> Tel: +44 (0)161 275 6871   Fax: +44 (0)161 275 5145
>> Email: hamied.haroon at manchester.ac.uk
>> Web: www.isbe.man.ac.uk/~hharoon
>> ________________________________________________
>>
>>
>>
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>
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