[caret-users] Paint Volume labels for Macaque F99

[Donna Dierker]

Hamied,

Yeah, I had run into similar issues with the PALS atlas composite paint 
files. The paint indices are not the same across hems. But rather than 
conclude this is a problem, I have just accepted that the index mapping 
is ephemeral, which is why it is encoded in the paint file header.

If you think about loading two paint files concurrently -- something 
David does all the time -- then you realize that it is likely that they 
share common paint indices, but that their mappings are almost certainly 
different. Whose should "win" in memory? Probably whichever was loaded 
first.

Lesson: Don't get attached to your paint index to paint name mappings.

Donna

On 07/28/2009 09:38 AM, Hamied Haroon wrote:
> Dear Donna,
>
> Thanks very much for your reply.
>
> You are absolutely right! The LUT_NAMES are reliable and do accurately
> map the paint name from its ordinal position under LUT_NAMES.
>
> I have now discovered that the LUT_NAMES listing is different in each
> hemisphere even for the same parcellation scheme/paint file. My mistake
> was in assuming that LUT_NAMES would be exactly the same for either
> hemisphere for the same parcellation scheme/paint file.
>
> I had uploaded some files today for you to look at, but this is no
> longer necessary so please feel free to delete these.
>
> Many thanks for your help.
>
> Best wishes,
>  
> Hamied
>  
>
> -----Original Message-----
> From: caret-users-bounces at brainvis.wustl.edu
> [mailto:caret-users-bounces at brainvis.wustl.edu] On Behalf Of Donna
> Dierker
> Sent: 27 July 2009 18:18
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] Paint Volume labels for Macaque F99
>
> Hamied,
>
> I wouldn't necessarily expect what we call the "paint index" from the 
> surface/node-based paint file to match the paint index in the LUT_NAMES 
> list.
>
> But I would expect the LUT_NAMES to accurately map the paint name from 
> its ordinal position.  This post explains how that works:
>
> http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00712.html
>
> If you think your paint volume has mislabeled some voxels, then upload 
> it here:
>
> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>
> ... and tell us exactly how you generated it.
>
> The LUT_NAMES should be reliable.
>
> But if you're expecting paint indices to remain constant across paint 
> files, mappings, etc., then don't.
>
> Donna
>
> On 07/27/2009 11:54 AM, Hamied Haroon wrote:
>   
>> Hi,
>>
>>  
>>
>> Following the kind advice provided by Donna and David, et al, 
>> previously, I have taken each of the Paint Columns available for the 
>> Macaque F99UA1 (i.e. Lobes, LVE00, Felleman-VE all, PHT 00, etc) and 
>> converted these to Paint Volumes in CARET, which I have then saved as 
>> AFNI image volumes on my local disk. This has allowed me to apply the 
>> various parcellations to MRI data that I have in the same species of 
>> macaque.
>>
>>  
>>
>> I originally assumed that the signal intensities in the AFNI (.BRIK) 
>> Paint Volume would correspond to the list of anatomical labels under 
>> LUT_NAMES in the header (.HEAD). However this correspondence does not 
>> seem to hold true for all the labels. For example, in LVE00, the 
>> region that has a signal intensity of 18 is certainly V1, but in the 
>> LUT_NAMES list 18 corresponds to V4.
>>
>>  
>>
>> Could there be any errors in the LUT_NAMES lists in the AFNI .HEAD 
>> files, or is there another way to (easily) get a reliable list of the 
>> anatomical labels that correspond to the signal intensities in the 
>> Paint Volume image file?
>>
>>  
>>
>> I look forward to hearing from you.
>>
>>  
>>
>> Many thanks.
>>
>>  
>>
>> Best wishes,
>>
>>  
>>
>> Hamied
>>
>>  
>>
>> _________________________________________________________
>>
>>  
>>
>>  Hamied A Haroon, PhD
>>
>>  Research Associate in MR Neuroimaging
>>
>>  Imaging Science and Biomedical Engineering Research Group
>>
>>  Research School of Cancer and Imaging Sciences
>>
>>  Faculty of Medical and Human Sciences
>>
>>  The University of Manchester
>>
>>  Room G.603, Stopford Building, Oxford Road, M13 9PT
>>
>>  Tel: 0161 275 6871   Fax: 0161 275 5145
>>
>>  Mobile: 07961 488 472
>>
>>  Email: hamied.haroon at manchester.ac.uk 
>> <mailto:hamied.haroon at manchester.ac.uk>
>>
>>  Web: http://personalpages.manchester.ac.uk/staff/hamied.haroon/
>>