Okay. What you've sent me is NOT a probability atlas, it is a label atlas, i.e., it does not contain one volume per region with values ranging from 0-100% but, instead, a single volume with discrete values 0-116 indicating each voxels classification. Using an existing Label atlas, e.g., Talairach, as a suitable prototype - rename aal-prob-2mm.nii to aal-labels-2mm.nii (just so it's clear what they are) then change the type and images parts of aal.xml as follows:
<type>Label</type>
<images>
<imagefile>/Users/fabbri/fsl/data/atlases/aal/aal-labels-2mm</imagefile>
<summaryimagefile>/Users/fabbri/fsl/data/atlases/aal/aal-labels-2mm</summaryimagefile>
</images>
Hope that helps,
Dave
On 25 Oct 2010, at 18:06, sere f wrote:
> Sure.....the atlas image is the number 794919.
> Thanks again.
> Serena.
>
> On Mon, Oct 25, 2010 at 6:06 PM, Dianne Patterson <[log in to unmask]> wrote:
> I'm VERY interested in finding out the resolution to this problem. I have some atlas aspirations too.
>
> Thankyou,
>
> Dianne
>
>
> On Mon, Oct 25, 2010 at 7:15 AM, David Flitney <[log in to unmask]> wrote:
> Thanks, but I already have the XML file. I really need both your atlas images files as well.
>
> On 25 Oct 2010, at 11:34, sere f wrote:
>
>> Hi David,
>> My FSLview works fine, in fact it has never crashed.
>> I have just uploaded my XML file.
>>
>> Thanks for your help.
>>
>> Serena.
>>
>>
>> On Mon, Oct 25, 2010 at 11:12 AM, David Flitney <[log in to unmask]> wrote:
>>
>> On 19 Oct 2010, at 15:40, sere f wrote:
>>
>>> Hi David,
>>>
>>> Thanks for your reply.
>>>
>>> I still have problem.
>>>
>>> I have run thresholding on my aal-prob-2mm.nii and now I have these files in the same directory:
>>> aal-maxprob-thr0-2mm.nii.gz
>>> aal-maxprob-thr25-2mm.nii.gz
>>> aal-maxprob-thr50-2mm.nii.gz
>>
>> Looks good...
>>
>>> and I have corrected xml in this way:
>>>
>>> <?xml version="1.0" encoding="ISO-8859-1"?>
>>> <atlas version="1.0">
>>> <header>
>>> <name>MRIcro 222 Atlas</name>
>>> <type>Label</type>
>>> <images>
>>> <imagefile>/aai/aal-prob-2mm</imagefile>
>>> <summaryimagefile>/aai/aal-maxprob-thr25-2mm</summaryimagefile>
>>> </images>
>>> </header>
>>> <data>
>>> <label index="1"> Precentral_L 2001</label>
>>> <label index="2"> Precentral_R 2002</label>
>>> <label index="3"> Frontal_Sup_L 2101</label>
>>> <label index="4"> Frontal_Sup_R 2102</label>
>>>
>>> .........
>>>
>>>
>>>
>>> <label index="115"> Vermis_9 9160</label>
>>> <label index="116"> Vermis_10 9170</label>
>>> </data>
>>> </atlas>
>>
>> ...as does this...
>>
>>> but aal atlas does not appear in "Atlas Selection" windows.
>>> I have looked a bit in archive and I have found this post:
>>>
>>>
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0910&L=FSL&D=0&1=FSL&9=A&I=-3&J=on&K=1&X=20ABF201A81057049C&Y=serenaf33%40gmail.com&d=No+Match%3BMatch%3BMatches&z=4&P=221013
>>>
>>> I have MAC 10.6.4 (Snow Leopard) and I am using FSL 4.1.5 I have not older FSL version.
>>> Could the version of my MAC be the problem?
>>
>> ...I don't think so... the post says that using atlas tools is crashing FSLview, you didn't mention that your FSLview is crashing? Perhaps you should upload your atlas files and the XML to our upload site and I'll have a closer look. Follow the instructions on http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>>
>> --
>> Dave Flitney, IT Manager
>> Oxford Centre for Functional MRI of the Brain
>> E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717
>> URL: http://www.fmrib.ox.ac.uk/~flitney
>>
>>
>>
>>
>
> --
> Dave Flitney, IT Manager
> Oxford Centre for Functional MRI of the Brain
> E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717
> URL: http://www.fmrib.ox.ac.uk/~flitney
>
>
>
>
>
>
> --
> Dianne Patterson, Ph.D.
> [log in to unmask]
> University of Arizona
> SLHS 314
> 621-9877
>
--
Dave Flitney, IT Manager
Oxford Centre for Functional MRI of the Brain
E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717
URL: http://www.fmrib.ox.ac.uk/~flitney
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