[caret-users] Stereotaxic foci meta-analyses

[David Van Essen]

Antonio et al.,

As Donna's email noted, we have substantially revamped the process of  
mapping stereotaxic foci onto the PALS atlas.  The revised mapping  
methods are best accessed at
http://sumsdb.wustl.edu/sums/stereotaxictocaretfoci.do
or, equivalently, from:
Tutorials: Converting
Stereotaxic Coordinates to Caret Foci Files from the SumsDB home page
(http://sumsdb.wustl.edu/sums/)

If you (or anyone else tuning in) have developed a substantial meta- 
analysis collection of published stereotaxic foci in this new format  
and are interested in contributing them to our growing repository of  
publicly searchable data, please let us know once a preliminary  
version of the dataset is ready for inspection.  We will make an  
initial quality control check, then add to the publicly accessible  
collection, along with an acknowledgment of individual(s) involved in  
carrying out the meta-analysis.

David VE

On Jul 30, 2007, at 9:58 AM, Donna Dierker wrote:

> Hi Antonino,
>
> Also, I forgot about this recent, possibly relevant post from David:
>
> http://brainvis.wustl.edu/pipermail/caret-users/2007-July/001250.html
>
> Donna
>
> On 07/30/2007 08:18 AM, Donna Dierker wrote:
>> Hi Antonino,
>>
>> Each tutorial has its own dataset, whose scenes correspond to the  
>> tutorial narrative.  For example, the June 2006 tutorial's dataset  
>> is here:
>>
>> CARET_TUTORIAL_WashU_JUNE06
>> http://sumsdb.wustl.edu/sums/directory.do?id=6499756
>>
>> Normally, this link is included in the tutorial document, but I  
>> see now that page 2 of this documents cites a link to the wrong  
>> tutorial directory:
>>
>> Access to data sets. This self-guiding tutorial document and the  
>> associated data sets are freely available in SumsDB (http:// 
>> sumsdb.wustl.edu/sums/directory.do?id=6457755;  
>> CARET_WASH_U_June06/ in the Tutorials directory). Download the pdf  
>> file (CARET_WASH_U_June06.pdf) and the data set  
>> (CARET_WASH_U_June06.zip).
>>
>> In fact, that link points to an older tutorial dataset.
>>
>> Here is a more recent tutorial than the June 2006 tutorial:
>>
>> CARET_TUTORIAL_SEPT-06
>> http://sumsdb.wustl.edu/sums/directory.do?id=6585200
>>
>> I'm relieved to see that this document points to the right  
>> dataset.  If foci are your interest, then I'd give this September  
>> tutorial a shot.
>>
>> Foci have gotten a lot of attention from David, John, Ping, and  
>> Erin recently.  There was another tutorial in the works, but I'm  
>> not sure what its status is.  David is just getting back from his  
>> trip down under; after he shakes off his jet lag, maybe he'll give  
>> us an update.
>>
>> Donna
>>
>> On 07/30/2007 05:37 AM, Antonino Casile wrote:
>>> Dear All,
>>> I am using Caret v5.51 (Jun 7 2007) in order to map foci of  
>>> several studies using Caret. I am following the steps of your  
>>> manual (Caret Tutorial - the Basic, 22 September 2006, pag.69)  
>>> and I am having the following problems:
>>>
>>> 1) In the manual (pag. 69) it is written to load the .spec file:
>>> PALS_B12.BOTH.TEMPLATE-Map-STEREOTAXIC-FOCI.73730.spec. However,  
>>> such a spec file cannot be downloaded from your on-line atlases  
>>> and I had to download PALS_B12.BOTH-HEMS.For-STEREOTAXIC-FOCI- 
>>> ANALYSES.73730.spec instead.
>>>
>>> 2) I follow the steps in section 5.2.1 (pag. 69) and I can  
>>> open .spec file with no problem.
>>>
>>> 3) The problems start with section 5.2.2: when I open the first  
>>> scene (by double clicking on "Avg Fiducial (FLIRT, Both Hems) for  
>>> stereotaxic foci analyses" in the Page Selection:Scene window I  
>>> get the following popup window:
>>>
>>> The following errors occurred while applying the scene:
>>>
>>> Error  NULL-metric_ForStartingParameters.73730.metric: Error NULL- 
>>> metric_ForStartingParameters.73730.metric: No such file or  
>>> directoryMetric File column named "NULL-metric for starting  
>>> paramters" not found.
>>> Metric File column named "NULL-metric for starting paramters" not  
>>> found.
>>> Metric File column named "NULL-metric for starting paramters" not  
>>> found.
>>> Metric File column named "NULL-metric for starting paramters" not  
>>> found.
>>>
>>>
>>> 4) I press close and simply ignore the message
>>>
>>> 5) When I get to the 10th step in section 5.2.2 I get the  
>>> following error message
>>>
>>> "These foci do not have associated stereotaxic spaces"
>>>
>>> The Focus is nonetheless visualized in the windows ... but what  
>>> is the meaning of the error messages? How can I get rid of them?
>>>
>>> Thanks a lot in advance.
>>>                 Regards, Antonino Casile
>>> _______________________________________________
>>> caret-users mailing list
>>> caret-users at brainvis.wustl.edu
>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>
>>
>>
>
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