Thanks Donna, everything seems to work now, so I’m happy :)

About the surfaces, I saw something in the archive, is it a white brain,
or deflated pial:
http://sumsdb.wustl.edu:8081/sums/search.do?category_id=6
and then click the first option with a brain icon on it that is possible
to view in the web browser.

There are 12 versions of each hemisphere so I presume that it is an
individual brain. Do you think is ok to use one of them, or do you happen
to have an average surface?

I think you are right, inflated brains may be best suited for visualizing
purposes, however, just in case some stubborn SPM guy would like once in a
while see he’s activation the way he is used to….
I think Freesurfer has a pial surface. Maybe it works to import that somehow?

Also, it would be nice to have the option to see the whole brain at once
(the non-split way) even inflated, but I guess that’s not yet possible….

Cheers,
Julian


> On 03/07/2007 10:27 AM, Julianm Macoveanu wrote:
>> Yes, I use the CARET_TUTORIAL_SEPT06/MAPPNING_PROCEDURES files, and load
>> the
>> Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec file.
>>
>> I think I got the hang of it. The break through was, after creating the
>> metric file load one of the predefined scenes before trying to open my
>> metric file. In this way it didn't complain anymore about different
>> number
>> of nodes.
>>
>> If I understand it right if I want now to see the activation on a pial
>> surface I should just open the coord file and add it to my template spec
>> file. Do you know where I could find this? I think it should also be
>> something between pial and fiducial.
>>
> The PALS_B12 atlas (and the colin atlas before it) has no pial
> surfaces.  One can generate pseudo-pial surfaces by using Surface:
> Geometry: Expand or Shrink surface to expand a fiducial surface, but
> I've never tried this with an average fiducial surface, and I don't
> really recommend it.  We prefer the inflated surface for visualization,
> unless you have activity in the operculum or insula that is difficult to
> see; in such cases, we then use the Very Inflated surface.  Activity in
> buried sulci isn't visible when viewed on a pial or a regular fiducial
> (less so with an average fiducial).
>
> I realize some people still prefer looking at a highly structured pial
> surface, but considering this is group data you're mapping, the
> structure of any one individual is not really representative of the
> "group" structure of your subjects.  We believe mapping to PALS_B12 and
> viewing the results on the inflated surface is a more faithful
> representation of your results than viewing them on, say, colin27's pial
> surface.  Slowly, we're hoping to win you over. ;-)
>
>> Also, L and R are overlaid wrong, what SPM reports as left, I see it on
>> the
>> right hemisphere in Caret. How can this be changed?
>>
> Use File: Open Data File: volume functional file and check the Volume is
> an SPM2 Volume with Right on Left checkbox.
>> Thanks,
>> Julian
>>
>> -----Original Message-----
>> From: [EMAIL PROTECTED]
>> [mailto:[EMAIL PROTECTED] On Behalf Of Donna
>> Dierker
>> Sent: Wednesday, March 07, 2007 4:05 PM
>> To: Caret, SureFit, and SuMS software users
>> Subject: [BULK] Re: [caret-users] Map SPM volume
>> Importance: Low
>>
>> Hi Julian,
>>
>> When mapping to atlas, are you selecting a spec file created from this
>> dataset:
>>
>> CARET_TUTORIAL_SEPT-06
>> http://sumsdb.wustl.edu/sums/directory.do?id=6585200
>>
>> ... using steps as described in Section 5.1 of this tutorial:
>>
>> Caret_Tutorial_Oct06.pdf
>> http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379
>>
>> It's tough to see how you could get this error under those
>> circumstances, since the files in that spec file (or derivative thereof)
>> all have the same 73730 standard mesh.
>>
>> While this spec won't have a pial surface, it will have left and right
>> versions of the following configurations:
>>
>> PALS_B12 average fiducial
>> inflated
>> very inflated
>> flat
>>
>> Since you're using SPM2, I'd suggest replacing the average fiducial
>> coord files with these files:
>>
>> Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord
>> Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord
>>
>> To do so, after opening
>> Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec, select File:
>> Open Data File: and select
>> Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord.  Repeat
>> for Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord.
>> Then, select Toolbar: Spec and use the X buttons to delete these
>> versions, which are similar but not as optimal as the SPM2 versions in
>> your case:
>>
>> Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord
>> Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord
>>
>> Both the SPM2 and FLIRT versions are in mni152 space, but the
>> contributing PALS_B12 anatomicals were normalized using SPM2 for the
>> SPM2 versions, while FSL's flirt (affine only) was used to normalize the
>> FLIRT versions.
>>
>> Donna
>>
>> On 03/07/2007 08:33 AM, Julianm Macoveanu wrote:
>>
>>> Hi guys,
>>>
>>> I need some help with basic stuff. I just want to use Caret to
>>> visualize my SPM2 activations on inflated/Fiducial surfaces. So I have
>>> the normalized volume file to start with.
>>>
>>>
>>>
>>> I have opened a spec file from the Caret tutorial, use the map volume
>>> to surface function, choose my volume, then Map to spec file with
>>> atlas (and without). I have also tried not to open any spec file to
>>> begin with, and then just open the one I chose as output during the
>>> mapping procedure
>>>
>>>
>>>
>>> As space I tried the SPM2, as this is the kind of volume I have (but
>>> also 711-sc).
>>>
>>>
>>>
>>> After the metric file is generated, I just try to open it, but I get
>>> the error that my metric file contains different number of nodes.
>>>
>>>
>>>
>>> What I would like to have is a spec file that have all different
>>> surfaces (including pial and multi-fiducial which I could not find in
>>> any examples of spec files) and then just create metric files from my
>>> SPM volumes in order to visualize the activations.
>>>
>>>
>>>
>>> Cheers,
>>>
>>> Julian
>>>
>>>
>>>
>>>
>>
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>
>
> --
> Donna L. Dierker
> (Formerly Donna Hanlon; no change in marital status -- see
> http://home.att.net/~donna.hanlon for details.)
>
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