[caret-users] Re: fMRI mapping & t-values

Katja Umla-Runge k.umla-runge at mx.uni-saarland.de
Wed Jun 20 07:05:18 CDT 2007


Hi Donna,

I loaded some files up concerning my issue. They are:

EwicPics.spec
PALS_BOTH_TEMPLATE-for-MAPPING.scene
RIB_ZIF_SPMTimg_interpolated_left.metric
RIB_ZIF_SPMTimg_interpolated_right.metric
spmT_0002.hdr
spmT_0002.img
spmfig_17May2006.ps

The latter is a postscript file containing the resulting activations  
in a table. If you need some other files to check, please let me know.
I used the "Average FIDUCIAL (FLIRT), LATERAL (PALS-B12_BOTH, average  
sulcal depth)" scene within the tutorial file  
PALS_BOTH_TEMPLATE-for-MAPPING.scene and within the "map volume(s) to  
surface(s)"-process, I entered mapping atlas --> space = SPM99 and  
atlas = PALS_..._LEFT (SPM99 space) on the "atlas surface selection"  
window. Then I repeated this step for atlas = PALS_..._RIGHT (SPM99  
space).
I also tried multi-fiducial mapping as you suggested using  
Human.PALS_B12.LR:MULTI_FIDUCIAL_SPM99_fMRI-MAPPER.B1-B2.LEFT.73730.spec But  
again, the occipital activation cluster does not occur when I enter a  
user specified threshold of 4,66. In fact, only few and very small  
clusters remain with this threshold. The occipital cluster is in the  
left hem and has a size of 36 voxels (in the postscript-file table).  
As to spiky t-values, the ones of the significant clusters in this  
contrast only range from 4.67 to 8.19.

Thank you for your help

Katja

-- 
Dipl.Psych. Katja Umla-Runge

Saarland University
Department of Psychology        phone: +49 - (0)681 - 302 4643
P.O.Box 151150                  fax:   +49 - (0)681 - 302 4049
D-66041 Saarbruecken            email: k.umla-runge at mx.uni-saarland.de

www.BrainCog.de


Zitat von caret-users-request at brainvis.wustl.edu:

> Send caret-users mailing list submissions to
> 	caret-users at brainvis.wustl.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://pulvinar.wustl.edu/mailman/listinfo/caret-users
> or, via email, send a message with subject or body 'help' to
> 	caret-users-request at brainvis.wustl.edu
>
> You can reach the person managing the list at
> 	caret-users-owner at brainvis.wustl.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of caret-users digest..."
>
>
> Today's Topics:
>
>    1. fMRI mapping & t-values (Katja Umla-Runge)
>    2. Re: fMRI mapping & t-values (Donna Dierker)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 19 Jun 2007 12:05:47 +0200
> From: Katja Umla-Runge <k.umla-runge at mx.uni-saarland.de>
> Subject: [caret-users] fMRI mapping & t-values
> To: Caret Mailing Liste <caret-users at brainvis.wustl.edu>
> Message-ID:
> 	<20070619120547.3v5v0k128kco0kwk at webmail.rz.uni-saarland.de>
> Content-Type: text/plain;	charset=ISO-8859-1;	DelSp="Yes";
> 	format="flowed"
>
> Dear Caret users,
>
> Mapping spmT*.img files (SPM99) to a surface in Caret, the resulting
> image seems (at first glance) to fit the data table I obtained from
> SPM. However, if I set the threshold to say t = 3,61 (metric -->
> settings --> threshold --> Pos User = 3,61 --> threshold type: User)
> which is the threshold I got from SPM for a given one-sample t-test,
> less activations remain as compared to the SPM data table. As an
> example, my results include an occipital activation with t = 4,67. If
> I want to see this structure activated on my Caret surface, I need to
> enter a threshold of about t = 1. Why do t-values and corresponding
> activations do not correspond between the two systems? How can make
> them correspond?
> Thank you in advance.
>
> Katja
>
> --
> Dipl.Psych. Katja Umla-Runge
>
> Saarland University
> Department of Psychology        phone: +49 - (0)681 - 302 4643
> P.O.Box 151150                  fax:   +49 - (0)681 - 302 4049
> D-66041 Saarbruecken            email: k.umla-runge at mx.uni-saarland.de
>
> www.BrainCog.de
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 19 Jun 2007 07:40:07 -0500
> From: Donna Dierker <donna at brainvis.wustl.edu>
> Subject: Re: [caret-users] fMRI mapping & t-values
> To: "Caret, SureFit, and SuMS software users"
> 	<caret-users at brainvis.wustl.edu>
> Message-ID: <4677CEA7.4020207 at brainvis.wustl.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Katja,
>
> A couple of things come to mind:
>
> * The 4.67 hot spot doesn't intersect the average fiducial surface.  Did
> you map to the average fiducial surface, or use multi-fiducial mapping
> (MFM)?  The latter method is less vulnerable to this problem.
>
> * There could be some very large "spiky" values throwing off the scale.
>
> I can take a quick look and let you know what I think:
>
> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>
> Is the 4.67 hot spot in the left or right hem?
>
> Donna
>
> On 06/19/2007 05:05 AM, Katja Umla-Runge wrote:
>> Dear Caret users,
>>
>> Mapping spmT*.img files (SPM99) to a surface in Caret, the resulting
>> image seems (at first glance) to fit the data table I obtained from
>> SPM. However, if I set the threshold to say t = 3,61 (metric -->
>> settings --> threshold --> Pos User = 3,61 --> threshold type: User)
>> which is the threshold I got from SPM for a given one-sample t-test,
>> less activations remain as compared to the SPM data table. As an
>> example, my results include an occipital activation with t = 4,67. If
>> I want to see this structure activated on my Caret surface, I need to
>> enter a threshold of about t = 1. Why do t-values and corresponding
>> activations do not correspond between the two systems? How can make
>> them correspond?
>> Thank you in advance.
>>
>> Katja
>>
>> --Dipl.Psych. Katja Umla-Runge
>>
>> Saarland University
>> Department of Psychology        phone: +49 - (0)681 - 302 4643
>> P.O.Box 151150                  fax:   +49 - (0)681 - 302 4049
>> D-66041 Saarbruecken            email: k.umla-runge at mx.uni-saarland.de
>>
>> www.BrainCog.de
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> caret-users mailing list
>> caret-users at brainvis.wustl.edu
>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>
>
>
> ------------------------------
>
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>
>
> End of caret-users Digest, Vol 45, Issue 8
> ******************************************
>







More information about the caret-users mailing list