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: [EMAIL PROTECTED]
www.BrainCog.de
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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 <[EMAIL PROTECTED]>
Subject: [caret-users] fMRI mapping & t-values
To: Caret Mailing Liste <caret-users@brainvis.wustl.edu>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
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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: [EMAIL PROTECTED]
www.BrainCog.de
------------------------------
Message: 2
Date: Tue, 19 Jun 2007 07:40:07 -0500
From: Donna Dierker <[EMAIL PROTECTED]>
Subject: Re: [caret-users] fMRI mapping & t-values
To: "Caret, SureFit, and SuMS software users"
<caret-users@brainvis.wustl.edu>
Message-ID: <[EMAIL PROTECTED]>
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: [EMAIL PROTECTED]
www.BrainCog.de
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