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

Donna Dierker donna at brainvis.wustl.edu
Wed Jun 20 09:02:37 CDT 2007


Hi Katja,

Here are my thoughts after looking at your files:

* There is a small cluster of activation in the left hemisphere near the 
occipital pole, but it is well below the 4.66 threshold.  In fact, the 
center of it was only about 0.6, as validated in both Caret and AFNI, by 
clicking on the center of the voxel and checking its intensity.  The 
attached capture afni_thresh_4.6.jpg shows what you see when you 
threshold this volume at 4.6 at axial slice 23, where the small left 
cluster seems to reach its maximum.

* There is a larger, more intense cluster near the right hem's occipital 
pole.  It was my understanding the SPM99 wrote its output in a 
right-handed coordinate system (left-on-left), but I raise this issue in 
case some right-left flipping may have crept in along the way.

* When you use MFM, you can enter a threshold like "4.66" at the 
beginning of the mapping process, but then when you visualize the 
results, you want to use the Avg Area theshold computed during the 
mapping process.  These numbers are automatically computed during 
mapping, so that the suprathreshold surface area is equivalent to the 
mean suprathreshold area of the contributing PALS subjects.  See the 
PALS tutorial for more details.

I sense a mismatch between expected and actual intensities in this cluster.

Donna

On 06/20/2007 07:05 AM, Katja Umla-Runge wrote:
> 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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: afni_thresh_4.6.jpg
Type: image/jpeg
Size: 4070 bytes
Desc: not available
URL: <http://brainvis.wustl.edu/pipermail/caret-users/attachments/20070620/7c4b4d9f/attachment-0001.jpg>


More information about the caret-users mailing list