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.psThe 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 Zitat von [EMAIL PROTECTED]:Send caret-users mailing list submissions to caret-users@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 [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] 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 <[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"; 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: [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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