if you are doing within-subject then why use the contrast images instead of the volumes themselves? And if the VBM is derived from the same anatomicals as the FS surfaces aren't they already in register? On Fri, 12 Feb 2010, Lena Palaniyappan wrote:
Bruce & Sita - many thanks for your comments.
I tried within-subject registration: still the alignment is poor (see attached)
I am looking at a VBM comparison that generated a contrast map of group differences. I want to extract thickness values corresponding to the clusters that appear deficient in one group using VBM procedure.
Contrast is not T1 weighted, it is derived from T1 images - does that mean I am barking up the wrong tree? Should I be using this contrast image as an overlay - but how?
Thanks Lena
On 12/02/2010 18:20, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Lena,
why do you want to use the contrast files and not the EPIs themselves? And why would the contrast by T1 weighted? In this context T1 means the stuff inside the surface (e.g. white matter) is brighter than the stuff outside the surface (e.g. gray matter). If the reverse is true then you want to use T2.
cheers Bruce On Fri, 12 Feb 2010, Lena Palaniyappan wrote:
On 12/02/2010 16:47, "Lena Palaniyappan" Lena.Palaniyappan@nottingham.ac.uk wrote:
I want to use contrast files that are outputs from SPM (in IMG HDR format) to overlay on inflated surfaces. But if I use bbregister and choose T1 as the image type, the regisration achieved is poor (image attached)
Is this the correct way of doing this or am I missing something?
Commands used:
bbregister --mov con_0001.img --t1 --s fsaverage --init-spm --reg register.dat
cat register.dat
tkregister2 --mov con_001.img --reg register.dat --surf
Many thanks Lena
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Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH