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
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH