Hi Mark,
Thanks for your reply, I have been really puzzled about this...I think it is something with the display range! I see some leftover brain in the top. how do I change it? Does this mean that if I load the files into matlab their data matrix will be aligned with the anatomy?
I need to register several functional runs to the native anatomy and then load them into matlab and run correlations between them (they need to be aligned for that purpose).
About the FOV, for some of my subjects I do see differences in "zoom" between the anatomy and the functional scans (the anatomy seems smaller).
Best,Francesca
2014-09-17 20:02 GMT+02:00 Mark Jenkinson <[log in to unmask]>:
Hi,
The command looks OK (except for the last name being .nii.gz_tmp rather than _tmp.nii.gz, but I assume this is a typo in this email).
Are you sure that the image contains zeros and not just that the display range is incorrect?Alternatively, the FOV of your new image might be too small in z.
All the best,Mark
On 15 Sep 2014, at 17:38, Francesca Strappini <[log in to unmask]> wrote:
Dear Mark,
Thank you for your suggestion. I have tried running it and when I open the output file in fslview, I see nothing (it uploads the file but there is no brain showing). The command I ran is as follows:
/usr/local/fsl/bin/fslcreatehd 70 70 34 1 3 3 3.3 1 0 0 0 16 <name of output nii>_tmp.nii.gz ; /usr/local/fsl/bin/flirt -in <name of input nii> -applyxfm -init <Feat directory>/reg/example_func2highres.mat -out <name of output nii> -paddingsize 0.0 -interp trilinear -ref <name of output nii>.nii.gz_tmp
Can you please tell me what is wrong with this command? or is there another way to view the output?
Thank you very much for all your help.