[Freesurfer] summing across FIR timepoints

2012-04-12 Thread Ellen Lau
Hi, We ran a first-level FIR analysis on our functional data with selxavg3-sess, which outputs a single ces.nii file for each subject containing the contrast images for all timepoints. Now we would like to create an image representing the sum of a subset of these images in a time-window of inte

[Freesurfer] mri_convert with flash - FS 4.5.0 vs 5.0

2010-10-08 Thread Ellen Lau
Hi, We're having trouble using mri_convert as wrapped within mne_flash_bem to create the bem surfaces from our FLASH volumes. The script runs but the inner_skull and outer_skull surfaces that it outputs seem to be rotated, for example if we display the surfaces on the T1 coronal, we see what looks