Hello all,

I am working with someone who has collected her data on Siemens Skyra 3T. Her scans are interleaved and oblique.

She found on the to 3d description: Some Siemens .ima files seems to have their EPI slices stored in
spatial order, and some in acquisition (interleaved) order. This
program doesn't try to figure this out. You can use the command
line option '-sinter' to tell the program to assume that the images
in a single .ima file are interleaved; for example, if there are
7 images in a file, then without -sinter, the program will assume
their order is '0 1 2 3 4 5 6'; with -sinter, the program will
assume their order is '0 2 4 6 1 3 5' (here, the number refers
to the slice location in space).


Also for oblıque datasets:
-oblique_origin
assume origin and orientation from oblique transformation matrix
rather than traditional cardinal information (ignores FOV/SLAB
options Sometimes useful for Siemens mosaic flipped datasets

I used the following command to reconstruct a resting state scan:


to3d -prefix ${subject}.REST2_test -save_outliers ${subject}_REST2_test.txt \
-time:zt 47 124 3s alt+z /Volumes/HaleDepo/STRESSSPGRREST_150816/${subject}/REST2/M*

I am wondering if this was the wrong way to go? It did seem to pick up that her scans were oblique. I know that "alt+z" indicates that they are interleaved.

Thanks,

Emily