Hi Ye
there's no way a 5 minute mprage would have only 3 slices. Or any mprage really, since they are always 3D. You need to find the rest of the slices (there are probably more than 128 of them)
Bruce
On Fri, 28 Jun 2013, ye tian wrote:
Dear Bruce and Greve,
Thank you very much. But I only have 3 images of MPRAGE though.
recon-all -s subject_directory -i /Path_to_MPRAGE finishes without error,
but gives two warnings of "input volume axes are not orthogonal"
recon-all -s subject_directory -autorecon1 exists "with ERRORS" almost
immediately. Besides one warning of "only one run found; motion correction
cannot be performed" and another warning of "input volumes are not
orthogonal", the log file basically just repeats the information of mri_info
MPRAGE.
Is it because I don't have enough images?
Thank you very much!
Sincerely,
Ye
On Fri, Jun 28, 2013 at 12:25 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
The MPRAGE is what you want
Bruce
On Fri, 28 Jun 2013, ye tian wrote:
Dear freesurfers,
My data seems not to be T1-weighted by look
(http://www.youtube.com/watch?v=W8ZFGvGvHVc). Would
you please help me
further identify by reading the following
experimental description?
Images were acquired with blood-oxygen level
dependent (BOLD) imaging on a 3
T Siemens Trio Scanner (Bandettini, Wong, Hinks,
Tikofsky, and Hyde, 1992).
A five-minute magnetization prepared,
rapid-acquisition gradient echo image
(MPRAGE) was acquired for anatomic overlays of
functional data and spatial
normalization (T1 MN1 Template). BOLD imaging used
a 33-slice whole-brain,
single-shot gradient echo (GE) echo-planar (EPI)
sequence (TR/TE = 2000/25
ms, FOV = 240 mm, matrix = 64 x 64, slice
thickness/gap = 4/0 mm). This
sequence delivers a nominal voxel resolution of 3 x
3 x 3 mm.
Also, if I do mri_info in freesurfer for the five
sequences of the data,
Series Number 1: TR: 8.6msec, TE: 4.00msec, T1:
-1.00msec, Flip Angle:
20.00degrees
Series Number 2: TR: 2000.00msec, TE: 25.0msec,
T1: -1.00msec, Flip
Angle: 90.00degrees
Series Number 3: TR: 2300.00msec, TE: 2.96msec;
T1: 900.00msec, Flip
Angle: 90.00degrees
Series Number 4&5: TR: 2000.00msec, TE: 25.00msec;
T1: -1.00msec, Flipe
Angle: 90.00degrees
Is my data NOT T1-weighted for sure?
Thank you very much!
Sincerely,
Ye
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