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.eduwrote:
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=W8ZFGvGvHVchttp://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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