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
 





The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.