Dear Bruce,
Thank you so much for being so patient with me!
I found them!!!!
Sincerely, Ye
On Fri, Jun 28, 2013 at 1:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
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<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, YeThe 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/**compliancelinehttp://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.