|
I was making a general statement for if your sequences produce outputs that don’t match the notes in the pipelines script. The specifics of figuring this out from the DICOM header is something Mike knows more about than I do.
Peace,
Matt.
From: <Book>, Gregory <gregory.b...@hhchealth.org>
Date: Monday, December 15, 2014 at 2:59 PM To: Matt Glasser <glass...@wusm.wustl.edu>, "Harms, Michael" <mha...@wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: RE: [HCP-Users] spin echo phase encoding direction I’m slightly more confused now. So, using the CMRR sequences, if I set the phase encoding direction on my spin echo to A>>P, and “Invert RO/PE Polarity” option is checked… a) what is the actual phase direction
of the data b) what is recorded in the DICOM header in the *.dInPlaneRot field? From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
If your phase encoding directions are inverted, I would recommend swapping the SpinEchoPositive and NegativeImage values. This would make the computed field map have the same sign as a typical
field map and then the PhaseEncodeList would not have to change. Peace, Matt. From: <Book>, Gregory <gregory.b...@hhchealth.org> Would that be the *.dInPlaneRot value for each slice in the CSA header? From: Harms, Michael [mailto:mha...@wustl.edu]
The value of "PhaseEncodingDirectionPositive" in the shadow field (0029,1020) reflects the combination of both "Phase enc. dir." on the Routine tab (e.g., "A>>P" vs. "P>>A") AND the setting of
"Invert RO/PE Polarity" on the Sequence/Special tab. As long as you have one of each polarity, you can use the spin echo field map correction. I highly recommend that you purposely try both possible assignments, and visually confirm which one is
giving the correct results. That's because the correct setting for PhaseEncodeList (e.g., "y-" vs. "y+") can in theory even be dependent on which DICOM to NIFTI converter you use. (e.g., if one converter returns a +LAS orientation, while another returns
a +LPS orientation, then the proper settings for PhaseEncodeList may be swapped). cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email:
mha...@wustl.edu From: <Book>, Gregory <gregory.b...@hhchealth.org> I have another question about the spin echo images, hopefully this will be my last question! It turns out that we’ve been collecting our spin echo images with the “Invert RO/PE Polarity” option selected, which apparently inverts the phase encoding direction 180deg, but does not record this to the DICOM
header. We’ve been collecting the EPI images without this inversion. So, for our data: EPI is A>>P “A>>P” SE is actually P>>A “P>>A” SE is actually A>>P Would we be able to use the spin echo correction if we simply switched the positive and negative images? So, would this work for our data? TaskList=”task1” PhaseEncodeList=”y-“ … SpinEchoPositiveImage=”the P>>A labeled image (actually acquired A>>P)” SpinEchoNegativeImage=”the A>>P labeled image (actually acquired P>>A)” -G _________________________________________________ Gregory Book Senior Technology Manager Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital 200 Retreat Avenue Hartford, CT 06106 Tel: 860-545-7267 Fax: 860-545-7797
_______________________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
or return mail. _______________________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
or return mail. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ |
- [HCP-Users] spin echo phase encoding direction Book, Gregory
- Re: [HCP-Users] spin echo phase encoding direction Harms, Michael
- Re: [HCP-Users] spin echo phase encoding directi... Book, Gregory
- Re: [HCP-Users] spin echo phase encoding dir... Glasser, Matthew
- Re: [HCP-Users] spin echo phase encoding... Book, Gregory
- Re: [HCP-Users] spin echo phase enc... Glasser, Matthew
- Re: [HCP-Users] spin echo phase enc... Harms, Michael
- Re: [HCP-Users] spin echo phase... Book, Gregory
- Re: [HCP-Users] spin echo p... Harms, Michael
- Re: [HCP-Users] spin echo p... Book, Gregory
- Re: [HCP-Users] spin echo p... Harms, Michael
