Hi Evgueni,
thank you very much for fixing it so quickly. I will try it tonight.
Regarding the meanings of the different ISMRMRD flags.
ENCODE_STEP1 - that is the phase encoding along ky
ENCODE_STEP2 - that is the phase encoding along kz (which is only relevant
for 3D MR datasets)
AVERAGE - in order to improve SNR or average over multiple motion states
to reduce motion artefacts, multiple copies of the same k-space data can
be acquired and are then averaged in the reconstruction
SLICE - this is the slice direction but only applies to acquisitions which
obtain multiple 2D slices, for a 3D acquisition this would also be 1
CONTRAST - depending on the timing of an MR sequence, different image
contrast can be achieved (T1-weighted, T2-weighted,...). One parameter to
determine the contrast is the echo time (i.e. time between excitation and
gradient/spin echo formation). In one scan, data can be acquired at
different echo times (which is for example done when acquiring the
fat-water-separated images used for AC calculation). The index "contrast"
would then refer to the first, second, third,... echo
PHASE - this varies a little but commonly it is used for different phases
of a cardiac cycle. In order to resolve the motion of the heart during the
cardiac cycle, the same k-space data is commonly acquired for each part of
the cardiac cycle and then labelled with the phase index
REPETITION - this index means that the same k-space is acquired multiple
times but not synchronised to the cardiac cycle (otherwise it would be a
phase) and not to be averaged in the reconstruction (otherwise it would be
an average)
SET and SEGMENT I am also not so sure about because I don't think I have
ever come accross it so far.
Hope this helps.
Regards,
Christoph
--
Dr. Christoph Kolbitsch
Medical Physics and Metrological Information Technologies
Physikalisch-Technische Bundesanstalt
Abbestr. 2-12
10587 Berlin, Germany
phone: +49 30 3481 7761
Von: <[log in to unmask]>
An: <[log in to unmask]>
Kopie: <[log in to unmask]>
Datum: 22.12.2016 22:34
Betreff: RE: github and coil map calculation
Hi Christoph,
I fixed the bug and pushed the latest changes, please try again.
I have not done fill yet ? I am still improving as_array() method (see my
latest commits). It would help me a lot if you could explain me the
meaning of ?encode_step1/2?, ?average?, ?contrast? and other things like
that. The list of relevant ISMRMRD flags is below ? for now, I only fully
understand the meaning of first and last in slice. I have some idea about
repetitions, but I have not seen any datasets that would use the
respective flags.
ISMRMRD_ACQ_FIRST_IN_ENCODE_STEP1 = 1,
ISMRMRD_ACQ_LAST_IN_ENCODE_STEP1 = 2,
ISMRMRD_ACQ_FIRST_IN_ENCODE_STEP2 = 3,
ISMRMRD_ACQ_LAST_IN_ENCODE_STEP2 = 4,
ISMRMRD_ACQ_FIRST_IN_AVERAGE = 5,
ISMRMRD_ACQ_LAST_IN_AVERAGE = 6,
ISMRMRD_ACQ_FIRST_IN_SLICE = 7,
ISMRMRD_ACQ_LAST_IN_SLICE = 8,
ISMRMRD_ACQ_FIRST_IN_CONTRAST = 9,
ISMRMRD_ACQ_LAST_IN_CONTRAST = 10,
ISMRMRD_ACQ_FIRST_IN_PHASE = 11,
ISMRMRD_ACQ_LAST_IN_PHASE = 12,
ISMRMRD_ACQ_FIRST_IN_REPETITION = 13,
ISMRMRD_ACQ_LAST_IN_REPETITION = 14,
ISMRMRD_ACQ_FIRST_IN_SET = 15,
ISMRMRD_ACQ_LAST_IN_SET = 16,
ISMRMRD_ACQ_FIRST_IN_SEGMENT = 17,
ISMRMRD_ACQ_LAST_IN_SEGMENT = 18,
By the way, I am not entirely comfortable with git, so if you could keep a
commented out copy of whatever you are changing/removing (we will get rid
of it eventually), then it would be much easier for me to see what you
have changed.
From: [log in to unmask] [mailto:[log in to unmask]]
Sent: 22 December 2016 20:51
To: Ovtchinnikov, Evgueni (STFC,RAL,SC)
Cc: [log in to unmask]
Subject: github and coil map calculation
Hi Evgueni,
I tried to push my latest modifications of the demos onto github but if I
look on the github homepage at my latest commit I also see changes in
cgadgetron.cpp for example. Is this ok or did my push overwrite some of
your latest changes?
Could you please have a look at the demo 'coil_sensitivity_maps.py'. In
line 102 I try to use the 'Inati' method but I run into an error there
because a function is missing. Could you have a look if this can be fixed
easily? Otherwise I would remove this part of the demo.
Did you already have time to write a fill-function to put k-space data
back into a reconstruction chain?
Regards,
Christoph
