it doesn't create it when it unpacks it - it is a separate series created
on the scanner. If you have the echoes in a single .mgz file named
echoes.mgz you would to:
foreach e (0 1 2 3)
mri_convert -nth $e echoes.mgz echo${e}.mgz
end
mri_average -sqr echo[0123].mgz rms.mgz
cheers
Bruce
On Tue, 10 Dec 2013, Chan, Noel Yan-Ki,Ph.D. wrote:
Thanks Bruce. I checked, it is multi-echo mprage, it's just when I unpack
it, it didn't automatically generate the RMS.
so can you walk me through when to do the mri-average-sqr?
So I just type the command:
unpacksdcmdir -src
/cluster/archive/304/siemens/Skyra-45407-20130822-092226-174000 -targ .
-scanonly unpacklogpre
Then it gives me:
Tue Dec 10 14:56:36 EST 2013
Log File is ./unpack.log
INFO: Logfile is ./unpack.log
SkipMoCo 0
Scanning source directory ...
INFO: summary file is ./dicomdir.sumfile
INFO: status file is ./parse.status
Scanning directory Tue Dec 10 14:56:36 EST 2013
mri_parse_sdcmdir --sortbyrun --d
/cluster/archive/304/siemens/Skyra-45407-20130822-092226-174000 --o
./dicomdir.sumfile --status ./parse.status
0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36
38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74
76 78 80 82 84 86 88 90 92 94 96 98 100
Done scanning Tue Dec 10 14:58:48 EST 2013
------------------------------------------
1 localizer ok 256 256 3 1
MR.1.3.12.2.1107.5.2.19.45407.2013082209234488137601798
2 localizer ok 256 256 3 1
MR.1.3.12.2.1107.5.2.19.45407.2013082209234486217101797
3 AAHead_Scout ok 160 160 128 1
MR.1.3.12.2.1107.5.2.19.45407.2013082209242568708801865
4 AAHead_Scout ok 162 162 5 1
MR.1.3.12.2.1107.5.2.19.45407.2013082209243010322103111
5 AAHead_Scout ok 162 162 3 1
MR.1.3.12.2.1107.5.2.19.45407.2013082209243010400603115
6 AAHead_Scout ok 162 162 3 1
MR.1.3.12.2.1107.5.2.19.45407.2013082209243010456303118
7 MEMPRAGE_tfl_mgh_multiecho_1mm_iso ok 256 256 176 4
MR.1.3.12.2.1107.5.2.19.45407.2013082209321083146803580
8 fMRI_resting_state ok 72 72 47 124
MR.1.3.12.2.1107.5.2.19.45407.2013082209330867404606382
How do I create the RMS?
Thanks,
Noel
---
Noel Yanki Chan, PhD
Department of Psychiatry Neuroscience
Laboratory of Sara Lazar, PhD
Harvard Medical School
Massachusetts General Hospital
Building 120, 2nd avenue, Suite 103
Charlestown, MA 02129
Tel: 617-643-5078 (lab) 607-229-7096 (cell)
On Dec 10, 2013, at 2:32 PM, Bruce Fischl wrote:
go back and look at the dicoms I guess. Can you post these
questions to the list so that others can answer?
thanks
Bruce
On Tue, 10 Dec 2013, Chan, Noel Yan-Ki,Ph.D. wrote:
How do I check if they are echoes of a multi-echo
mprage? They should
have... I mean all other subjects are fine (all
others generated RMS
automatically) besides these 2 subjects, I don't
know if that's something
wrong at the time with the data collection.
On Dec 10, 2013, at 2:03 PM, Bruce Fischl wrote:
you can use mri_average -sqr ... I believe, as
long as these
really are the echoes of a multi-echo mprage.
Are you sure you
didn't just point recon-all at the wrong
series? It should have
generated one automatically
On Tue, 10 Dec 2013, Chan, Noel Yan-Ki,Ph.D.
wrote:
Hi Bruce,
Only these two subjects didn't create the
RMS
automatically, I don't know
why. How can I generate the RMS?
Thanks,
Noel
On Dec 10, 2013, at 1:52 PM, Bruce Fischl
wrote:
Hi Noel
what were the acquisitions? If they
were
multi-echo mprage than
you will either have to generate the
RMS or
find the series that
is the RMS (since it should have
been generated
automatically)
cheers
Bruce
On Tue, 10 Dec 2013, Chan, Noel
Yan-Ki,Ph.D.
wrote:
Hi,
I'm trying to do recon-all for
a file,
and it gave
me this multiple frame
error message:
#@# MotionCor Mon Nov 25
13:11:40 EST
2013
Found 1 runs
/autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/mri/
orig/001.mgz
Checking for (invalid)
multi-frame
inputs...
ERROR: input(s) cannot have
multiple
frames!
/autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/mri/
orig/001.mgz has 4 frames
If this is a multi-frame
MEMPRAGE image,
use mri_concat --rms to
combine echo
frames.
Linux compute-0-73
2.6.32-358.23.2.el6.x86_64 #1 SMP
Wed Oct 16 18:37:12 UTC
2013 x86_64 x86_64 x86_64
GNU/Linux
recon-all -s
BHI_BJU-345_pre_lazar exited
with
ERRORS at Mon Nov 25 13:11:47
EST 2013
For more details,
seethelogfile/autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_
laz
ar/
scri
pts/recon-all.log
To report a problem,
see http://surfer.nmr.mgh.harvard.edu/fswiki/BugRepor
ting
May I ask what should I do to
solve this
problem?
There are actually two files
which give
me the same
error message:
BHI_BJU-345_pre_lazar
(pbsjob_30) and
BHI_JJA-329_pre_lazar
(pbsjob_33)
Thanks,
Noel ---
Noel Yanki Chan, PhD
Department of Psychiatry
Neuroscience
Laboratory of Sara Lazar, PhD
Harvard Medical School
Massachusetts General Hospital
Building 120, 2nd avenue,
Suite 103
Charlestown, MA 02129
Tel: 617-643-5078 (lab)
607-229-7096
(cell)
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