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, see thelogfile/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/BugReporting
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)
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)
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Chan, Noel Yan-Ki,Ph.D.