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)