New subject: DICOM input format and structure

6 Mar 2014


      Hi Sravan , please post to the list and not to us personally. Thanks!
This is just a list of what you (or whoever you are working with 
acquired), so I don't know what is in there. Probably #2 is what you 
want, less sure about #4
doug
On 03/06/2014 03:34 PM, Mattevada, Sravan wrote:
...
Hello Doug,
I ran the dcmunpac command and below is what I got.
Sorry I am new to freesurfer, Linux and MRI Images as well.
Are no. 2 and no. 4 the T1s ? which one do I need to pass to the recon-all ?
Thank you very much for your response. It helps a lot.
[freesurfer@localhost freesurfer]# dcmunpack -src /home/freesurfer/Documents/Sub_9884/DICOM
cd /home/freesurfer
/usr/local/freesurfer/bin/dcmunpack -src /home/freesurfer/Documents/Sub_9884/DICOM
-rwxr-xr-x. 1 root root 23416 May 13  2013 /usr/local/freesurfer/bin/dcmunpack

Searching for matching files
Thu Mar  6 14:22:14 CST 2014
Thu Mar  6 14:22:14 CST 2014
Found 229 total files.
   Interrogating each and every one of them.
   Be patient.
If you have collected the data in the Martinos center, this
will run faster if you kill this job and re-run with -martinos
Found 9 unique series: 1 2 3 4 5 6 7 8 9
Subject 9884^9884^^^
Date 20131203
Time 082101.937000
Institution RADIOLOGY ASSOCIATES-CDI
1 LOCALIZER3PLANE 5 20 40 0.546875 ROW 180 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000000/IM000003
2 T1SESAG 8 345 90 0.8984375 ROW 140 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000001/IM000011
3 T2TSEAX 85 4010 180 0.8984375 ROW 110 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000002/IM000011
4 T1SEAX 8 500 90 0.8984375 ROW 140 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000003/IM000011
5 T2FLAIRAX 117 9000 180 0.8984375 ROW 130 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000004/IM000011
6 T2AXHEMO 27 1220 25 0.44921875 ROW 195 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000005/IM000011
7 AXep2d_diff_2scan_trace 98 4100 90 1.796875\1.796875 COL 1260 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000006/IM000011
8 AXep2d_diff_2scan_trace_ADC 98 4100 90 1.796875\1.796875 COL 1260 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000007/IM000011
9 T2TSECOROBL 87 4260 180 0.4296875 ROW 110 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000008/IM000011
Thu Mar  6 14:22:43 CST 2014
dcmunpack done
-Sravan

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu]
Sent: Thursday, March 06, 2014 1:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] DICOM input format and structure
They do not have to have a dcm extension. The 180 files represent many
slices from a single volume (or multiple volumes). You need to find out
which ones are which. One way to do this is to run
dcmunpack -src path-to-dicom folder
this will look through all the folders and files under path-to-dicom and
sort them into acqusitions. It will print out a list of each volume and
a single dicom file that belongs to that volume. When you find the T1
that you want to run thru FS, pass that single dicom file to recon-all
with the -i flag
duog
On 03/06/2014 12:57 PM, Mattevada, Sravan wrote:
...
Hello,
           I am new to freesurfer. I went through the Wiki and

FAQ's but couldn't find information on
               the format  of the input for recon-all. I understand
that one of the input files must have a ".dcm" extension.
             I have a CD which has MRI scanned images.

                  The folder structure is E:\DICOM\PA000000\ST000000

                  under ST000000 there are 8 folders SE000000,

SE000001,... SE000008
                      Each SE00000* folder has files IM000000,
IM000001, ...
                  There are about 180 files all together in the 8

folders.
                  At first there were no extentions to any of the

image files, so, I add an extension ".dcm" to all of the files.
                  I ran recon-all got an error.

                  the error.log file has "MRIresample(): source

matrix has zero determinant; matrix is:"
                  Am I on the right path ? or am I missing something ?
                  So I need to convert the images before running

the recon ?
                      I see that only 8 files in the first folder in
the series are being read, Do I need to input the files in a different
structure ?
I am trying to do a proof of concept with our data before buying a
machine for running Linux CentOS for freesurfer.
recon-all command generates the following
[freesurfer@localhost freesurfer]# recon-all -i
Documents/Sub_9884/SE000000/IM000000.dcm -subject test -all
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22
03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/subjects/test
mri_convert /home/freesurfer/Documents/Sub_9884/SE000000/IM000000.dcm
/usr/local/freesurfer/subjects/test/mri/orig/001.mgz
mri_convert /home/freesurfer/Documents/Sub_9884/SE000000/IM000000.dcm
/usr/local/freesurfer/subjects/test/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/freesurfer/Documents/Sub_9884/SE000000/IM000000.dcm...
Getting Series No
INFO: Found 8 files in /home/freesurfer/Documents/Sub_9884/SE000000
INFO: Scanning for Series Number 1
Scanning Directory
INFO: found 6 files in series
INFO: loading series header info.
RunNo = 0
INFO: sorting.
INFO: (512 512   6), nframes = 1, ismosaic=0
PE Dir ROW ROW
AutoAlign matrix detected
AutoAlign Matrix ---------------------
  1.000   0.000   0.000   0.000;
  0.000   1.000   0.000   0.000;
  0.000   0.000   1.000   0.000;
  0.000   0.000   0.000   1.000;
FileName /home/freesurfer/Documents/Sub_9884/SE000000/IM000004.dcm
Identification
     NumarisVer        syngo MR A35 4VA35A
     ScannerModel      Symphony
     PatientName       9884^9884^^^
Date and time
     StudyDate         20131203
     StudyTime         082101.937000
     SeriesTime        082131.093000
     AcqTime           082138.020010
Acquisition parameters
     PulseSeq          *fl2d1
     Protocol          LOCALIZER  3 PLANE
     PhEncDir          ROW
     EchoNo            0
     FlipAngle         40
     EchoTime          5
     InversionTime     -1
     RepetitionTime    20
     PhEncFOV          280
     ReadoutFOV        280
Image information
     RunNo             0
     SeriesNo          1
     ImageNo           3
     NImageRows        512
     NImageCols        512
     NFrames           1
     SliceArraylSize   6
     IsMosaic          0
     ImgPos            140.0000   6.0000 140.0000
     VolRes              0.5469   0.5469  12.0000
     VolDim            512      512        6
     Vc                 -1.0000  -0.0000   0.0000
     Vr                 -0.0000  -0.0000  -1.0000
     Vs                 -1.0000  -0.0000   0.0000
     VolCenter         -36.0000   6.0000   0.0000
     TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
INFO: no Siemens slice order reversal detected (good!).
TR=20.00, TE=5.00, TI=-1.00, flip angle=40.00
warning: input volume axes are not orthogonal:i_dot_j = 0.000000,
i_dot_k = 1.000000, j_dot_k = 0.000000
i_ras = (-1, -0, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, -0, 0)
warning: output volume axes are not orthogonal:i_dot_j = 0.000000,
i_dot_k = 1.000000, j_dot_k = 0.000000
i_ras = (-1, -0, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, -0, 0)
writing to /usr/local/freesurfer/subjects/test/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Thu Mar  6 11:02:35 CST 2014
Found 1 runs
/usr/local/freesurfer/subjects/test/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
cp /usr/local/freesurfer/subjects/test/mri/orig/001.mgz
/usr/local/freesurfer/subjects/test/mri/rawavg.mgz
/usr/local/freesurfer/subjects/test
mri_convert /usr/local/freesurfer/subjects/test/mri/rawavg.mgz
/usr/local/freesurfer/subjects/test/mri/orig.mgz --conform
mri_convert /usr/local/freesurfer/subjects/test/mri/rawavg.mgz
/usr/local/freesurfer/subjects/test/mri/orig.mgz --conform
MRIresample(): source matrix has zero determinant; matrix is:
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/freesurfer/subjects/test/mri/rawavg.mgz...
TR=20.00, TE=5.00, TI=-1.00, flip angle=40.00
warning: input volume axes are not orthogonal:i_dot_j = 0.000000,
i_dot_k = 1.000000, j_dot_k = 0.000000
i_ras = (-1, -0, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, -0, 0)
Original Data has (0.546875, 0.546875, 12) mm size and (512, 512, 6)
voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
-0.547  -0.000  -12.000   140.000;
-0.000  -0.000  -0.000   6.000;
  0.000  -0.547   0.000   140.000;
  0.000   0.000   0.000   1.000;
Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22
03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s test exited with ERRORS at Thu Mar  6 11:02:38 CST 2014
For more details, see the log file
/usr/local/freesurfer/subjects/test/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/