Hi Changming,
unpacksdcmdir only works with Siemens dicoms I think (that's what the "s"
is for). Try giving mri_convert the name of *one* slice in the anatomical
series as input.
cheers
Bruce
On Thu, 29 Apr 2010, [gbk] ²ýÃ÷ wrote:
Dear Freesurfers:
i failed every time i tried to transform my dicom GE structrual images
into mgz format, because i am quite new for this software, so i'd like to ask
some help from you. i will be very grateful if you can tell me what the reason
is, or give me some suggestions on how to fix the problem.
my command lines and the error messages are as below.
thank you very much!
changming
[chenchangming...@localhost ~]$ cd
/media/12D8F3B3D8F392E9/chenchangming/20071119/csq
[chenchangming...@localhost csq]$ cd .
[chenchangming...@localhost csq]$ ls
0001.dcm 0023.dcm 0045.dcm 0067.dcm 0089.dcm 0111.dcm 0133.dcm 0155.dcm
0002.dcm 0024.dcm 0046.dcm 0068.dcm 0090.dcm 0112.dcm 0134.dcm 0156.dcm
0003.dcm 0025.dcm 0047.dcm 0069.dcm 0091.dcm 0113.dcm 0135.dcm 0157.dcm
0004.dcm 0026.dcm 0048.dcm 0070.dcm 0092.dcm 0114.dcm 0136.dcm 0158.dcm
0005.dcm 0027.dcm 0049.dcm 0071.dcm 0093.dcm 0115.dcm 0137.dcm 0159.dcm
0006.dcm 0028.dcm 0050.dcm 0072.dcm 0094.dcm 0116.dcm 0138.dcm 0160.dcm
0007.dcm 0029.dcm 0051.dcm 0073.dcm 0095.dcm 0117.dcm 0139.dcm 0161.dcm
0008.dcm 0030.dcm 0052.dcm 0074.dcm 0096.dcm 0118.dcm 0140.dcm 0162.dcm
0009.dcm 0031.dcm 0053.dcm 0075.dcm 0097.dcm 0119.dcm 0141.dcm 0163.dcm
0010.dcm 0032.dcm 0054.dcm 0076.dcm 0098.dcm 0120.dcm 0142.dcm 0164.dcm
0011.dcm 0033.dcm 0055.dcm 0077.dcm 0099.dcm 0121.dcm 0143.dcm 0165.dcm
0012.dcm 0034.dcm 0056.dcm 0078.dcm 0100.dcm 0122.dcm 0144.dcm 0166.dcm
0013.dcm 0035.dcm 0057.dcm 0079.dcm 0101.dcm 0123.dcm 0145.dcm 0167.dcm
0014.dcm 0036.dcm 0058.dcm 0080.dcm 0102.dcm 0124.dcm 0146.dcm 0168.dcm
0015.dcm 0037.dcm 0059.dcm 0081.dcm 0103.dcm 0125.dcm 0147.dcm 0169.dcm
0016.dcm 0038.dcm 0060.dcm 0082.dcm 0104.dcm 0126.dcm 0148.dcm 0170.dcm
0017.dcm 0039.dcm 0061.dcm 0083.dcm 0105.dcm 0127.dcm 0149.dcm 0171.dcm
0018.dcm 0040.dcm 0062.dcm 0084.dcm 0106.dcm 0128.dcm 0150.dcm 0172.dcm
0019.dcm 0041.dcm 0063.dcm 0085.dcm 0107.dcm 0129.dcm 0151.dcm
0020.dcm 0042.dcm 0064.dcm 0086.dcm 0108.dcm 0130.dcm 0152.dcm
0021.dcm 0043.dcm 0065.dcm 0087.dcm 0109.dcm 0131.dcm 0153.dcm
0022.dcm 0044.dcm 0066.dcm 0088.dcm 0110.dcm 0132.dcm 0154.dcm
[chenchangming...@localhost ~]$ unpacksdcmdir -scanonly scan.dat -src . -targ .
$Id: unpacksdcmdir,v 1.19.2.2 2008/03/11 19:56:38 nicks Exp $
/home/chenchangmingswu
-scanonly scan.dat -src . -targ .
Thu Apr 29 07:05:51 EDT 2010
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name:
stable4 $ TimeStamp: 2010/04/29-11:05:51-GMT BuildTimeStamp: Aug 11 2009
08:24:20 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
User: chenchangmingswu Machine: localhost.localdomain Platform: Linux
PlatformVersion: 2.6.31.5-127.fc12.i686.PAE CompilerName: GCC
CompilerVersion: 30400
localhost.localdomain
Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7
21:25:57 EST 2009 i686 athlon i386 GNU/Linux
Thu Apr 29 07:05:51 EDT 2010
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 Thu Apr 29 07:05:51 EDT 2010
mri_parse_sdcmdir --sortbyrun --d . --o ./dicomdir.sumfile --status
./parse.status
0
Done scanning Thu Apr 29 07:05:51 EDT 2010
------------------------------------------
ERROR: no dicom files found in .
[chenchangming...@localhost csq]$ recon-all -force -i
/media/12D8F3B3D8F392E9/chenchangming/20071119/csq -subjid csq
INFO: /media/12D8F3B3D8F392E9/chenchangming/fs-analysis/csq exists with -i, but
-force specified.
Deleting any previous source volumes
Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0
INFO: SUBJECTS_DIR is /media/12D8F3B3D8F392E9/chenchangming/fs-analysis
Actual FREESURFER_HOME /home/chenchangmingswu/software/freesurfer
-rwxrwxrwx. 1 chenchangmingswu chenchangmingswu 15854 Apr 28 12:46
/media/12D8F3B3D8F392E9/chenchangming/fs-analysis/csq/scripts/recon-all.log
Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7
21:25:57 EST 2009 i686 athlon i386 GNU/Linux
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /home/chenchangmingswu/software/freesurfer/
Previous: /home/chenchangmingswu/software/freesurfer
/media/12D8F3B3D8F392E9/chenchangming/fs-analysis/csq
mri_convert /media/12D8F3B3D8F392E9/chenchangming/20071119/csq
/media/12D8F3B3D8F392E9/chenchangming/fs-analysis/csq/mri/orig/001.mgz
mri_convert /media/12D8F3B3D8F392E9/chenchangming/20071119/csq
/media/12D8F3B3D8F392E9/chenchangming/fs-analysis/csq/mri/orig/001.mgz
corRead(): can't open file
/media/12D8F3B3D8F392E9/chenchangming/20071119/csq/COR-.info
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from /media/12D8F3B3D8F392E9/chenchangming/20071119/csq...
Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7
21:25:57 EST 2009 i686 athlon i386 GNU/Linux
recon-all exited with ERRORS at Thu Apr 29 07:53:34 EDT 2010
_______________________________________________
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.
