Dear FreeSurfers,
Our group has encountered an error while unpacking the first set of data we acquired on Bay 2 since the upgrade. Here's our command line:
unpacksdcmdir -src 07120620/ -targ . -generic -scanonly SUBJ.out
We then modify the .out file from
1 localizer ok 512 512 3 1 74858975 2 AAScout ok 128 128 128 2 74859004 3 T1_MPRAGE_sag ok 256 256 128 1 74856609 4 gre_2d_2mm ok 256 256 55 1 74855396 5 gre_2d_2mm ok 256 256 55 1 74852997 6 field_mapping_2mmthickness ok 128 128 35 2 74853893 7 field_mapping_2mmthickness ok 128 128 35 1 74851708 8 ep2d_t1w ok 64 64 35 1 74848994 9 epzshim_cjw02_nonalternat ok 64 64 35 222 74849554 10 epzshim_cjw02_nonalternat ok 64 64 35 222 74846612 11 epzshim_cjw02_nonalternat ok 64 64 35 222 74843672 12 epzshim_cjw02_nonalternat ok 64 64 35 222 74837495
to
3 T1_MPRAGE_sag COR T1_MPRAGE 8 ep2d_t1w bshort f 9 epzshim_cjw02_nonalternat bshort f 10 epzshim_cjw02_nonalternat bshort f 11 epzshim_cjw02_nonalternat bshort f 12 epzshim_cjw02_nonalternat bshort f
and save as SUBJ.cfg
Next command line is: unpacksdcmdir -src 07120620/ -targ .. -cfg SUBJ.cfg -fsfast
We get this error when it encounters the first functional run:
--------------------------------------------------------- Run 9 ----------------------------------------- Mon Dec 10 12:43:27 EST 2007 9 epzshim_cjw02_nonalternat bshort f ERROR: mri_convert child process exited abnormally
We've re-run the second unpack command after putting different functional runs (or even single functional runs) in the first position processed, and the same error message occurs each time. We've also tried the process on functional runs that do not have a z-shim (thought that might be causing trouble), but the error still comes up.
Any ideas?
Thanks in advance.
Dan Dillon (on behalf of Elena Goetz)
Is this data on line here at the NMR center? Can you point me to it?
Dan Dillon wrote:
Dear FreeSurfers,
Our group has encountered an error while unpacking the first set of data we acquired on Bay 2 since the upgrade. Here's our command line:
unpacksdcmdir -src 07120620/ -targ . -generic -scanonly SUBJ.out
We then modify the .out file from
1 localizer ok 512 512 3 1 74858975 2 AAScout ok 128 128 128 2 74859004 3 T1_MPRAGE_sag ok 256 256 128 1 74856609 4 gre_2d_2mm ok 256 256 55 1 74855396 5 gre_2d_2mm ok 256 256 55 1 74852997 6 field_mapping_2mmthickness ok 128 128 35 2 74853893 7 field_mapping_2mmthickness ok 128 128 35 1 74851708 8 ep2d_t1w ok 64 64 35 1 74848994 9 epzshim_cjw02_nonalternat ok 64 64 35 222 74849554 10 epzshim_cjw02_nonalternat ok 64 64 35 222 74846612 11 epzshim_cjw02_nonalternat ok 64 64 35 222 74843672 12 epzshim_cjw02_nonalternat ok 64 64 35 222 74837495
to
3 T1_MPRAGE_sag COR T1_MPRAGE 8 ep2d_t1w bshort f 9 epzshim_cjw02_nonalternat bshort f 10 epzshim_cjw02_nonalternat bshort f 11 epzshim_cjw02_nonalternat bshort f 12 epzshim_cjw02_nonalternat bshort f
and save as SUBJ.cfg
Next command line is: unpacksdcmdir -src 07120620/ -targ .. -cfg SUBJ.cfg -fsfast
We get this error when it encounters the first functional run:
Run 9 ----------------------------------------- Mon Dec 10 12:43:27 EST 2007 9 epzshim_cjw02_nonalternat bshort f ERROR: mri_convert child process exited abnormally
We've re-run the second unpack command after putting different functional runs (or even single functional runs) in the first position processed, and the same error message occurs each time. We've also tried the process on functional runs that do not have a z-shim (thought that might be causing trouble), but the error still comes up.
Any ideas?
Thanks in advance.
Dan Dillon (on behalf of Elena Goetz)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I can unpack these without a problem locally. Nick is preparing a new minor stable release in which these fixes will be present.
doug
ps. If you just can't wait, you can get new versions of the following (linux) binaries
mri_convert mri_parse_sdcmdir mri_probedicom
here:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
doug
Dan Dillon wrote:
Dear FreeSurfers,
Our group has encountered an error while unpacking the first set of data we acquired on Bay 2 since the upgrade. Here's our command line:
unpacksdcmdir -src 07120620/ -targ . -generic -scanonly SUBJ.out
We then modify the .out file from
1 localizer ok 512 512 3 1 74858975 2 AAScout ok 128 128 128 2 74859004 3 T1_MPRAGE_sag ok 256 256 128 1 74856609 4 gre_2d_2mm ok 256 256 55 1 74855396 5 gre_2d_2mm ok 256 256 55 1 74852997 6 field_mapping_2mmthickness ok 128 128 35 2 74853893 7 field_mapping_2mmthickness ok 128 128 35 1 74851708 8 ep2d_t1w ok 64 64 35 1 74848994 9 epzshim_cjw02_nonalternat ok 64 64 35 222 74849554 10 epzshim_cjw02_nonalternat ok 64 64 35 222 74846612 11 epzshim_cjw02_nonalternat ok 64 64 35 222 74843672 12 epzshim_cjw02_nonalternat ok 64 64 35 222 74837495
to
3 T1_MPRAGE_sag COR T1_MPRAGE 8 ep2d_t1w bshort f 9 epzshim_cjw02_nonalternat bshort f 10 epzshim_cjw02_nonalternat bshort f 11 epzshim_cjw02_nonalternat bshort f 12 epzshim_cjw02_nonalternat bshort f
and save as SUBJ.cfg
Next command line is: unpacksdcmdir -src 07120620/ -targ .. -cfg SUBJ.cfg -fsfast
We get this error when it encounters the first functional run:
Run 9 ----------------------------------------- Mon Dec 10 12:43:27 EST 2007 9 epzshim_cjw02_nonalternat bshort f ERROR: mri_convert child process exited abnormally
We've re-run the second unpack command after putting different functional runs (or even single functional runs) in the first position processed, and the same error message occurs each time. We've also tried the process on functional runs that do not have a z-shim (thought that might be causing trouble), but the error still comes up.
Any ideas?
Thanks in advance.
Dan Dillon (on behalf of Elena Goetz)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Dan Dillon -
Doug Greve