Hi Steve, if the same volume is distributed over multiple directories, then it will surely fail (actually, it is mri_convert that assumes that all files for a given volume will be in the same directory). I don't know of anyone else who has had this problem, even those who are scanning for 20 min (maybe they are not unpacking from CDs). doug
Steven Lehar wrote: > > There is a bug in the new *dcmunpack* that replaces the > earlier *unpacksdcmdir* when it is unpacking a "fragmented" dicom > directory, i.e. one in which the files were saved to DVD incrementally > during the scan, as opposed to dicom files that are saved all at once, > after all the scanning is complete. > > The difference can be seen with a 'du' command, here is a fragmented, > dicom "PRL007", compared to a consolidated one "PRL007C" of the same > data: > > $ *du* > 166156 ./PRL007/DICOM/11020419/14200000 *unconsolidated* > 166160 ./PRL007/DICOM/11020419 > 5188 ./PRL007/DICOM/11020418/50520000 > 207448 ./PRL007/DICOM/11020418/57160000 > 101648 ./PRL007/DICOM/11020418/03040000 > 502616 ./PRL007/DICOM/11020418/42140000 > 205384 ./PRL007/DICOM/11020418/17590000 > 1022288 ./PRL007/DICOM/11020418 > 1188452 ./PRL007/DICOM > 1204460 ./PRL007 > > 1022256 ./PRL007C/DICOM/11020418/03040000 *consolidated* > 1022260 ./PRL007C/DICOM/11020418 > 1022264 ./PRL007C/DICOM > 1038264 ./PRL007C > > When *dcmunpack* unpacks a fragmented dicom, the unpacking /appears/ > to succeed without errors, but the resulting f.nii file is missing a > bunch of acquisitions. Calling dcmunpack on an unconsolidated and > consolidated dicom respectively produces the f.nii files below: > > *unconsolidated*: > /space/ficus/4/users/PRL_sessions/*PRL042*/prl_moco/006/f.nii > $ ls -l f.nii > -rw-rw-r-- 1 slehar harrisgp 125043040 Jan 6 17:04 f.nii > > *consolidated*: > /space/ficus/4/users/PRL_sessions/*PRL042C*/prl_moco/006/f.nii > $ ls -l f.nii > -rw-rw-r-- 1 slehar harrisgp 201720160 Jan 11 20:48 f.nii > > Examination with osirix reveals the unconsolidated image to have only > 318 acquisitions, the consolidated one has 513 acquisitions. > > And just FYI, I wrote a script called *consolidate* (see attached) > that does the consolidation you see above, after which *dcmunpack* > unpacked it without loss of acquisitions. > > This may be an issue that only affects *us* because we do very long > ~20 min. functional scans with hundreds of aquisitions, people with > more typical scans may not ever experience this issue, and likewise > for people who save their scans all at once at the end. > > Steve Lehar > ------------------------------------------------------------------------ > > _______________________________________________ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
