There are lots of warnings in the log file. Have you anonymized this data or done anything to the DICOM files since they came from the scanner?
On 12/18/2013 03:44 AM, Rujing Zha wrote: > Dear Doug, > Thanks for your kindhearted help, Doug. > I upload the standard output and error message file named > "unpack_log", and the unpack log file named unpack.log in the attachment. > Thanks in advance. > All the best. > 2013-12-18 > ------------------------------------------------------------------------ > /Rujing Zha/ > ------------------------------------------------------------------------ > *发件人：*Douglas N Greve <gr...@nmr.mgh.harvard.edu> > *发送时间：*2013-12-18 00:51 > *主题：*Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from > the command-line ERROR > *收件人：*"Rujing Zha"<charujing...@163.com> > *抄送：*"freesurfer"<freesurfer@nmr.mgh.harvard.edu> > Is that all it says? Can you send the log file? > On 12/16/2013 10:00 PM, Rujing Zha wrote: > > Hi Doug, > > Thanks Doug. > > I tried the "-run 15" option, it generate a "015" folder. However > > unpacksdcmdir code echo ERROR message: > > "ERROR:mri_convert > > child killed: segmentation violation ", > > and the script terminated. > > All the best. > > 2013-12-17 > > ------------------------------------------------------------------------ > > > /Rujing Zha/ > > ------------------------------------------------------------------------ > > > *发件 人：*Douglas N Greve <gr...@nmr.mgh.harvard.edu> > > *发送时间：*2013-12-17 02:56 > > *主 题：*Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from > > the command-line ERROR > > *收件 人：*"freesurfer"<freesurfer@nmr.mgh.harvard.edu> > > *抄送：* > > If you passed "-run 015" it should have generated a 015 folder and not a > > > 013 folder. The only thing I can think may have gone wrong is that it > > expected 15 instead of 015. > > doug > > On 12/16/2013 09:24 AM, Bruce Fischl wrote: > > > sorry, I don't know that code very well. Doug is probably the right > > > one to help you > > > Bruce > > > > > > > > > On Mon, 16 Dec 2013, Rujing Zha wrote: > > > > > >> Dear Bruce, > > >> I did setup the "-run 015" not "013" in unpacksdcmdir as I told in > > >> previous > > >> message. But it generated the "013" folder automatically after running > > > >> unpacksdcdir, which made me so confused. > > >> As it created the "013" folder, I guess unpacksdcmdir didnot recognized > > > > > >> structure image correctly which was in the "15th" line of the scan.info. > > > > > >> Thanks Bruce. > > >> All the best. > > >> > > >> 2013-12-16 > > >> > > >> ____________________________________________________________________________ > > >> > > > > > >> > > >> Rujing Zha > > >> > > >> ____________________________________________________________________________ > > >> > > > > > >> > > >> 发 件 人：Bruce Fischl <fis...@nmr.mgh.harvard.edu> > > >> 发送时间：2013-12-16 22:12 > > >> 主 > > 题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the > > >> command-line ERROR > > >> 收件 人："Rujing Zha"<charujing...@163.com> > > >> 抄 送："freesurfer"<freesurfer@nmr.mgh.harvard.edu> > > >> > > >> but why are you giving recon-all the path to run 013 instead of 015? I > > > >> don't know the fsfast file structure, but your scan.info says that > > >> 013 is > > > ?? ?an EPI fun and 015 is the mprage > > >> > > >> On Sat, > > >> 14 Dec 2013, Rujing Zha wrote: > > >> > > >> > Hi Bruce, > > >> > It generated a 013 subfolder in after running this code "unpacksdcmdir > > > > > >> > -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 > > >> 3danat mg > > >> z > > >> > 001.mgz". It is 15 that I can see the number of > > >> t1_mpr_ns_sag_iso_zhang > > > ?? ?in > > >> > the unpack.log. > > >> > Then I ran "recon-all -i ../work/liujunhao/3danat/013/001.mgz -s > > >> liujunha > > >> o", > > >> > and it finished without error. > > >> > "recon-all -s liujunhao -all" was run and ERROR would be displayed: > > > >> > ERROR: input(s) cannot have multiple frames! > > >> > The recon-all.log unpack.log and scan.info were unloaded in the > > >> attachmen > > >> t. > > >> > Thanks. > > >> > All the best. > > >> > > > >> > 2013-12-14 > > >> > > > >> > > > >> _________________________________________________________________________ > > >> > > > > > >> > > >> ___ > > >> > Rujing Zha > > >> > > > >> > > > >> _______________________________________________ > > >> 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 i > > >> s > > >> addressed. If you believe this e-mail was sent to you in error and > > >> the e-ma > > >> il > > >> contains patient information, please contact the Partners Compliance > > >> HelpLi > > >> ne at > > >> http://www.partners.org/complianceline . If the e-mail was sent to > > >> you in e > > >> rror > > >> but does not contain patient information, please contact the sender > > >> and pro > > >> perly > > >> dispose of the e-mail. > > >> > > >> > > >> > > > > > > > > > _______________________________________________ > > > 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: 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 > -- > 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: 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 -- 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: 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
