Re: [Freesurfer] Found 0 unique series
ue
> continue
> @ nth = $nth + 1 ;
> @ nth = 60 + 1
> set filetype = `mri_probedicom --i $f --d filetype`
> set filetype = `mri_probedicom --i $f --d filetype`
> mri_probedicom --i
> /autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071011020919522481256
> --d filetype
> if ( $filetype == notdicom ) continue ;
> if ( notdicom == notdicom ) continue
> continue
> @ nth = $nth + 1 ;
> @ nth = 61 + 1
> set filetype = `mri_probedicom --i $f --d filetype`
> set filetype = `mri_probedicom --i $f --d filetype`
> mri_probedicom --i
> /autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010591916939874147
> --d filetype
> if ( $filetype == notdicom ) continue ;
> if ( notdicom == notdicom ) continue
> continue
> @ nth = $nth + 1 ;
> @ nth = 62 + 1
> set filetype = `mri_probedicom --i $f --d filetype`
> set filetype = `mri_probedicom --i $f --d filetype`
> mri_probedicom --i
> /autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010591415652273938
> --d filetype
> if ( $filetype == notdicom ) continue ;
> if ( notdicom == notdicom ) continue
> continue
> @ nth = $nth + 1 ;
> @ nth = 63 + 1
> set filetype = `mri_probedicom --i $f --d filetype`
> set filetype = `mri_probedicom --i $f --d filetype`
> mri_probedicom --i
> /autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010592441576274365
> --d filetype
> if ( $filetype == notdicom ) continue ;
> if ( notdicom == notdicom ) continue
> continue
> @ nth = $nth + 1 ;
> @ nth = 64 + 1
> set filetype = `mri_probedicom --i $f --d filetype`
> set filetype = `mri_probedicom --i $f --d filetype`
> mri_probedicom --i
> /autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071011015419083680629
> --d filetype
> if ( $filetype == notdicom ) continue ;
> if ( notdicom == notdicom ) continue
> continue
> rm -f $dumpfile
> rm -f /tmp/dcmunpack.dump.21578
>
>
> set SeriesNos = ( `cat $infofile | awk '{print $2}' | sort -n | uniq` )
> set SeriesNos = ( `cat $infofile | awk '{print $2}' | sort -n | uniq` )
> cat
> /autofs/cluster/cagn/1/users/traney/Projects/FC-REVEAL-practice/DEMA65e/imagelist.dat
> awk {print $2}
> uniq
> sort -n
> cat:
> /autofs/cluster/cagn/1/users/traney/Projects/FC-REVEAL-practice/DEMA65e/imagelist.dat:
> No such file or directory
> echo "Found $#SeriesNos unique series: $SeriesNos" | tee -a $LF
> echo Found 0 unique series:
> tee -a
> /autofs/cluster/cagn/1/users/traney/Projects/FC-REVEAL-practice/DEMA65e/dcmunpack.log
> Found 0 unique series:
>
> echo "Subject $Patient"
> Patient: Undefined variable.
>
> It's just weird because it runs for most subjects but not a particular few.
> Thanks!
> Best,
> Talia
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, June 15, 2016 4:43 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Found 0 unique series
>
> The problem appears to be
>
> cat: /imagelist.dat: No such file or directory
>
>
> Not sure what is going on there. Make sure you're not in / when running
> it or that the output points to /. Try running it with -debug as the
> first argument and sending the output.
>
> On 06/15/2016 04:36 PM, Raney, Talia L. wrote:
>> My command line is dcmunpack -src $dcmdir -targ $homedir/$subj -fsfast -run
>> $run_num restingstate nii.gz f.nii.gz and the output is
>> ---
>> 1 24 restingstate f 0 0
>> ---
>> Searching for matching files
>> Wed Jun 15 16:34:27 EDT 2016
>> Wed Jun 15 16:34:27 EDT 2016
>> Found 65 total files.
>> cat: /imagelist.dat: No such file or directory
>> Found 0 unique series:
>> Patient: Undefined variable.
>>
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Wednesday, June 15, 2016 4:08 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject:
Re: [Freesurfer] Found 0 unique series
gn/1/users/traney/Projects/FC-REVEAL-practice/DEMA65e/dcmunpack.log Found 0 unique series: echo "Subject $Patient" Patient: Undefined variable. It's just weird because it runs for most subjects but not a particular few. Thanks! Best, Talia From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, June 15, 2016 4:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Found 0 unique series The problem appears to be cat: /imagelist.dat: No such file or directory Not sure what is going on there. Make sure you're not in / when running it or that the output points to /. Try running it with -debug as the first argument and sending the output. On 06/15/2016 04:36 PM, Raney, Talia L. wrote: > My command line is dcmunpack -src $dcmdir -targ $homedir/$subj -fsfast -run > $run_num restingstate nii.gz f.nii.gz and the output is > --- >1 24 restingstate f 0 0 > --- > Searching for matching files > Wed Jun 15 16:34:27 EDT 2016 > Wed Jun 15 16:34:27 EDT 2016 > Found 65 total files. > cat: /imagelist.dat: No such file or directory > Found 0 unique series: > Patient: Undefined variable. > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, June 15, 2016 4:08 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Found 0 unique series > > what is your command line and what is the full terminal output > > On 06/15/2016 04:06 PM, Raney, Talia L. wrote: >> Hi FreeSurfer users, >> I've been running dcmunpack and I get an error that said Found 0 unique >> series, even though it has dicom files. What does this mean and what could I >> do to fix the problem? >> Best, >> Talia >> ___ >> 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 > ___ > 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 ___ 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.
Re: [Freesurfer] Found 0 unique series
The problem appears to be cat: /imagelist.dat: No such file or directory Not sure what is going on there. Make sure you're not in / when running it or that the output points to /. Try running it with -debug as the first argument and sending the output. On 06/15/2016 04:36 PM, Raney, Talia L. wrote: > My command line is dcmunpack -src $dcmdir -targ $homedir/$subj -fsfast -run > $run_num restingstate nii.gz f.nii.gz and the output is > --- >1 24 restingstate f 0 0 > --- > Searching for matching files > Wed Jun 15 16:34:27 EDT 2016 > Wed Jun 15 16:34:27 EDT 2016 > Found 65 total files. > cat: /imagelist.dat: No such file or directory > Found 0 unique series: > Patient: Undefined variable. > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, June 15, 2016 4:08 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Found 0 unique series > > what is your command line and what is the full terminal output > > On 06/15/2016 04:06 PM, Raney, Talia L. wrote: >> Hi FreeSurfer users, >> I've been running dcmunpack and I get an error that said Found 0 unique >> series, even though it has dicom files. What does this mean and what could I >> do to fix the problem? >> Best, >> Talia >> ___ >> 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 > ___ > 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 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.
Re: [Freesurfer] Found 0 unique series
My command line is dcmunpack -src $dcmdir -targ $homedir/$subj -fsfast -run $run_num restingstate nii.gz f.nii.gz and the output is --- 1 24 restingstate f 0 0 --- Searching for matching files Wed Jun 15 16:34:27 EDT 2016 Wed Jun 15 16:34:27 EDT 2016 Found 65 total files. cat: /imagelist.dat: No such file or directory Found 0 unique series: Patient: Undefined variable. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, June 15, 2016 4:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Found 0 unique series what is your command line and what is the full terminal output On 06/15/2016 04:06 PM, Raney, Talia L. wrote: > Hi FreeSurfer users, > I've been running dcmunpack and I get an error that said Found 0 unique > series, even though it has dicom files. What does this mean and what could I > do to fix the problem? > Best, > Talia > ___ > 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 ___ 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.
Re: [Freesurfer] Found 0 unique series
what is your command line and what is the full terminal output On 06/15/2016 04:06 PM, Raney, Talia L. wrote: > Hi FreeSurfer users, > I've been running dcmunpack and I get an error that said Found 0 unique > series, even though it has dicom files. What does this mean and what could I > do to fix the problem? > Best, > Talia > ___ > 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 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.
