Hi,
I am trying to unpack dicom files and convert them to nifti, but am running into an error. I ran the following command with no issue:
unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir/scan.info
however, when I try to run the next command to actually unpack the data:
unpacksdcmdir -src 0008 -targ NIFTI -fsfast \ ? -run 7 3danat mgz 001.mgz <<NIFTI>>
I get the following error message: Missing name for redirect.
Thanks,
Caroline
Remove the <<NIFTI>>
On 05/22/2014 03:45 PM, Caroline Lewis wrote:
Hi,
I am trying to unpack dicom files and convert them to nifti, but am running into an error. I ran the following command with no issue: unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir/scan.info http://scan.info
however, when I try to run the next command to actually unpack the data:
unpacksdcmdir -src 0008 -targ NIFTI -fsfast \ ? -run 7 3danat mgz 001.mgz <<NIFTI>>
I get the following error message: Missing name for redirect. Thanks,
Caroline
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Douglas. Now I am running into other errors. I ran the command:
unpacksdcmdir -src 0008 -targ 0008/mri/orig -fsfast \ ? -run 8 bold nii 001.nii
ERROR: reading 0008/11147SACC000.MR.RESEARCH_NEURO.8.1.2014.05.13.14.42.14.530.48877356.dcm tag 28 30
Also, some of the runs in the "scan.info" file say "err" where it should say "ok"
Do you have any idea why I'm getting these errors?
Thanks,
Caroline
On Thu, May 22, 2014 at 4:16 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Remove the <<NIFTI>>
On 05/22/2014 03:45 PM, Caroline Lewis wrote:
Hi,
I am trying to unpack dicom files and convert them to nifti, but am running into an error. I ran the following command with no issue: unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir/
scan.info http://scan.info
however, when I try to run the next command to actually unpack the data:
unpacksdcmdir -src 0008 -targ NIFTI -fsfast \ ? -run 7 3danat mgz 001.mgz <<NIFTI>>
I get the following error message: Missing name for redirect. Thanks,
Caroline
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 greve@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.
hmmm, if it does not have tag 28 30, then something is really wrong. This is a Siemens dicom, right? What scanner? doug
On 05/22/2014 06:05 PM, Caroline Lewis wrote:
Thanks Douglas. Now I am running into other errors. I ran the command:
unpacksdcmdir -src 0008 -targ 0008/mri/orig -fsfast \ ? -run 8 bold nii 001.nii
ERROR: reading 0008/11147SACC000.MR.RESEARCH_NEURO.8.1.2014.05.13.14.42.14.530.48877356.dcm tag 28 30
Also, some of the runs in the "scan.info http://scan.info" file say "err" where it should say "ok"
Do you have any idea why I'm getting these errors?
Thanks,
Caroline
On Thu, May 22, 2014 at 4:16 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Remove the \<<NIFTI>> On 05/22/2014 03:45 PM, Caroline Lewis wrote: > Hi, > > I am trying to unpack dicom files and convert them to nifti, but am > running into an error. I ran the following command with no issue: > unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir/scan.info <http://scan.info> <http://scan.info> > > > however, when I try to run the next command to actually unpack the data: > > unpacksdcmdir -src 0008 -targ NIFTI -fsfast \ > ? -run 7 3danat mgz 001.mgz \<<NIFTI>> > > I get the following error message: Missing name for redirect. > Thanks, > > Caroline > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That doesn't sound good. Does tag 28, 30 mean the voxel size is missing, why would this be? It is a Siemens dicom from a 3T scanner - not sure which model but I can find out.
Do you have any idea why I am getting errors for some runs in the scan. info file as such?:
7 t1_mprage_tra_p2_iso_1.0 err 0 0 0 160 11147SACC000.MR.RESEARCH_NEURO.
Thanks Doug,
Caroline
On Thu, May 22, 2014 at 6:52 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
hmmm, if it does not have tag 28 30, then something is really wrong. This is a Siemens dicom, right? What scanner? doug
On 05/22/2014 06:05 PM, Caroline Lewis wrote:
Thanks Douglas. Now I am running into other errors. I ran the command:
unpacksdcmdir -src 0008 -targ 0008/mri/orig -fsfast \ ? -run 8 bold nii 001.nii
ERROR: reading
0008/11147SACC000.MR.RESEARCH_NEURO.8.1.2014.05.13.14.42.14.530.48877356.dcm
tag 28 30
Also, some of the runs in the "scan.info http://scan.info" file say "err" where it should say "ok"
Do you have any idea why I'm getting these errors?
Thanks,
Caroline
On Thu, May 22, 2014 at 4:16 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Remove the \<<NIFTI>> On 05/22/2014 03:45 PM, Caroline Lewis wrote: > Hi, > > I am trying to unpack dicom files and convert them to nifti, but am > running into an error. I ran the following command with no issue: > unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir/scan.info <http://scan.info> <http://scan.info> > > > however, when I try to run the next command to actually unpack the data: > > unpacksdcmdir -src 0008 -targ NIFTI -fsfast \ > ? -run 7 3danat mgz 001.mgz \<<NIFTI>> > > I get the following error message: Missing name for redirect. > Thanks, > > Caroline > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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.
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 greve@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
What is the model of the scanner? I think there is an error in there because it can' find the parameters it needs. You can also try something like
mri_convert 160 11147SACC000.MR.RESEARCH_NEURO. test.mgh
this might print something more informative to the terminal. You can also try
mri_probedicom --i 11147SACC000.MR.RESEARCH_NEURO.
doug
On 05/23/2014 10:18 AM, Caroline Lewis wrote:
That doesn't sound good. Does tag 28, 30 mean the voxel size is missing, why would this be? It is a Siemens dicom from a 3T scanner - not sure which model but I can find out.
Do you have any idea why I am getting errors for some runs in the scan. info file as such?:
7 t1_mprage_tra_p2_iso_1.0 err 0 0 0 160 11147SACC000.MR.RESEARCH_NEURO.
Thanks Doug,
Caroline
On Thu, May 22, 2014 at 6:52 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
hmmm, if it does not have tag 28 30, then something is really wrong. This is a Siemens dicom, right? What scanner? doug On 05/22/2014 06:05 PM, Caroline Lewis wrote: > Thanks Douglas. Now I am running into other errors. I ran the command: > > unpacksdcmdir -src 0008 -targ 0008/mri/orig -fsfast \ > ? -run 8 bold nii 001.nii > > ERROR: reading > 0008/11147SACC000.MR.RESEARCH_NEURO.8.1.2014.05.13.14.42.14.530.48877356.dcm > tag 28 30 > > Also, some of the runs in the "scan.info <http://scan.info> <http://scan.info>" file say > "err" where it should say "ok" > > Do you have any idea why I'm getting these errors? > > Thanks, > > Caroline > > > On Thu, May 22, 2014 at 4:16 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Remove the \<<NIFTI>> > > On 05/22/2014 03:45 PM, Caroline Lewis wrote: > > Hi, > > > > I am trying to unpack dicom files and convert them to nifti, but am > > running into an error. I ran the following command with no issue: > > unpacksdcmdir -src dicomdir -targ targetdir -scanonly > targetdir/scan.info <http://scan.info> <http://scan.info> <http://scan.info> > > > > > > however, when I try to run the next command to actually unpack > the data: > > > > unpacksdcmdir -src 0008 -targ NIFTI -fsfast \ > > ? -run 7 3danat mgz 001.mgz \<<NIFTI>> > > > > I get the following error message: Missing name for redirect. > > Thanks, > > > > Caroline > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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
freesurfer@nmr.mgh.harvard.edu
-
Caroline Lewis -
Douglas N Greve