Re: [Freesurfer] unpacking error

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
>     >
>     >
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>     --
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>     MGH-NMR Center
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--
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/

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