Hello Experts,

I am trying to run the mri_convert command prior to the recon-all command on Siemens T1 dicoms (as suggested in the archives). I am using freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0, Mac OS X Lion 10.7.5

I am using the command below:

mri_convert -it siemens_dicom -ot mgz 1002/IM-0001-0001.dcm 2001.mgz

Below is the command line error I receive, it is a similar error I receive when I try to use the command recon-all on the Siemens dicoms.

I have used freesurfer before on GE dicoms and never had a problem running recon-all. Is this error message particular to the Siemens dicoms, and would you be able to tell me how to proceed?

Thank you very much for you help,

Cat

reading from 1002/IM-0001-0001.dcm...

Getting Series No

Scanning Directory

INFO: Found 130 files in 1002

INFO: Scanning for Series Number 2

INFO: found 128 files in series

INFO: loading series header info.

INFO: sorting.

RunNo = 1

WARNING: Run 1 appears to be truncated

  Files Found: 128, Files Expected (lRep+1): 1

FileName                    1002/IM-0001-0001.dcm

Identification

            NumarisVer        syngo MR D11

            ScannerModel      Skyra

            PatientName       RS-FMRI^RS-FMRI

Date and time

            StudyDate         20130222

            StudyTime         082109.140000

            SeriesTime        082812.906000

            AcqTime           082237.315000

Acquisition parameters

            PulseSeq          *tfl3d1_16ns

            Protocol          SAG MP Rage

            PhEncDir          ROW

            EchoNo            1

            FlipAngle         8

            EchoTime          3.03

            InversionTime     1000

            RepetitionTime    2400

            PhEncFOV          0

            ReadoutFOV        0

Image information

            RunNo             1

            SeriesNo          2

            ImageNo           1

            NImageRows        256

            NImageCols        256

            NFrames           128

            SliceArraylSize   0

            IsMosaic          1

            ImgPos            -78.6002 128.0000  93.1332

            VolRes              1.0000   1.0000   1.2500

            VolDim              0        0        0

            Vc                 -0.0000  -1.0000   0.0000

            Vr                 -0.0000  -0.0000  -1.0000

            Vs                  0.0000   0.0000   0.0000

            VolCenter           0.0000   0.0000   0.0000

            TransferSyntaxUID 1.2.840.10008.1.2.1

WARNING: file 1002/IM-0001-0001.dcm does not contain a Siemens ASCII header

has this file been anonymized?

ERROR: cannot unpack mosiacs without ASCII header