Hi Kambiz, what is the source of this dicom file? It is missing the image orientation tag, which is pretty fundamental. Did this come directly off the scanner? Or has it been manipulated in some way? Is this raw image data or did the scanner created it based on some processing? doug

On 05/02/2012 01:55 PM, Kambiz Tavabi wrote:

Hello, The command

mri_convert -it dicom -ot mgz 0001_9746dc8ab0544b3c8460cc2925682ba3.dcm 001.mgz

gives the following output:

mri_convert -it dicom -ot mgz 0001_9746dc8ab0544b3c8460cc2925682ba3.dcm 001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from 0001_9746dc8ab0544b3c8460cc2925682ba3.dcm... Starting DICOMRead2() dcmfile = /home/kambiz/data/freesurfer/ilabs/tmp/206/DICOM/0001_9746dc8ab0544b3c8460cc2925682ba3.dcm dcmdir = /home/kambiz/data/freesurfer/ilabs/tmp/206/DICOM Ref Series No = 301 Found 707 files, checking for dicoms WARNING: tag image orientation not found Found 705 dicom files in series. WARNING: tag image orientation not found First Sorting Computing Slice Direction Vs: 85.2923 -138.9 161.601 Vs: 0.371599 -0.605155 0.704061 Second Sorting Counting frames nframes = 1 nslices = 705 ndcmfiles = 705 MRIalloc(0, 0, 705): bad parm ERROR: mri alloc failed

I am running freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on RedHat 5.8 I don't understand what the problem is?

Thanks in advance Kambiz