Hi Bruce,

OK, thanks.

I will try MRIcron.

Pom

On Thu, Jul 25, 2013 at 7:59 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

Hi Pom

are these the dicoms straight off your Philips scanner? We don't have a ton of experience with philips. Maybe you could use something else to convert them to NIFTI, like MRIcron, then pass them to us?

cheers Bruce

On Thu, 25 Jul 2013, Pom Sailasuta wrote:

...

Hello,

I am resending this post since there is no reply for 2 days, I really appreciate your help.

thanks so much.

I have several errors using mri_convert to convert 3T Philips T1-wt, DTI and fMRI images. The last one on T1-wt images tells me to send email to freesurfer, so here is the error messages:

[pom@PomLinux /home/pom]% !mri mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from IM_0001... Starting DICOMRead2() dcmfile = /home/pom/Software/freesurfer/**subjects/S009002A/mri/orig/** orig2/IM_0001 dcmdir = /home/pom/Software/freesurfer/**subjects/S009002A/mri/orig/** orig2 WARNING: tag image orientation not found Ref Series No = 2 ERROR: bits = 8 not supported. Send email to freesurfer@nmr.mgh.harvard.edu

for DTI images, here is the errors:

MRIalloc(0, 0, 1855): bad parm [pom@PomLinux /home/pom]% mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from IM_0001... Starting DICOMRead2() dcmfile = /home/pom/Software/freesurfer/**subjects/S009002A/mri/orig/IM_* *0001 dcmdir = /home/pom/Software/freesurfer/**subjects/S009002A/mri/orig Ref Series No = 501 Found 1874 files, checking for dicoms WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found Found 1855 dicom files in series. WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found First Sorting Computing Slice Direction Vs: -117.09 -112.869 17.456 Vs: -0.715854 -0.690047 0.106721 Second Sorting Counting frames nframes = 1 nslices = 1855 ndcmfiles = 1855 MRIalloc(0, 0, 1855): bad parm ERROR: mri alloc failed

I would greatly appreciate any help.

-- Pom

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