Hi Bruce
That right. After the dicom were converted to nii.gz it imported and processed into recon-all without any problem. Please see my other mail with mri_info.
mri_convert /home/freesurfer/subjects/9999/mri/rawavg.mgz /home/freesurfer/subjects/9999/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/freesurfer/subjects/9999/mri/rawavg.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.10523, -0.994448, 0) j_ras = (-0.0616664, 0.00652535, 0.998075) k_ras = (0.992534, -0.105027, 0.0620106) Original Data has (1.25, 1.25, 1.2) mm size and (192, 192, 160) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation
cheers Knut J
On 07/05/2014 03:46 PM, Bruce Fischl wrote:
Hi Knut
is the FOV really 384mm?? That's awfully big and seems more likely to be an error in the dicoms than real.
cheers Bruce On Sat, 5 Jul 2014, Knut J Bjuland wrote:
Dear FreeSurfers,
I have imported several dicom files with recon-all -i -subjid id. All files were imported correctly, apart from one subjects. When I try to convert it direcelty with mri_convert -ot mgz dicom/9999/1.dcm -s 9999
I get this error message.
WARNING: files are not found to be different and cannot be sorted File1: ../../../../dicom/9999/162.dcm File2: ../../../../dicom/9999/2.dcm
When I process the subject with recon-all -s 9999 -all. I got this message.
WARNING ==================++++++++++++++++++++++++======================================= The physical sizes are (240.00 mm, 240.00 mm, 384.00 mm), which cannot fit in 256^3 mm^3 volumes. The resulting volume will have 384 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu)
Can you please advise me how to import the dicom files? Should I convert them to nifti. Will this affect the end results compared to the other subjects that were imported correctly?
Knut J
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