Hi Akshay
the -cs flag specifies the voxel size, not the field of view, so you are creating a volume with 256mm voxels! Try --cw256 instead.
cheers Bruce On Tue, 7 May 2013, Akshay wrote:
mri_convert path-to-nifti file mask.mgz --resample_type nearest -cs 256
On 5/7/13 2:55 PM, Bruce Fischl wrote:
can you send me the full mri_convert command line that is run? On Tue, 7 May 2013, Akshay wrote:
Hi Bruce
Please find the file attached
Best,
Akshay
On 5/7/13 2:40 PM, Bruce Fischl wrote:
Hi Akshay
is you send us that file we'll take a look.
cheers Bruce On Tue, 7 May 2013, Akshay wrote:
Hi All,
I am re-posting this question since there was no response to my previous attempt.
I have a problem conforming certain nifti files, the following is the log when i try to convert them,
reading from /home/akshay/ADNI/137_S_1041/MIDAS_Whole_Brain_Mask/2006-11-09_09_35_11.0/S22310/ADNI_137_S_1041_MR_MIDAS_Whole_Brain_Mask_Br_20120723235935683_S22310_I317755.nii... INFO: using NIfTI-1 qform TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -4.99113e-10, -1) j_ras = (-4.99113e-10, -1, 4.99113e-10) k_ras = (-1, 4.99113e-10, 0) WARNING ==================++++++++++++++++++++++++======================================= The physical sizes are (281.25 mm, 280.14 mm, 216.72 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 282 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ==================================================++++++++++++++++++++++++===============
Original Data has (1.09862, 1.09429, 1.20399) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 282 voxels for all directions Reslicing using nearest
This is understood, however I want them to be conformed to 256^3 mm. If I use -cs 256 flag, it does resample the image to 256^3mm but the image is blank.
Is there something wrong I am doing? How do I conform these files to 256^3mm?
Any help will be greatly appreciated.
Best,
Akshay
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