I am using recon-all command to process some analyze images. But it seems that this command does not work for all .img images. For example, I have an image with the following information:
256x256x124 0.7mm x 0.7mm x 1.5mm data type: uint8 description: position:0 0 0 file orientation: 1 0 0 0 1 0 0 0 1
working orientation: 1 0 0 0 1 0 0 0 1
Will the dimension, resolution, and data type all matter in the process?
Hi Jie,
it should be ok. We typically don't recommend this type of "french fry" voxel with one dimension beting almost 4 times as long as the others. You are usually better off getting closer to isotropic. That said, if the SNR is good enough try giving it to recon-all. One thing to be wary of though is the orientation. Do you have a .mat file to go with the .hdr/.img? Otherwise you won't be able to tell left from right. Can you get them in some other format, such as nifti?
cheers Bruce
On Fri, 7 Oct 2011, Jie Shi wrote:
I am using recon-all command to process some analyze images. But it seems that this command does not work for all .img images. For example, I have an image with the following information:
256x256x124 0.7mm x 0.7mm x 1.5mm data type: uint8 description: position:0 0 0 file orientation: 1 0 0 0 1 0 0 0 1
working orientation: 1 0 0 0 1 0 0 0 1
Will the dimension, resolution, and data type all matter in the process?
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Jie Shi