That is probably just the way they are oriented in the nii file. BTW, why are you using bshort? I'm trying to push people into using nii.

doug

Leila Reddy wrote:

Hi,

I am trying to convert SPM5 .nii files into bshort and I used the following command:

mri_concat fkoch-0007*.nii --o bold/007/fspm_000.bshort

The command seems to work in that I have a bunch of bshort files in my bold/007 directory but when I try to view the slices (using sliceview-sess for example) the slices are all upside-down (rotated by 180 degrees). Is there an option I can use to get them the right side up?

I'm using FS v3 on an IntelMac and my version of mri_concat is stable3. Here is the output of bugr:

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FREESURFER_HOME: /Applications/freesurfer

Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5

Kernel info: Darwin 8.11.1 i386

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Thanks, Leila

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