Anil Roy wrote:

Hello All,

I wanted to convert the brainmask volume to analyze format. I'm not very familiar with the analyze format and had two questions.

1. The wiki mentions that converting to SPM-Analyze format could

involve converting to multiple or single frames. What exactly are multiple or single frames? Are they just different slices?

This refers to different time points. Eg, in a functional run, you might have 100 time points. Each of these is a frame.

2. When converting, I get the message INFO: set hdr.hist.orient to

'coronal flipped'. What does that refer to?

That is a field in the analyze header that is supposed to indicate the orientation.

I have posted the output from mri_convert below.

Thanks,

Anil.

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[root@slr08 freesurfer]# mri_convert -ot spm $SUBJECTS_DIR/O-06-002/mri/brainmask.mgz /root/test.img mri_convert -ot spm /mnt/win/MRI_data/MWIN4/Freesurfer//O-06-002/mri/brainmask.mgz /root/test.img $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from /mnt/win/MRI_data/MWIN4/Freesurfer//O-06-002/mri/brainmask.mgz... TR=2300.00, TE=3.36, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /root/test.img... Analyze Output Matrix -1.000 0.000 0.000 129.678; 0.000 0.000 1.000 -82.220; 0.000 -1.000 0.000 140.347; 0.000 0.000 0.000 1.000;

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INFO: set hdr.hist.orient to 'coronal flipped' [root@slr08 freesurfer]#

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