from a freesurfer standpoint, it looks like you've done the right thing. Sorry, can't help out much on slicer. It is possible that slicer is expecting an integer data set, so you can try
mri_convert FSParcel_FSorient.mgz FSParcel_FSorient.int.mgz --out_data_type int
doug
joel bruss wrote:
I must have posted this to an incorrect address before so I'll try this again:
Hello-
I'm running freesurfer-Linux-centos4- stable-pub-v4.0.5 on Suse 11.
I've used the output of FreeSurfer, specifically wmparc.mgz to create a 32-bit volume to which I've applied edits. The two commands I used were:
mri_vol2vol --mov mri/wmparc.mgz --targ mri/rawavg.mgz --o wmparc-in-native.mgz --regheader --interp nearest
mri_convert --in_type mgz --out_type analyze wmparc-in-native.mgz wmparc_in_native_analyze
(The new Analzye set was renamed FSParcel.hdr/img)
After making the appropriate edits, I wanted to put this file back into mgz format/freesurfer space so I ran:
mri_convert --in_type analyze --out_type mgz FSParcel 3065_FSParcel.mgz
mri_vol2vol --mov FSParcel.mgz --targ mri/wmparc.mgz --o FSParcel_FSorient.mgz --regheader --interp nearest
(I assumed that a target of wmparc would be most appropriate sinc that's what I started with but I've tried aseg as well)
I've been playing around with Slicer and trying load the file as a label file to which I create (I believe) vtk models. If I convert wmparc to an Analyze set and then back to FreeSurfer mgz without any edits, I get an exact copy, as would be expected. If I make any alterations to the file and follow my steps, Slicer gripes that it can't parse the header. No matter what dims I use, I get pixels scattered across the screen and it appears that the volume is scrunched to 1 slice. If I run tkregister (as mri_vol2vol suggests)
tkregister2 --mov FSParcel_FSorient.mgz --targ $SUBJECTS_DIR/sub1/mri/aseg.mgz --reg FSParcel_FSorient.mgz.reg
everything looks fine. I find the Slicer documentation a bit lacking and don't know who to turn to. Is there something inherently wrong with my commands or is there a way to write header params to the mgz file so that Slicer will just work?
-Joel
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