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Dear list,
I'm new to freesurfer and would like to create a volumetric region of interest from the Destrieux atlas labels, to mask my spm12 results. All my images have been normalised so I just need the mask in avg305T1 space.
I tried running the following command:
mri_label2vol --label ctx-lh-S_intraparietal-and_Parietal_transverse.label --temp [MATLAB_PATH]/spm12/canonical/avg305T1.nii --o [PATH_TO_OUTPUT_DIR]/test.mgz --reg /usr/local/freesurfer/subjects/fsaverage/mri/brainmask.mgz
I get the following print-out and error message:
$Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
Template RAS-to-Vox: --------
-0.50000 -0.00000 -0.00000 45.50000;
-0.00000 -0.00000 -0.50000 54.50000;
-0.00000 0.50000 -0.00000 45.50000;
-0.00000 -0.00000 -0.00000 1.00000;
Loading registration from /usr/local/freesurfer/subjects/fsaverage/mri/brainmask.mgz
regio_read_register(): Success
Error reading inplaneres from /usr/local/freesurfer/subjects/fsaverage/mri/brainmask.mgz
As I'm new to freesurfer, I'm probably missing something simple. I've tried searching the archives (e.g., I found this
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/018159.html)
and notice that many use register.dat as the --reg input, and I assume this is where the problem arises here. However, I'm not sure how to go about generating this file, as I'm using the average brain: Do I need to run a full surface reconstruction on the
avg305T1.nii file? Or is there a simpler way to get around this? I have mni152.register.dat in my freesurfer directory but no mni305.register.dat equivalent.
Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
uname -a: Linux localhost.localdomain 3.10.0-957.10.1.el7.x86_64 #1 SMP Mon Mar 18 15:06:45 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
Platform: Windows 8.1, running through VirtualBox 6.0.6
Thanks in advance for your help with this,
Emma