Hello Lindsay,
It is best to run art_slice on the raw images before any preprocessing is done. That way all the volumes are perfectly aligned. Also, please note that ArtRepair works on 3D volumes, but was not upgraded to be compatible with 4D nifti.
-Paul
----- Original Message -----
From: "Lindsay Hanford" <[log in to unmask]>
To: [log in to unmask]
Sent: Sunday, May 10, 2015 8:38:38 AM
Subject: Re: [SPM] Artifact repair toolbox with SPM5 and coronal volumes
Hello SPM Community,
I am having the same issue as this post, when I try to perform the art_slice command from the art repair toolbox on SPM8.
My commands and output is below...
EDU>> art_slice
-> I selected my raw images
-> and selected the median filter all data and eliminate data outside the head
-> automatic mask
NEW IMAGE FILES WILL BE CREATED
The filtered scan data will be saved in the same directory
with fh pre-pended to their filenames.
Generated mask image is written to file ArtifactMask.img.
** The images do not all have same orientation and/or voxel sizes. **
The function assumes that a voxel in one image corresponds exactly
with the same voxel in another. This is not a safe assumption if
the orientation information in the headers or .mat files says that
the images are oriented differently. Please ensure that you process
all data correctly. For example, you may have realigned the images,
but not actually resliced them to be in voxel-wise alignment.
Here are the orientation matrices of the image volumes. This list
can be used to determine which file(s) are causing the problem.
[-3.75 0 0 118.32; 0 3.75 0 -105.68; 0 0 4 -59.2352] /Users/LindsayHanford/Documents/BDoff_Thesis_Project/dicom_files_full/exam_567/EmoA/preproc_nii/EmoA_567.nii
...
Error using spm_check_orientations (line 54)
The orientations etc must be identical for this procedure.
Error in spm_read_vols (line 26)
spm_check_orientations(V);
Error in art_automask (line 72)
Y = spm_read_vols(V);
Error in art_slice (line 114)
Automask = art_automask(Pnames(1,:),-1,1);
I didn't see a response to the post, I am not sure how to resolve this issue.
Any ideas?
Lindsay
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