Hello,
This probably isn't an issue with data-type - the command "/usr/local/fsl/bin/fslmaths thresh_zstat1 -mas /Users/.../Desktop/SCANS/Masks/seg_mask.nii.gz thresh_zstat1" is failing because the mask has a different geometry to the functional data. From the output below, it looks like your mask is 185x207x209 in 1mm resolution, does this match the functional data? Can you let me know the results of running fslhd on both the functional data and the mask?
Kind Regards
Matthew
> Dear All,
>
> I want to conduct fMRI FEAT analyses at the individual level with subject specific MRIs and manual segmentation masks. The masks were created in ITK-snap and INT16 type, not FLOAT32 as the other images are.
>
> data_type INT16
>
> dim1 185
>
> dim2 207
>
> dim3 209
>
> dim4 1
>
> datatype 4
>
> pixdim1 1.000000
>
> pixdim2 1.000000
>
> pixdim3 1.000000
>
> pixdim4 0.000000
>
> cal_max 0.0000
>
> cal_min 0.0000
>
> file_type NIFTI-1+
>
>
> Therefore, when I am running the feat, I get an error at post stats:
>
> WARNING:: Inconsistent orientations for individual images in pipeline!
> Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
>
> Image Exception : #3 :: Attempted to multiply images/ROIs of different sizes
> libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException
>
> FATAL ERROR ENCOUNTERED:
> COMMAND:
> /usr/local/fsl/bin/fslmaths thresh_zstat1 -mas /Users/.../Desktop/SCANS/Masks/seg_mask.nii.gz thresh_zstat1
> ERROR MESSAGE:
> child killed: SIGABRT
> END OF ERROR MESSAGE
> child killed: SIGABRT
> while executing
> "if { [ catch {
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
> switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr arginde..."
> (file "/usr/local/fsl/bin/feat" line 310)
> Error encountered while running in main feat script, halting.
> child killed: SIGABRT
>
>
> I am as sure that the images are labelled correctly, so assume the data type is the problem.
>
> Does this sound correct? And if so, how do I safely convert the mask to the correct data type?
>
> Many thanks in advance.
>
> Clare
|