Dear Matthew,
Thanks for the reply. I have ran fslhd on the functional data and mask and they do not match:
filename con_012_func1.nii.gz
sizeof_hdr 348
data_type INT16
dim0 4
dim1 64
dim2 64
dim3 44
dim4 261
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.000000
pixdim1 3.000000
pixdim2 3.000000
pixdim3 3.000000
pixdim4 2.410000
pixdim5 1.000000
pixdim6 1.000000
pixdim7 58545.914062
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -3.000000 0.000000 -0.000000 96.000000
qto_xyz:2 0.000000 2.598076 -1.500000 -44.900520
qto_xyz:3 0.000000 1.500000 2.598076 -106.426422
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -3.000000 0.000000 0.000000 96.000000
sto_xyz:2 0.000000 2.598076 -1.500000 -44.900520
sto_xyz:3 0.000000 1.500000 2.598076 -106.426422
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip
aux_file
filename con_012_seg.nii.gz
sizeof_hdr 348
data_type UINT16
dim0 3
dim1 185
dim2 207
dim3 209
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units Unknown
datatype 512
nbyper 2
bitpix 16
pixdim0 0.000000
pixdim1 1.000000
pixdim2 1.000000
pixdim3 1.000000
pixdim4 0.000000
pixdim5 0.000000
pixdim6 0.000000
pixdim7 0.000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Aligned Anat
qform_code 2
qto_xyz:1 -1.000000 -0.000000 -0.000000 92.965897
qto_xyz:2 0.000000 1.000000 -0.000000 -79.256493
qto_xyz:3 -0.000000 0.000000 1.000000 -103.286942
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -1.000000 -0.000000 0.000000 92.965897
sto_xyz:2 -0.000000 1.000000 -0.000000 -79.256493
sto_xyz:3 0.000000 0.000000 1.000000 -103.286942
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip
aux_file
I also want to use the individual T1 and the fslhd info for this is:
filename con_012_mprage_brain.nii.gz
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 174
dim2 192
dim3 192
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 0.000000
pixdim1 1.000000
pixdim2 1.000000
pixdim3 1.000000
pixdim4 1.000000
pixdim5 0.000000
pixdim6 0.000000
pixdim7 0.000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -1.000000 0.000000 -0.000000 87.713997
qto_xyz:2 0.000000 0.982935 -0.183951 -65.430283
qto_xyz:3 0.000000 0.183951 0.982935 -122.346207
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -1.000000 0.000000 0.000000 87.713997
sto_xyz:2 0.000000 0.982935 -0.183951 -65.430283
sto_xyz:3 0.000000 0.183951 0.982935 -122.346207
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip FSL5.0
aux_file
I hope this is helpful? Many thanks again,
BW
Clare
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Matthew Webster [[log in to unmask]]
Sent: 19 November 2015 13:44
To: [log in to unmask]
Subject: Re: [FSL] Convert data type to FLOAT32
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
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