Hello again,
Now that I found the following "The cluster program uses the input image's header information to calculate mm-coordinates" perhaps this suggests the problem I am encountering is related to my image? Here is what fslhd tells me about my input file:
filename 5v5_Right-Pallidum_tstat3.nii.gz
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 182
dim2 218
dim3 182
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 0.0000000000
pixdim1 1.0000000000
pixdim2 1.0000000000
pixdim3 1.0000000000
pixdim4 1.0000000000
pixdim5 0.0000000000
pixdim6 0.0000000000
pixdim7 0.0000000000
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 Unknown
qform_code 0
qto_xyz:1 1.000000 0.000000 0.000000 0.000000
qto_xyz:2 0.000000 1.000000 0.000000 0.000000
qto_xyz:3 0.000000 0.000000 1.000000 0.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Unknown
sform_code 0
sto_xyz:1 0.000000 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 0.000000 0.000000 0.000000
sto_xyz:3 0.000000 0.000000 0.000000 0.000000
sto_xyz:4 0.000000 0.000000 0.000000 0.000000
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
file_type NIFTI-1+
file_code 1
descrip FSL5.0
aux_file
As I don't understand all of these fields I was wondering if someone could tell me if they see any problem with this in usage in the cluster command? Thanks in advance.
Best,
Jake
On May 7, 2013, at 2:33 PM, Jake wrote:
> Hello,
>
> I'm using FSL 5.0.2 and trying to get coordinates using the cluster command. However, I seem to be getting the same result regardless of whether I am using --mm or not. My maps are in standard 1mm space. Does anyone know what I might be doing wrong? Thanks in advance!!
>
> Best,
> Jake
>
>
> 1. cluster -i 5v5_Right-Pallidum_tstat3.nii.gz -t 3.355
>
> Cluster Index Voxels MAX MAX X (vox) MAX Y (vox) MAX Z (vox) COG X (vox) COG Y (vox) COG Z (vox)
> 3 43 5.98 81 122 61 82.2 121 60.8
> 2 5 4.05 87 109 72 86.6 110 72
> 1 3 3.85 79 126 62 79.3 126 62.3
>
> 2. cluster -i 5v5_Right-Pallidum_tstat3.nii.gz -t 3.355 --mm
>
> Cluster Index Voxels MAX MAX X (mm) MAX Y (mm) MAX Z (mm) COG X (mm) COG Y (mm) COG Z (mm)
> 3 43 5.98 81 122 61 82.2 121 60.8
> 2 5 4.05 87 109 72 86.6 110 72
> 1 3 3.85 79 126 62 79.3 126 62.3
>
>
>
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
|