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January 13, 2014 06:39PM
Hi All

I have 3dretroicor working with both resp and card data, as long as the 4D data set is in the original dimensions.

When I upsample or downsample isotropically ( 4 or 5mm using flirt ), retroicor throws the error:
*** Error transforming resp data

I diffed the headers and can't understand why non-time dimension inforamtion should make any difference.

My data sets are fMRI 4D nifti files,.

I tried matching everything but the i,j,k and x,y,z dim values to match. The card data always works....

Thank you in advance,
dpc

EDIT: I also tried making the dtype of the image int16. That did not help and there was a warning that the data was being
cast into float32.


### WORKING data set Header 
[$ fslhd bold_native.nii 
filename       bold_native.nii

sizeof_hdr     348
data_type      INT16
dim0           4
dim1           64
dim2           64
dim3           32
dim4           274
dim5           1
dim6           1
dim7           1
vox_units      mm
time_units     s
datatype       4
nbyper         2
bitpix         16
pixdim0        0.0000000000
pixdim1        3.7500000000
pixdim2        3.7500000000
pixdim3        5.0000000000
pixdim4        1.0000000000
pixdim5        0.0000000000
pixdim6        0.0000000000
pixdim7        0.0000000000
vox_offset     352
cal_max        11573.0000
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      -3.750000  0.000000  0.000000  115.530998
qto_xyz:2      0.000000  -3.750000  0.000000  145.613007
qto_xyz:3      0.000000  0.000000  5.000000  -62.979599
qto_xyz:4      0.000000  0.000000  0.000000  1.000000
qform_xorient  Right-to-Left
qform_yorient  Anterior-to-Posterior
qform_zorient  Inferior-to-Superior
sform_name     Scanner Anat
sform_code     1
sto_xyz:1      -3.750000  0.000000  0.000000  115.530998
sto_xyz:2      0.000000  -3.750000  0.000000  145.613007
sto_xyz:3      0.000000  0.000000  5.000000  -62.979599
sto_xyz:4      0.000000  0.000000  0.000000  1.000000
sform_xorient  Right-to-Left
sform_yorient  Anterior-to-Posterior
sform_zorient  Inferior-to-Superior
file_type      NIFTI-1+
file_code      1
descrip        FSL5.0
aux_file

#NOT WORKING
fslhd bold_5mm_cal.nii 
filename       bold_5mm_cal.nii

sizeof_hdr     348
data_type      FLOAT32
dim0           4
dim1           47
dim2           47
dim3           31
dim4           274
dim5           1
dim6           1
dim7           1
vox_units      mm
time_units     s
datatype       16
nbyper         4
bitpix         32
pixdim0        0.0000000000
pixdim1        5.0000000000
pixdim2        5.0000000000
pixdim3        5.0000000000
pixdim4        2200.0000000000
pixdim5        0.0000000000
pixdim6        0.0000000000
pixdim7        0.0000000000
vox_offset     352
cal_max        11573.0000
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      -5.000000  0.000000  0.000000  109.280998
qto_xyz:2      0.000000  -5.000000  0.000000  145.613007
qto_xyz:3      0.000000  0.000000  5.000000  -62.979599
qto_xyz:4      0.000000  0.000000  0.000000  1.000000
qform_xorient  Right-to-Left
qform_yorient  Anterior-to-Posterior
qform_zorient  Inferior-to-Superior
sform_name     Scanner Anat
sform_code     1
sto_xyz:1      -5.000000  0.000000  0.000000  109.280998
sto_xyz:2      0.000000  -5.000000  0.000000  145.613007
sto_xyz:3      0.000000  0.000000  5.000000  -62.979599
sto_xyz:4      0.000000  0.000000  0.000000  1.000000
sform_xorient  Right-to-Left
sform_yorient  Anterior-to-Posterior
sform_zorient  Inferior-to-Superior
file_type      NIFTI-1+
file_code      1
descrip        FSL5.0
aux_file



Edited 1 time(s). Last edit at 01/13/2014 07:41PM by danielcuneo.
Subject Author Posted

3dretroicor fails with resp data on resampled data sets

danielcuneo January 13, 2014 06:39PM

Re: 3dretroicor fails with resp data on resampled data sets

danielcuneo January 13, 2014 08:35PM



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