Dear Jesper!

Thank you for your comment.

Yes, I did not see that the warpfields were not goodlooking.

However I found that they have very different dimensions and orientation (see fslhd on them below) even though they were created by similar fnirt calls...

Would this give an explanation?

Thank you again!
With best wishes,  Markus

filename       T1_2_FA1_warpcoef.nii.gz
=============================
sizeof_hdr     348
data_type      FLOAT32
dim0           4
dim1           128
dim2           128
dim3           64
dim4           3
dim5           1
dim6           1
dim7           1
vox_units      mm
time_units     s
datatype       16
nbyper         4
bitpix         32
pixdim0        0.0000000000
pixdim1        1.7968750000
pixdim2        1.7968750000
pixdim3        2.0000000000
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      0.000000
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      -1.796875  0.000000  -0.000000  117.711868
qto_xyz:2      0.000000  1.796875  -0.000000  -102.796608
qto_xyz:3      0.000000  0.000000  2.000000  -51.474575
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      -1.796875  0.000000  -0.000000  117.711868
sto_xyz:2      0.000000  1.796875  -0.000000  -102.796608
sto_xyz:3      0.000000  0.000000  2.000000  -51.474575
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        FSL4.0
aux_file


filename       T1_2MNI_warpcoef.nii.gz
============================
sizeof_hdr     348
data_type      FLOAT32
dim0           4
dim1           21
dim2           24
dim3           21
dim4           3
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        1.0000000000
pixdim5        0.0000000000
pixdim6        0.0000000000
pixdim7        0.0000000000
vox_offset     352
cal_max        0.0000
cal_min        0.0000
scl_slope      0.000000
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    2007
intent_name
intent_p1      2.000000
intent_p2      2.000000
intent_p3      2.000000
qform_name     Scanner Anat
qform_code     1
qto_xyz:1      5.000000  0.000000  0.000000  91.000000
qto_xyz:2      0.000000  5.000000  0.000000  109.000000
qto_xyz:3      0.000000  0.000000  5.000000  91.000000
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     Scanner Anat
sform_code     1
sto_xyz:1      1.113220  -0.000225  -0.000151  -6.675520
sto_xyz:2      -0.033047  1.067810  0.293899  -29.982800
sto_xyz:3      0.021964  -0.324781  1.023180  -41.905102
sto_xyz:4      0.000000  0.000000  0.000000  1.000000
sform_xorient  Left-to-Right
sform_yorient  Posterior-to-Anterior
sform_zorient  Inferior-to-Superior
file_type      NIFTI-1+
file_code      1
descrip        FSL4.0
aux_file

2009/7/1 Jesper Andersson <[log in to unmask]>

Dear Markus,

I am having trouble with making work a convertwarp command.

I have warped dti_FA to T1 and T1 to MNI_2mm.

I then inverted each  warp_coef and would like to combine both into a MNI_2FA_warpcoef in order to apply this one to pieces out of an MNI_Atlas.

I used the following command:

convertwarp --ref=dtifit/dti_FA.nii.gz --warp1=Warps/T1_2_FA_warpcoef.nii.gz --warp2=T1/MNI_2T1_warpcoef.nii.gz --out=Warps/MNI_2FA_warpcoef.nii.gz

your command looks OK. What does the individual inverted warpfields look like? Are they both OK?

Jesper

--
Dr. med. Markus Gschwind, M.D.
Laboratory for Neurology and Imaging of Cognition
Dept of Neurosciences
University Medical Center (CMU)
1 Michel-Servet - 1211 GENEVA - CH

Tel 0041 (0) 22 379 5324
Fax 0041 (0) 22 379 5402
email: [log in to unmask]
http://labnic.unige.ch