Hi again,
> FSL 4.1.9 has a change to the ROI library functions, which I believe fixes the bug below,
Apparently, fslroi affects the data now in a different manner. After
reducing the image volume with fslroi, mm coordinates refer to the same
location in the brain as in the full volume. However, when I resample
both images to overlay them with an anatomical image (flirt
transformation with the identity matrix), the smaller volume is shifted
while the large image is matching the brain reasonable well (I pasted
some lines of the header for the full volume and the fslroi'd volume below).
Is this now the expected behaviour? I would expect, that the same
transformation of both, a full image volume and a smaller volume after
using fslroi, does not change the spatial alignment to a reference
image. Am I wrong and everything is working in the intended way?
Thanks for all the support,
wolf
____________________________________________
EPI_full_brain.nii.gz
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 121
dim2 163
dim3 121
[...]
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -1.399333 -0.021830 -0.037304 84.721703
qto_xyz:2 -0.029030 1.369892 0.287320 -94.615875
qto_xyz:3 -0.032021 -0.287955 1.369698 -45.274288
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 -1.399333 -0.021831 -0.037297 84.721703
sto_xyz:2 -0.029030 1.369893 0.287320 -94.615875
sto_xyz:3 -0.032015 -0.287956 1.369698 -45.274288
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
____________________________________________
EPI_red_brain.nii.gz
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 99
dim2 74
dim3 90
[...]
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -1.399333 -0.021830 -0.037303 63.992867
qto_xyz:2 -0.029030 1.369892 0.287320 -79.045303
qto_xyz:3 -0.032021 -0.287955 1.369698 -10.468461
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 -1.399333 -0.021831 -0.037297 63.993023
sto_xyz:2 -0.029030 1.369893 0.287320 -79.045303
sto_xyz:3 -0.032015 -0.287956 1.369698 -10.468370
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
On 26/10/11 14:29, Matthew Webster wrote:
> Hello Wolf,
> FSL 4.1.9 has a change to the ROI library functions, which I believe fixes the bug below,
>
> Many Regards
>
> Matthew
>> Hi,
>>
>> Thanks for the new version.
>>
>> There was recently a discussing about a minor bug with fslroi (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;2163c160.1109). The problem was, that it does not change the qform. Was this fixed with the current release, or is the suggested workaround still required? I guess applying such a correction when fslroi itself is already modifying the qform is not such a good idea...
>>
>> thanks for the support,
>> wolf
>>
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