Hi Forrest,
Sorry from my part as well for the late reply.
In the meantime I have downgraded to FSL 5.0.9 where the old eddy_correct command seems to work just fine...What problems could arise if I go with this instead of the newer eddy_openmp for tractography? When running dtifit afterwards the results seem to look okay.
Also, to answer your questions:
- I did not apply any prior steps to the data - my data is a single-encoding direction dataset, so I think TOPUP is out of the question, right? so just dcm2nii and then the eddy
- the bvecs:
-0 -0.4700424563067426 -0.5771884316852347 0.6677637990258092 -0.6108900408789216 -0.1889680457014771 0.03679057954370148 0.443813693534889 0.7326297386042989 -0.6111162551227854 -0.279261232460045 0.3057036567944051 0.5413202039729733 0.7378275850490816 -0.6885765660645333 -0.467014098468295 0.5598922965830152 0.7196851993990488 -0.7404915075211436 -0.7682923038712941 0.6399694631252499 0.3942707424034287 -0.7410794373297502 -0.7043499541292001 -0.7435442832192238 -0.3767844117123791 0.2065178563836324 0.6671485555240039 0.6403044696667902 -0.7433277700549104 -0.05532777976686304 0.6668461786554045 0.6505629294471666 -0
0 0.5917009066770422 0.3553142500018258 0.7236282030481019 0.3598528560337313 0.7758507495760995 0.8153061106813484 0.6938120361583378 0.2971622380344863 0.3598761956349324 0.7930299581135309 0.8147735308302673 0.6165504610187826 0.4231150675534205 0.5264319776771538 0.7665302376051654 0.7435524533916604 0.5804157706008328 0.6696794393355899 0.3505624056022695 0.4045461691649309 0.6267325993204964 0.6683115397042908 0.2870135389188655 0.6594922299265584 0.5778732523468872 0.6002333585513155 0.7222940378480961 0.2079583740249427 0.6606629216380304 0.5789309601822158 0.7216535299120325 -0.091200661458442 0
0 -0.6549428567320946 0.7352586535022261 0.1745101215664876 -0.7052086499622692 -0.6019524287727724 -0.577860174219706 -0.5671457619379467 -0.612330250763489 -0.7050007398272504 -0.5414024818171241 -0.4926351791552509 -0.5716974703408255 -0.5259126112113922 -0.4987299802836956 -0.440827910654883 -0.3655822692933153 -0.3810127806058409 0.05658358679480708 0.5355678815369941 0.6532850763405187 0.6721286435580921 0.06450571264673748 0.6492413614360725 0.1105075949447791 0.7239448085141673 0.7727032341172843 0.1822200901791821 0.7394346254890098 0.1048249270773547 0.8134972604657826 0.185829003180869 0.7539564178055133 0
- the bvals:
0 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800
- output of fslhd:
sizeof_hdr 348
data_type INT16
dim0 4
dim1 128
dim2 128
dim3 60
dim4 34
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.000000
pixdim1 1.750000
pixdim2 1.750000
pixdim3 2.000000
pixdim4 9.021528
pixdim5 1.000000
pixdim6 1.000000
pixdim7 81391.289062
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 -1.742647 -0.066802 -0.166478 117.844009
qto_xyz:2 -0.090016 1.724087 0.327111 -105.056290
qto_xyz:3 -0.132586 -0.292512 1.966033 41.381149
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 -1.742647 -0.066802 -0.166478 117.844009
sto_xyz:2 -0.090016 1.724086 0.327111 -105.056290
sto_xyz:3 -0.132586 -0.292512 1.966033 41.381149
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 TE=59.77899933;sec=81391.2900
aux_file
Best,
Sabina
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