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Dear Anderson, Thank you very much for your reply! I will resample my results to 1mm (I could not do this in the ICA, as I had too much data and the pc could not handle it). Thank you for your help! Best Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg [log in to unmask] www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================ ________________________________________ Van: FSL - FMRIB's Software Library [[log in to unmask]] namens Anderson M. Winkler [[log in to unmask]] Verzonden: dinsdag 11 juni 2013 5:13 Aan: [log in to unmask] Onderwerp: Re: [FSL] autoaq problem PS: not 27 mL (!), much less than that... Still, 3 mm is quite a big voxel! 2013/6/10 Anderson M. Winkler <[log in to unmask]<mailto:[log in to unmask]>> Hi Heidi, I suggest that you resample your data to 1 or 2mm, instead of the atlas. It's much less error prone from you side, as you'd have just one set of images to manipulate (yours), rather than two (yours and the atlas). Plus, by resampling the atlas, you'd have to make sure that the 'atlasquery' command locates and uses it correctly, and also deal yourself even with minor issues as the fact that 182 and 218 (dimensions of the 1 mm atlas) aren't divisible by 3. Save yourself the hassle and use your data with 2 or 1 mm resolution. And if you could do it from the very beginning of the analysis, even better, as each 3mm voxel has volume of 27 mL -- a very coarse resolution to conclude anything. Finally, remember that the use of autoaq is just for a quick, overall anatomic reference. You can still get the same information if you look at your images side-by-side with the atlas, or follow an anatomy textbook. All the best, Anderson 2013/6/10 Jacobs H (NP) <[log in to unmask]<mailto:[log in to unmask]>> Dear Anderson, I have been using autoaq for my resting state analyses. Looking at the results in fslview, shows that the results are localized in posterior regions. However the autoaq command shows that the results are in the frontal areas. I think this difference stems from a difference in image dimensions. In melodic I resampeled everything into 3mm. The dimensions of my dual regression images are provided below. I created an atlas that fits these dimensions (with applying FLIRT on the Harvard Oxford atlas). Unfortunately, autoaq does not provide me the correct output. I am not sure which atlas it uses or whether I can tell it to use the one that I created. Any ideas how I can solve this? Should I warp my dual regression to fit the 1mm atlas? How can I do that? Thanks! Best Heidi sizeof_hdr 348 data_type FLOAT32 dim0 3 dim1 60 dim2 72 dim3 60 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units s datatype 16 nbyper 4 bitpix 32 pixdim0 0.0000000000 pixdim1 3.0000000000 pixdim2 3.0000000000 pixdim3 3.0000000000 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 MNI_152 qform_code 4 qto_xyz:1 -3.000000 0.000000 -0.000000 90.000000 qto_xyz:2 0.000000 3.000000 -0.000000 -126.000000 qto_xyz:3 0.000000 0.000000 3.000000 -72.000000 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 MNI_152 sform_code 4 sto_xyz:1 -3.000000 0.000000 0.000000 90.000000 sto_xyz:2 0.000000 3.000000 0.000000 -126.000000 sto_xyz:3 0.000000 0.000000 3.000000 -72.000000 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 FSL4.1 aux_file ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg [log in to unmask]<mailto:[log in to unmask]> www.maastrichtuniversity.nl<http://www.maastrichtuniversity.nl> www.heidijacobs.nl<http://www.heidijacobs.nl> Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090<tel:%2B31%2043%2038%2084%20090> F +31 43 38 84 092<tel:%2B31%2043%2038%2084%20092> ================================================