PMC:3839092 / 10019-13540
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3839092","sourcedb":"PMC","sourceid":"3839092","source_url":"http://www.ncbi.nlm.nih.gov/pmc/3839092","text":"Data acquisition and analysis\nDiffusion data were acquired on a Siemens Allegra 3.0 T scanner at the NYU Center for Brain Imaging using a single-channel head coil. Diffusion-weighted echo-planar images (EPI) were acquired along 12 diffusion gradient directions for acquisition of 35 slices through the whole brain (TR = 6000 ms, TE = 82 ms, flip angle = 90°, b value = 1000 s/mm2, FOV = 192 mm, 128 × 128 matrix, slice thickness = 2.5 mm, with four averages). High-resolution T1-weighted anatomical images were acquired using a magnetization-prepared gradient echo sequence (TR = 2530 ms; TE = 3.25 ms; TI = 1100 ms; flip angle = 7°; 128 slices; FOV = 256 mm; acquisition voxel size = 1.3 mm × 1 mm × 1.3 mm).\nAll preprocessing was performed using FMRIB’s Software Library (FSL; Oxford, UK): FMRIB’s Diffusion Toolbox (FDT). Preprocessing began with eddy current correction to correct for gradient-coil distortions and small head motions, using affine registration to a b0 reference volume. A diffusion tensor model was fitted to each voxel along the principal λ1, λ2, λ3 directions to generate FA, MD, RD, and AD. We then implemented FSL’s tract-based spatial statistics pipeline [TBSS; (28)], in which a non-linear registration aligned each subject to the FMRIB58_FA template in 1 mm × 1 mm × 1 mm standard space, and then warped each subject into standard Montreal Neurological Institute space (MNI152). A WM “skeleton” was then generated representing a single line running down the centers of all of the common WM fibers by using an FA cut-off of 0.2, and relevant diffusivity measures (i.e., FA, MD, RD, AD) were projected onto the skeleton. Group statistical analysis was then conducted only on voxels within the WM skeleton mask, therefore restricting the voxel-wise analysis only to voxels with high confidence of lying within equivalent major WM pathways in each individual.\nIn order to assess differences in FA, MD, RD, and AD between the MDD and HC groups, we used FSL’s Randomise with 5000 permutations to perform voxel-wise independent samples t-tests using voxel-based thresholding while controlling for age and sex. Group comparisons did not withstand stringent correction for multiple comparisons using family-wise error correction (FWE; implemented by Randomise) or FDR correction (implemented by FSL’s FDR program). As such, we performed a second, more exploratory analysis in which we accepted clusters of at least 10 contiguous voxels at p \u003c 0.001.\nTo investigate relationships with depression severity, anhedonia, and irritability, Randomise was again used to perform a series of one-sample t-tests using the score for each category, respectively, while controlling for age and gender. Due to the low variability in scores in the HC group, as well as the nature of the study topic, the analysis was limited to the MDD group whose scores were normally distributed. Once again, tests did not withstand correction for multiple comparisons and we used the more exploratory approach of accepting clusters of at least 10 contiguous voxels at p \u003c 0.001. We used FSL’s cluster program to extract all clusters across the brain, and anatomical localization of each cluster was determined using the FSLView atlas toolbox and the relevant gray matter (Harvard-Oxford Cortical/Subcortical) and WM (Johns Hopkins University WM tractography) atlases. Brain imaging results were prepared for display using FSL’s tbss_fill script, which displays results superimposed upon the WM skeleton from the group TBSS analysis.","divisions":[{"label":"Title","span":{"begin":0,"end":29}}],"tracks":[{"project":"2_test","denotations":[{"id":"24324445-16624579-41737772","span":{"begin":1189,"end":1191},"obj":"16624579"}],"attributes":[{"subj":"24324445-16624579-41737772","pred":"source","obj":"2_test"}]},{"project":"NEUROSES","denotations":[{"id":"T291","span":{"begin":460,"end":464},"obj":"PATO_0000469"},{"id":"T292","span":{"begin":1803,"end":1807},"obj":"PATO_0000469"},{"id":"T293","span":{"begin":919,"end":924},"obj":"PATO_0000587"},{"id":"T294","span":{"begin":983,"end":989},"obj":"PATO_0000918"},{"id":"T295","span":{"begin":1210,"end":1216},"obj":"PATO_0001199"},{"id":"T296","span":{"begin":1540,"end":1543},"obj":"PATO_0001978"},{"id":"T297","span":{"begin":1647,"end":1652},"obj":"CHEBI_24433"},{"id":"T298","span":{"begin":2131,"end":2136},"obj":"CHEBI_24433"},{"id":"T299","span":{"begin":2754,"end":2759},"obj":"CHEBI_24433"},{"id":"T300","span":{"begin":2839,"end":2844},"obj":"CHEBI_24433"},{"id":"T301","span":{"begin":3501,"end":3506},"obj":"CHEBI_24433"},{"id":"T302","span":{"begin":1949,"end":1952},"obj":"CHEBI_566274"},{"id":"T303","span":{"begin":2835,"end":2838},"obj":"CHEBI_566274"},{"id":"T304","span":{"begin":2118,"end":2121},"obj":"PATO_0000011"},{"id":"T305","span":{"begin":2691,"end":2694},"obj":"PATO_0000011"},{"id":"T306","span":{"begin":2118,"end":2121},"obj":"CHEBI_84123"},{"id":"T307","span":{"begin":2691,"end":2694},"obj":"CHEBI_84123"},{"id":"T308","span":{"begin":2149,"end":2152},"obj":"CHEBI_52027"},{"id":"T309","span":{"begin":2903,"end":2906},"obj":"CHEBI_52027"},{"id":"T310","span":{"begin":2192,"end":2200},"obj":"PATO_0002118"},{"id":"T311","span":{"begin":2936,"end":2944},"obj":"PATO_0002118"},{"id":"T312","span":{"begin":2413,"end":2421},"obj":"CHEBI_33731"},{"id":"T313","span":{"begin":3012,"end":3020},"obj":"CHEBI_33731"},{"id":"T314","span":{"begin":3082,"end":3089},"obj":"CHEBI_33731"},{"id":"T315","span":{"begin":3113,"end":3121},"obj":"CHEBI_33731"},{"id":"T316","span":{"begin":3176,"end":3183},"obj":"CHEBI_33731"},{"id":"T317","span":{"begin":2437,"end":2447},"obj":"PATO_0001961"},{"id":"T318","span":{"begin":3036,"end":3046},"obj":"PATO_0001961"},{"id":"T319","span":{"begin":2820,"end":2827},"obj":"PATO_0000392"},{"id":"T320","span":{"begin":2872,"end":2883},"obj":"PATO_0001566"},{"id":"T321","span":{"begin":2503,"end":2513},"obj":"PM3425"},{"id":"T322","span":{"begin":2503,"end":2513},"obj":"PM3425"}],"attributes":[{"subj":"T291","pred":"source","obj":"NEUROSES"},{"subj":"T292","pred":"source","obj":"NEUROSES"},{"subj":"T293","pred":"source","obj":"NEUROSES"},{"subj":"T294","pred":"source","obj":"NEUROSES"},{"subj":"T295","pred":"source","obj":"NEUROSES"},{"subj":"T296","pred":"source","obj":"NEUROSES"},{"subj":"T297","pred":"source","obj":"NEUROSES"},{"subj":"T298","pred":"source","obj":"NEUROSES"},{"subj":"T299","pred":"source","obj":"NEUROSES"},{"subj":"T300","pred":"source","obj":"NEUROSES"},{"subj":"T301","pred":"source","obj":"NEUROSES"},{"subj":"T302","pred":"source","obj":"NEUROSES"},{"subj":"T303","pred":"source","obj":"NEUROSES"},{"subj":"T304","pred":"source","obj":"NEUROSES"},{"subj":"T305","pred":"source","obj":"NEUROSES"},{"subj":"T306","pred":"source","obj":"NEUROSES"},{"subj":"T307","pred":"source","obj":"NEUROSES"},{"subj":"T308","pred":"source","obj":"NEUROSES"},{"subj":"T309","pred":"source","obj":"NEUROSES"},{"subj":"T310","pred":"source","obj":"NEUROSES"},{"subj":"T311","pred":"source","obj":"NEUROSES"},{"subj":"T312","pred":"source","obj":"NEUROSES"},{"subj":"T313","pred":"source","obj":"NEUROSES"},{"subj":"T314","pred":"source","obj":"NEUROSES"},{"subj":"T315","pred":"source","obj":"NEUROSES"},{"subj":"T316","pred":"source","obj":"NEUROSES"},{"subj":"T317","pred":"source","obj":"NEUROSES"},{"subj":"T318","pred":"source","obj":"NEUROSES"},{"subj":"T319","pred":"source","obj":"NEUROSES"},{"subj":"T320","pred":"source","obj":"NEUROSES"},{"subj":"T321","pred":"source","obj":"NEUROSES"},{"subj":"T322","pred":"source","obj":"NEUROSES"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#eca193","default":true},{"id":"NEUROSES","color":"#939eec"}]}]}}