Dear Sir / madam, After going through some publications i have found that Subcortical ROIs, such as the brainstem and thalamus can be extracted from the Harvard–Oxford subcortical structural atlas, For the cortical core region of the PIVC many publications have used ,Jue-lich histological (cyto- and myelo-architectonic) atlas.
Could you please let me know how could i possibly do the registration of multiple images from HCP data to these common standard space atlases to perform group connectivity analysis, in FSL you would use 2-stage registration with FLIRT & FNIRT , is there any alternative with Workbench?. Thanks Vasudev On 28 June 2016 at 22:04, Timothy Coalson <[email protected]> wrote: > Connectome Workbench doesn't include data (by design, so there are never > hidden inputs to an operation). Someone else can probably point you to > atlases containing the regions you want. > > Tim > > > On Tue, Jun 28, 2016 at 9:44 AM, Dev vasu < > [email protected]> wrote: > >> Dear madam, >> >> Is there any way to extract the ROIs from probabilistic atlases included >> within workbench,I would like to define Vestibulospinal tract as seed and >> Parieto insular vestibular cortex(PIVC) as target mask with Brain stem, >> Medial and laterall vestibular nuclei as way points. >> >> >> Is there any way i can obtain co-ordinates for these regions ?. >> >> >> Thanks >> Vasudev >> >> On 28 June 2016 at 16:05, Dev vasu <[email protected]> >> wrote: >> >>> Dear madam, >>> >>> >>> I would like to study the distribution of vestibular tracks from >>> thalamus to vestibular cortex for which by i would like to define a ROI >>> mask ( seed mask) from all voxels in the right thalamus and using >>> vestibular cortex region as target mask. >>> >>> >>> I would first like to create a volume mask and convert them into >>> cortical surface masks to perform tractography.this is my main goal. I have >>> 30 subjects ( male ) -from HCP , I have finished with Pre-processing of all >>> the data now i would like to perform analysis. >>> >>> If you have any other better way to map vestibular thalamic connectivity >>> , i would really appreciate your suggestions. >>> >>> >>> Thanks >>> Vasudev >>> >>> >>> On 28 June 2016 at 15:50, Dierker, Donna <[email protected]> wrote: >>> >>>> Hi Vasudev, >>>> >>>> You'll probably need to be more specific about your goals, as there are >>>> many ways to define a ROI. The most common is to threshold some functional >>>> map (dscalar.nii or func.gii/nifti) at something like p=.05, but there are >>>> many other ways to do it. >>>> >>>> If you need to draw a ROI manually in workbench, you can load something >>>> like a curvature, myelin, or functional map and display it in multiple tabs >>>> or windows (e.g., midthickness surface in one view, very inflated in >>>> another). You can draw borders on the very inflated map, and see how they >>>> look on the midthickness. Adjust as needed. >>>> >>>> Then wb_command -border-to-rois can fill in the vertices encircled by >>>> the borders to create a cortical ROI. >>>> >>>> For drawing volumetric ROIs, there are all sorts of options out there. >>>> >>>> Donna >>>> >>>> >>>> On Jun 27, 2016, at 9:45 AM, Dev vasu < >>>> [email protected]> wrote: >>>> >>>> > Dear Sir, >>>> > >>>> > I would like to know how to define structural and functional ROI in >>>> workbench,should we define the ROI manually ? or is there any alternate >>>> procedure for it, I am aware of process in SPM but not in workbench. >>>> > >>>> > >>>> > >>>> > Thanks >>>> > Vasudev >>>> > _______________________________________________ >>>> > HCP-Users mailing list >>>> > [email protected] >>>> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> > >>>> >>>> >>> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
