Dear madam,
I have a slight confusion pertaining to HCP data, when i download HCP preprocessed data, i do not see all the files that i would generally obtain after running HCP-minimal preprocessing pipeline. Could you please let me know the reason for this. I have verified if registration was done using HOA atlas and it seems fine, could you please let me know how to register the images ( both volume and surface ) to Jue-lich histological (cyto- and myelo-architectonic) atlas. Thanks Vasudev On 29 June 2016 at 16:25, Dierker, Donna <[email protected]> wrote: > Vasudev, > > I would expect the volumes (*.nii.gz) and surfaces (*.surf.gii) under the > MNINonLinear subdirectory to already be in register with the Harvard-Oxford > Atlas (HOA). The files under this directory were all fnirted to MNI. > > You can test it yourself by overlaying the HOA volume over individual T1's > or T2's under the MNINonLinear subdirectory. > > Donna > > > On Jun 29, 2016, at 7:19 AM, Dev vasu < > [email protected]> wrote: > > > 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
