Vasudev, I must repeat Mike Harms' advice: Start separate threads with appropriate subject lines, rather than pile disparate topics onto existing threads, or combine separate topics into a single thread. Having a subject line that accurately reflects your issue is especially key to getting the attention of experts who might be, say, at the OHBM conference, with no shortage of distractions.
With 1200 subjects and thousands of large files, it was necessary to keep packages to the minimum of what most users would want/need. For the Juelich atlas, I'd read the references cited here for insight: http://neuro.debian.net/pkgs/fsl-juelich-histological-atlas.html Good luck! Donna On Jun 29, 2016, at 10:04 AM, Dev vasu <[email protected]> wrote: > 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
