Re: [HCP-Users] Define the ROI and signal extraction in ROI
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 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 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 > 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 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 > > 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 > > 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 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 > > > > >
Re: [HCP-Users] Define the ROI and signal extraction in ROI
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 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 < > vasudevamurthy.devulapa...@gmail.com> 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 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 < > vasudevamurthy.devulapa...@gmail.com> 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 > 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 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 < > vasudevamurthy.devulapa...@gmail.com> 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 > > > HCP-Users@humanconnectome.org > > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > > > > > > > ___ > > HCP-Users mailing list > > HCP-Users@humanconnectome.org > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > > > > ___
Re: [HCP-Users] Define the ROI and signal extraction in ROI
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 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 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 > 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 > 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 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 > 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 > > HCP-Users@humanconnectome.org > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Define the ROI and signal extraction in ROI
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 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 < > vasudevamurthy.devulapa...@gmail.com> 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 >> 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 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 < vasudevamurthy.devulapa...@gmail.com> 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 > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > >>> >> ___ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Define the ROI and signal extraction in ROI
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 < vasudevamurthy.devulapa...@gmail.com> 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 > 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 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 < >>> vasudevamurthy.devulapa...@gmail.com> 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 >>> > HCP-Users@humanconnectome.org >>> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> > >>> >>> >> > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Define the ROI and signal extraction in ROI
The freesurfer segmentation includes a right thalamus definition, among other things, and if you are working in a standard grayordinate space, you can use -cifti-separate with "-volume THALAMUS_RIGHT data_rthal.nii.gz -roi roi_rthal.nii.gz". Subcortical masks will never be able to be meaningfully mapped onto cortex, they lie outside of cortex. Pick a separate surface ROI of interest or just track to the entire surface. Tim On Tue, Jun 28, 2016 at 9:05 AM, Dev vasu < vasudevamurthy.devulapa...@gmail.com> 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 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 < >> vasudevamurthy.devulapa...@gmail.com> 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 >> > HCP-Users@humanconnectome.org >> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > >> >> > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Define the ROI and signal extraction in ROI
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 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 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 < >> vasudevamurthy.devulapa...@gmail.com> 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 >> > HCP-Users@humanconnectome.org >> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > >> >> > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Define the ROI and signal extraction in ROI
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 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 < > vasudevamurthy.devulapa...@gmail.com> 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 > > HCP-Users@humanconnectome.org > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Define the ROI and signal extraction in ROI
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 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 > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Define the ROI and signal extraction in ROI
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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
