Re: [HCP-Users] Extraction of mean myelination values from a custom roi
Hi Timothy, sorry for the late response. Thanks, this helped. I ran the command you wrote but used the value of 1.3(=p-value of 0.05). After this, when using cifti-stats with the created ROI the output values were different from when I used the whole output of PALM as ROI. Thanks again for your help! Lisa On 21 October 2017 at 06:34, Timothy Coalson <tsc...@mst.edu> wrote: > I think I misunderstood the problem, a single ROI should work fine. > > Are you talking about thresholding in the display settings (the wrench > icon on the layer in wb_view)? That doesn't actually threshold the file > into an ROI, that just changes the display of it to not color the > outside-threshold values. To actually threshold it to make an ROI file, > you need to do something like this: > > wb_command -cifti-math 'x > 5.3' ROI.dscalar.nii -var x > inputstatistic.dscalar.nii > > Tim > > > On Thu, Oct 19, 2017 at 2:02 AM, Lisa Kramarenko < > lisa.kramare...@gmail.com> wrote: > >> Hey Timothy, >> >> thanks for your response. Before continuing with the questions about the >> exact implementation I am not very sure as to why you refer to my ROIs in >> plural. As ROI, I used the dscalar file which I got as an output of PALM, >> i.e. it is a file showing where there was a significant difference between >> two groups. I threshholded it in the Workbench and saved the changes, so >> that the file now only shows the really significantly different areas. In >> my understanding this is only one ROI/one map. Do I understand it wrongly? >> I can attach the file if you want. >> >> I just want to see what the mean myelination in these exact areas that >> turned out to be significant is in the groups I compared. Hope it makes >> sense. >> >> Thanks again! >> >> Lisa >> >> On 18 October 2017 at 01:12, Timothy Coalson <tsc...@mst.edu> wrote: >> >>> The -cifti-parcellate command is currently the easier way to do this, if >>> your ROIs don't overlap. The -roi option to -cifti-stats currently uses >>> only the first map, and only tests for whether the value is greater than 0, >>> so probably the first map in your roi input is actually all positive. Also >>> note that MEAN does not take a dash in front of it, which would cause an >>> error. >>> >>> Tim >>> >>> >>> On Tue, Oct 17, 2017 at 5:57 PM, Glasser, Matthew <glass...@wustl.edu> >>> wrote: >>> >>>> It might only be using the first ROI. Tim will know better what is the >>>> issue. You might try converting the ROIs to a parcellation and then >>>> parcellating the myelin map and converting the parcellated file to text or >>>> whatever you need. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa >>>> Kramarenko <lisa.kramare...@gmail.com> >>>> Date: Tuesday, October 17, 2017 at 7:11 AM >>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>> Subject: [HCP-Users] Extraction of mean myelination values from a >>>> custom roi >>>> >>>> Dear experts, >>>> >>>> I have a question about extracting average myelination value from a >>>> custom roi. What I did was the following: >>>> >>>> wb_command -cifti-stats merged_myelin_maps_group1.dscalar.nii -reduce >>>> -MEAN -roi file_with_significant_differences_between_the_groups_thresho >>>> lded_at_1.3.dscalar.nii >>>> >>>> I get a series of numbers (for every of the merged maps), however they >>>> don't change if I omit the roi part which leads me to believe that the >>>> average is calculated across the whole cortex and not specifically in areas >>>> I want to specify. >>>> >>>> What would be the best way to find out the mean myelination values in a >>>> specific roi (which is defined by the file with significantly different >>>> areas)? >>>> >>>> I hope you understand what I mean. >>>> >>>> Thanks a lot for your help! >>>> >>>> Best, >>>> Lisa >>>> >>>> ___ >>>> 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] Extraction of mean myelination values from a custom roi
I think I misunderstood the problem, a single ROI should work fine. Are you talking about thresholding in the display settings (the wrench icon on the layer in wb_view)? That doesn't actually threshold the file into an ROI, that just changes the display of it to not color the outside-threshold values. To actually threshold it to make an ROI file, you need to do something like this: wb_command -cifti-math 'x > 5.3' ROI.dscalar.nii -var x inputstatistic.dscalar.nii Tim On Thu, Oct 19, 2017 at 2:02 AM, Lisa Kramarenko <lisa.kramare...@gmail.com> wrote: > Hey Timothy, > > thanks for your response. Before continuing with the questions about the > exact implementation I am not very sure as to why you refer to my ROIs in > plural. As ROI, I used the dscalar file which I got as an output of PALM, > i.e. it is a file showing where there was a significant difference between > two groups. I threshholded it in the Workbench and saved the changes, so > that the file now only shows the really significantly different areas. In > my understanding this is only one ROI/one map. Do I understand it wrongly? > I can attach the file if you want. > > I just want to see what the mean myelination in these exact areas that > turned out to be significant is in the groups I compared. Hope it makes > sense. > > Thanks again! > > Lisa > > On 18 October 2017 at 01:12, Timothy Coalson <tsc...@mst.edu> wrote: > >> The -cifti-parcellate command is currently the easier way to do this, if >> your ROIs don't overlap. The -roi option to -cifti-stats currently uses >> only the first map, and only tests for whether the value is greater than 0, >> so probably the first map in your roi input is actually all positive. Also >> note that MEAN does not take a dash in front of it, which would cause an >> error. >> >> Tim >> >> >> On Tue, Oct 17, 2017 at 5:57 PM, Glasser, Matthew <glass...@wustl.edu> >> wrote: >> >>> It might only be using the first ROI. Tim will know better what is the >>> issue. You might try converting the ROIs to a parcellation and then >>> parcellating the myelin map and converting the parcellated file to text or >>> whatever you need. >>> >>> Peace, >>> >>> Matt. >>> >>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa >>> Kramarenko <lisa.kramare...@gmail.com> >>> Date: Tuesday, October 17, 2017 at 7:11 AM >>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>> Subject: [HCP-Users] Extraction of mean myelination values from a >>> custom roi >>> >>> Dear experts, >>> >>> I have a question about extracting average myelination value from a >>> custom roi. What I did was the following: >>> >>> wb_command -cifti-stats merged_myelin_maps_group1.dscalar.nii -reduce >>> -MEAN -roi file_with_significant_differences_between_the_groups_thresho >>> lded_at_1.3.dscalar.nii >>> >>> I get a series of numbers (for every of the merged maps), however they >>> don't change if I omit the roi part which leads me to believe that the >>> average is calculated across the whole cortex and not specifically in areas >>> I want to specify. >>> >>> What would be the best way to find out the mean myelination values in a >>> specific roi (which is defined by the file with significantly different >>> areas)? >>> >>> I hope you understand what I mean. >>> >>> Thanks a lot for your help! >>> >>> Best, >>> Lisa >>> >>> ___ >>> 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] Extraction of mean myelination values from a custom roi
Hey Timothy, thanks for your response. Before continuing with the questions about the exact implementation I am not very sure as to why you refer to my ROIs in plural. As ROI, I used the dscalar file which I got as an output of PALM, i.e. it is a file showing where there was a significant difference between two groups. I threshholded it in the Workbench and saved the changes, so that the file now only shows the really significantly different areas. In my understanding this is only one ROI/one map. Do I understand it wrongly? I can attach the file if you want. I just want to see what the mean myelination in these exact areas that turned out to be significant is in the groups I compared. Hope it makes sense. Thanks again! Lisa On 18 October 2017 at 01:12, Timothy Coalson <tsc...@mst.edu> wrote: > The -cifti-parcellate command is currently the easier way to do this, if > your ROIs don't overlap. The -roi option to -cifti-stats currently uses > only the first map, and only tests for whether the value is greater than 0, > so probably the first map in your roi input is actually all positive. Also > note that MEAN does not take a dash in front of it, which would cause an > error. > > Tim > > > On Tue, Oct 17, 2017 at 5:57 PM, Glasser, Matthew <glass...@wustl.edu> > wrote: > >> It might only be using the first ROI. Tim will know better what is the >> issue. You might try converting the ROIs to a parcellation and then >> parcellating the myelin map and converting the parcellated file to text or >> whatever you need. >> >> Peace, >> >> Matt. >> >> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa >> Kramarenko <lisa.kramare...@gmail.com> >> Date: Tuesday, October 17, 2017 at 7:11 AM >> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Subject: [HCP-Users] Extraction of mean myelination values from a custom >> roi >> >> Dear experts, >> >> I have a question about extracting average myelination value from a >> custom roi. What I did was the following: >> >> wb_command -cifti-stats merged_myelin_maps_group1.dscalar.nii -reduce >> -MEAN -roi file_with_significant_differences_between_the_groups_ >> thresholded_at_1.3.dscalar.nii >> >> I get a series of numbers (for every of the merged maps), however they >> don't change if I omit the roi part which leads me to believe that the >> average is calculated across the whole cortex and not specifically in areas >> I want to specify. >> >> What would be the best way to find out the mean myelination values in a >> specific roi (which is defined by the file with significantly different >> areas)? >> >> I hope you understand what I mean. >> >> Thanks a lot for your help! >> >> Best, >> Lisa >> >> ___ >> 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] Extraction of mean myelination values from a custom roi
The -cifti-parcellate command is currently the easier way to do this, if your ROIs don't overlap. The -roi option to -cifti-stats currently uses only the first map, and only tests for whether the value is greater than 0, so probably the first map in your roi input is actually all positive. Also note that MEAN does not take a dash in front of it, which would cause an error. Tim On Tue, Oct 17, 2017 at 5:57 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > It might only be using the first ROI. Tim will know better what is the > issue. You might try converting the ROIs to a parcellation and then > parcellating the myelin map and converting the parcellated file to text or > whatever you need. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa > Kramarenko <lisa.kramare...@gmail.com> > Date: Tuesday, October 17, 2017 at 7:11 AM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] Extraction of mean myelination values from a custom > roi > > Dear experts, > > I have a question about extracting average myelination value from a custom > roi. What I did was the following: > > wb_command -cifti-stats merged_myelin_maps_group1.dscalar.nii -reduce > -MEAN -roi file_with_significant_differences_between_the_ > groups_thresholded_at_1.3.dscalar.nii > > I get a series of numbers (for every of the merged maps), however they > don't change if I omit the roi part which leads me to believe that the > average is calculated across the whole cortex and not specifically in areas > I want to specify. > > What would be the best way to find out the mean myelination values in a > specific roi (which is defined by the file with significantly different > areas)? > > I hope you understand what I mean. > > Thanks a lot for your help! > > Best, > Lisa > > ___ > 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] Extraction of mean myelination values from a custom roi
It might only be using the first ROI. Tim will know better what is the issue. You might try converting the ROIs to a parcellation and then parcellating the myelin map and converting the parcellated file to text or whatever you need. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Tuesday, October 17, 2017 at 7:11 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Extraction of mean myelination values from a custom roi Dear experts, I have a question about extracting average myelination value from a custom roi. What I did was the following: wb_command -cifti-stats merged_myelin_maps_group1.dscalar.nii -reduce -MEAN -roi file_with_significant_differences_between_the_groups_thresholded_at_1.3.dscalar.nii I get a series of numbers (for every of the merged maps), however they don't change if I omit the roi part which leads me to believe that the average is calculated across the whole cortex and not specifically in areas I want to specify. What would be the best way to find out the mean myelination values in a specific roi (which is defined by the file with significantly different areas)? I hope you understand what I mean. Thanks a lot for your help! Best, Lisa ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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] Extraction of mean myelination values from a custom roi
Dear experts, I have a question about extracting average myelination value from a custom roi. What I did was the following: wb_command -cifti-stats merged_myelin_maps_group1.dscalar.nii -reduce -MEAN -roi file_with_significant_differences_between_the_groups_thresholded_at_1.3.dscalar.nii I get a series of numbers (for every of the merged maps), however they don't change if I omit the roi part which leads me to believe that the average is calculated across the whole cortex and not specifically in areas I want to specify. What would be the best way to find out the mean myelination values in a specific roi (which is defined by the file with significantly different areas)? I hope you understand what I mean. Thanks a lot for your help! Best, Lisa ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
