Re: [caret-users] mapping ALE on surface: error for number of nodes
Could you zip up the Output spec file and its contents and upload the zip file here: http://pulvinar.wustl.edu/cgi-bin/upload.cgi Also, do you already have a spec file loaded when you select Attributes: Map volume to surface? If so, try this without loading a spec file first. On May 7, 2014, at 2:09 PM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: I understand that the map I see is in fact the myelin smooting something. So, ine the spec file, when I go to metric open my metric file, I have a Choose Column to load window but no column has been loaded, and when I click ok, I receive the same error messag: Error PDHCEM_Conte69_LEFT_midthickness_164k_fs_LR_7_May_2014_14_58_48.metric: contains a different number of nodes than Conte69.L.midthickness.164k_fs_LR.coord.gii Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Wed, May 7, 2014 at 2:52 PM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Ok I see an overlay! I didn't know I had to use Scene. So that's good! But the problem now is that I the overlay is not related to my statistical data, as you can see with the screen shot of my file in Mango vs in Caret. Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Wed, May 7, 2014 at 2:20 PM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Hi, My volume is in Tal space. Is this a problem? Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Wed, May 7, 2014 at 11:30 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Another thought occurred to me: If you select a 32k version of the Conte69 atlas as your spec file, then you'll get an error when you try to open the 164k vertex metric file. I'm sure there is a way to downsample the metric file, and there are also mapping features in Workbench's wb_command, if you want to map directly to 32k mesh surfaces. But we don't have a 32k version of Conte69 in caret5. On May 7, 2014, at 9:58 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Audrey-Anne, Erin and I tried to do that, but you can't see the menu picks very clearly in the video: https://www.youtube.com/watch?v=jED8sg9szdU But here are the steps: Download conte69 atlas: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8293720archive_name=Conte69_atlas_v2.LR.164k_fs_LR.c5.zip Unpack and cd to the Conte69_164k_fs_LR.c5 directory. Launch caret5. Cancel when spec file dialog comes up. Attributes: Map volume to surface Data mapping type: Metric; Next Add volumes from disk; select volume in MNI space; next Map to spec file with atlas Note: If you don't see this, then your caret installation is incomplete or confused about its parent directory. Launch from command line. Output spec file: select Conte69_atlas-v2.L.164k_fs_LR.c5.spec Space: FNIRT Atlas: Conte69 Map LEFT midthickness... Next Accept default metric filename Mapping Algorithm: Enclosing and interpolated are the most popular Next Close when Summary appears File: Open Spec File: Conte69_atlas-v2.L.164k_fs_LR.c5.spec Load scenes Double-click first scene (Conte69 midthickness and inflated...) Toolbar: Spec: Metric: map_data_0_Conte69... Erase all existing columns Toolbar: D/C: Page Selection: Overlay/underlay Surface Primary overlay Data type metric metric You should see it. Donna On May 6, 2014, at 7:36 PM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Hi Donna, As you suggested, I tried with the Conte69 atlas (164k and 74k), but same results. The metric file is recorded in the spec file, but the same error shows about different number of nodes. Thanks for paying attention to my problem. Would it be possible for you to make an online demonstration, with a screen sharing or a screen cast tool? In this way, we may find a way to solve the issue faster. Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Tue, May 6, 2014 at 9:50 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Audrey, I will look at this more closely later, but this is the step where you should be downloading the Conte69 atlas and using one of its visualization specs instead of this spec out of the distribution directory: 8. select in fmri_mapping_files Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you suggested The Conte69 atlas is here: http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas I wonder if your writing to the fmri_mapping_files that are intended to be read-only might cause trouble. Also, I would not expect to find a SPHERE or CMW configuration in that fmri_mapping_files spec. Will look more at this later, but here are some hints as to what looks
Re: [caret-users] mapping ALE on surface: error for number of nodes
Hi Audrey-Anne, Erin and I tried to do that, but you can't see the menu picks very clearly in the video: https://www.youtube.com/watch?v=jED8sg9szdU But here are the steps: Download conte69 atlas: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8293720archive_name=Conte69_atlas_v2.LR.164k_fs_LR.c5.zip Unpack and cd to the Conte69_164k_fs_LR.c5 directory. Launch caret5. Cancel when spec file dialog comes up. Attributes: Map volume to surface Data mapping type: Metric; Next Add volumes from disk; select volume in MNI space; next Map to spec file with atlas Note: If you don't see this, then your caret installation is incomplete or confused about its parent directory. Launch from command line. Output spec file: select Conte69_atlas-v2.L.164k_fs_LR.c5.spec Space: FNIRT Atlas: Conte69 Map LEFT midthickness... Next Accept default metric filename Mapping Algorithm: Enclosing and interpolated are the most popular Next Close when Summary appears File: Open Spec File: Conte69_atlas-v2.L.164k_fs_LR.c5.spec Load scenes Double-click first scene (Conte69 midthickness and inflated...) Toolbar: Spec: Metric: map_data_0_Conte69... Erase all existing columns Toolbar: D/C: Page Selection: Overlay/underlay Surface Primary overlay Data type metric metric You should see it. Donna On May 6, 2014, at 7:36 PM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Hi Donna, As you suggested, I tried with the Conte69 atlas (164k and 74k), but same results. The metric file is recorded in the spec file, but the same error shows about different number of nodes. Thanks for paying attention to my problem. Would it be possible for you to make an online demonstration, with a screen sharing or a screen cast tool? In this way, we may find a way to solve the issue faster. Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Tue, May 6, 2014 at 9:50 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Audrey, I will look at this more closely later, but this is the step where you should be downloading the Conte69 atlas and using one of its visualization specs instead of this spec out of the distribution directory: 8. select in fmri_mapping_files Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you suggested The Conte69 atlas is here: http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas I wonder if your writing to the fmri_mapping_files that are intended to be read-only might cause trouble. Also, I would not expect to find a SPHERE or CMW configuration in that fmri_mapping_files spec. Will look more at this later, but here are some hints as to what looks amiss. Donna On May 5, 2014, at 10:28 AM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Here the attached image Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Mon, May 5, 2014 at 11:23 AM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Dear Donna, It is not a read-only issue since the spec files are modified when I do the mapping. Here is exactly what I did: 1. open CARET v5.65 2. Attributes Map volume(s) to surface(s) 3. chose Metric for Data mapping type 4. Enable entry of volume threshold 5. Add volumes from disk -- selected my ALE map, which is a nifti image, in Talairach format 6. Entered the volume thresholding in the pop-up window (positive: 0.028; negative: 0.00) 7. Map to spec file with Atlas 8. select in fmri_mapping_files Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you suggested 9. Space : FNIRT; Atlas: Conte69 Map LEFT midthickness (164k_LR nodes) 10. idem 8 and 9, but with RIGHT 11. renamed by data files (L and R) 12. Mapping algorith: METRIC_ENCLOSING_VOXEL 13. ok (or next), heard a bip like there was an error, but the summary shows 14. Close 15. Open spec file Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec 16. check my metric file (please see joint image) load 17. Got this error message Error PDHCEM_Conte69_LEFT_midthickness_164k_fs_LR_5_May_2014_11_13_13.metric: Error PDHCEM_Conte69_LEFT_midthickness_164k_fs_LR_5_May_2014_11_13_13.metric: contains a different number of nodes than Conte69.L.midthickness.164k_fs_LR.coord.gii Pressed ok 18. The brain image is displayed, but without my data on it Can you see if I did something wrong? Thanks very much Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Wed, Apr 30, 2014 at 3:22 PM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Audrey, Hmmm. I wonder if this might be because the spec file you name below is part of the Caret distribution, and it might be read-only. In fact, it's a good idea for it to be read-only. The files under data_files are
Re: [caret-users] mapping ALE on surface: error for number of nodes
Another thought occurred to me: If you select a 32k version of the Conte69 atlas as your spec file, then you'll get an error when you try to open the 164k vertex metric file. I'm sure there is a way to downsample the metric file, and there are also mapping features in Workbench's wb_command, if you want to map directly to 32k mesh surfaces. But we don't have a 32k version of Conte69 in caret5. On May 7, 2014, at 9:58 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Audrey-Anne, Erin and I tried to do that, but you can't see the menu picks very clearly in the video: https://www.youtube.com/watch?v=jED8sg9szdU But here are the steps: Download conte69 atlas: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8293720archive_name=Conte69_atlas_v2.LR.164k_fs_LR.c5.zip Unpack and cd to the Conte69_164k_fs_LR.c5 directory. Launch caret5. Cancel when spec file dialog comes up. Attributes: Map volume to surface Data mapping type: Metric; Next Add volumes from disk; select volume in MNI space; next Map to spec file with atlas Note: If you don't see this, then your caret installation is incomplete or confused about its parent directory. Launch from command line. Output spec file: select Conte69_atlas-v2.L.164k_fs_LR.c5.spec Space: FNIRT Atlas: Conte69 Map LEFT midthickness... Next Accept default metric filename Mapping Algorithm: Enclosing and interpolated are the most popular Next Close when Summary appears File: Open Spec File: Conte69_atlas-v2.L.164k_fs_LR.c5.spec Load scenes Double-click first scene (Conte69 midthickness and inflated...) Toolbar: Spec: Metric: map_data_0_Conte69... Erase all existing columns Toolbar: D/C: Page Selection: Overlay/underlay Surface Primary overlay Data type metric metric You should see it. Donna On May 6, 2014, at 7:36 PM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Hi Donna, As you suggested, I tried with the Conte69 atlas (164k and 74k), but same results. The metric file is recorded in the spec file, but the same error shows about different number of nodes. Thanks for paying attention to my problem. Would it be possible for you to make an online demonstration, with a screen sharing or a screen cast tool? In this way, we may find a way to solve the issue faster. Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Tue, May 6, 2014 at 9:50 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Audrey, I will look at this more closely later, but this is the step where you should be downloading the Conte69 atlas and using one of its visualization specs instead of this spec out of the distribution directory: 8. select in fmri_mapping_files Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you suggested The Conte69 atlas is here: http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas I wonder if your writing to the fmri_mapping_files that are intended to be read-only might cause trouble. Also, I would not expect to find a SPHERE or CMW configuration in that fmri_mapping_files spec. Will look more at this later, but here are some hints as to what looks amiss. Donna On May 5, 2014, at 10:28 AM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Here the attached image Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Mon, May 5, 2014 at 11:23 AM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Dear Donna, It is not a read-only issue since the spec files are modified when I do the mapping. Here is exactly what I did: 1. open CARET v5.65 2. Attributes Map volume(s) to surface(s) 3. chose Metric for Data mapping type 4. Enable entry of volume threshold 5. Add volumes from disk -- selected my ALE map, which is a nifti image, in Talairach format 6. Entered the volume thresholding in the pop-up window (positive: 0.028; negative: 0.00) 7. Map to spec file with Atlas 8. select in fmri_mapping_files Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you suggested 9. Space : FNIRT; Atlas: Conte69 Map LEFT midthickness (164k_LR nodes) 10. idem 8 and 9, but with RIGHT 11. renamed by data files (L and R) 12. Mapping algorith: METRIC_ENCLOSING_VOXEL 13. ok (or next), heard a bip like there was an error, but the summary shows 14. Close 15. Open spec file Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec 16. check my metric file (please see joint image) load 17. Got this error message Error PDHCEM_Conte69_LEFT_midthickness_164k_fs_LR_5_May_2014_11_13_13.metric: Error PDHCEM_Conte69_LEFT_midthickness_164k_fs_LR_5_May_2014_11_13_13.metric: contains a different number of nodes than Conte69.L.midthickness.164k_fs_LR.coord.gii Pressed ok 18. The brain image is displayed, but without
Re: [caret-users] mapping ALE on surface: error for number of nodes
Hi, My volume is in Tal space. Is this a problem? Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Wed, May 7, 2014 at 11:30 AM, Donna Dierker do...@brainvis.wustl.eduwrote: Another thought occurred to me: If you select a 32k version of the Conte69 atlas as your spec file, then you'll get an error when you try to open the 164k vertex metric file. I'm sure there is a way to downsample the metric file, and there are also mapping features in Workbench's wb_command, if you want to map directly to 32k mesh surfaces. But we don't have a 32k version of Conte69 in caret5. On May 7, 2014, at 9:58 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Audrey-Anne, Erin and I tried to do that, but you can't see the menu picks very clearly in the video: https://www.youtube.com/watch?v=jED8sg9szdU But here are the steps: Download conte69 atlas: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8293720archive_name=Conte69_atlas_v2.LR.164k_fs_LR.c5.zip Unpack and cd to the Conte69_164k_fs_LR.c5 directory. Launch caret5. Cancel when spec file dialog comes up. Attributes: Map volume to surface Data mapping type: Metric; Next Add volumes from disk; select volume in MNI space; next Map to spec file with atlas Note: If you don't see this, then your caret installation is incomplete or confused about its parent directory. Launch from command line. Output spec file: select Conte69_atlas-v2.L.164k_fs_LR.c5.spec Space: FNIRT Atlas: Conte69 Map LEFT midthickness... Next Accept default metric filename Mapping Algorithm: Enclosing and interpolated are the most popular Next Close when Summary appears File: Open Spec File: Conte69_atlas-v2.L.164k_fs_LR.c5.spec Load scenes Double-click first scene (Conte69 midthickness and inflated...) Toolbar: Spec: Metric: map_data_0_Conte69... Erase all existing columns Toolbar: D/C: Page Selection: Overlay/underlay Surface Primary overlay Data type metric metric You should see it. Donna On May 6, 2014, at 7:36 PM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Hi Donna, As you suggested, I tried with the Conte69 atlas (164k and 74k), but same results. The metric file is recorded in the spec file, but the same error shows about different number of nodes. Thanks for paying attention to my problem. Would it be possible for you to make an online demonstration, with a screen sharing or a screen cast tool? In this way, we may find a way to solve the issue faster. Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Tue, May 6, 2014 at 9:50 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Audrey, I will look at this more closely later, but this is the step where you should be downloading the Conte69 atlas and using one of its visualization specs instead of this spec out of the distribution directory: 8. select in fmri_mapping_files Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you suggested The Conte69 atlas is here: http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas I wonder if your writing to the fmri_mapping_files that are intended to be read-only might cause trouble. Also, I would not expect to find a SPHERE or CMW configuration in that fmri_mapping_files spec. Will look more at this later, but here are some hints as to what looks amiss. Donna On May 5, 2014, at 10:28 AM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Here the attached image Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Mon, May 5, 2014 at 11:23 AM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Dear Donna, It is not a read-only issue since the spec files are modified when I do the mapping. Here is exactly what I did: 1. open CARET v5.65 2. Attributes Map volume(s) to surface(s) 3. chose Metric for Data mapping type 4. Enable entry of volume threshold 5. Add volumes from disk -- selected my ALE map, which is a nifti image, in Talairach format 6. Entered the volume thresholding in the pop-up window (positive: 0.028; negative: 0.00) 7. Map to spec file with Atlas 8. select in fmri_mapping_files Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you suggested 9. Space : FNIRT; Atlas: Conte69 Map LEFT midthickness (164k_LR nodes) 10. idem 8 and 9, but with RIGHT 11. renamed by data files (L and R) 12. Mapping algorith: METRIC_ENCLOSING_VOXEL 13. ok (or next), heard a bip like there was an error, but the summary shows 14. Close 15. Open spec file Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec 16. check my metric file (please see joint image) load 17. Got this error message Error
Re: [caret-users] mapping ALE on surface: error for number of nodes
We don't have a version of the Conte69 midthickness in talairach space, but we do have a PALS version that is in TT space. Use the AFNI PALS surface. But this would not cause the mesh error (wrong number of vertices) issue that you were having. If you tried to view a 74k PALS mesh metric on a Conte69 164k mesh surface, then you'd get a problem like the one you had. From: Audrey-Anne Dubé audreyanned...@gmail.com To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Sent: Wednesday, May 7, 2014 1:20 PM Subject: Re: [caret-users] mapping ALE on surface: error for number of nodes Hi, My volume is in Tal space. Is this a problem? Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Wed, May 7, 2014 at 11:30 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Another thought occurred to me: If you select a 32k version of the Conte69 atlas as your spec file, then you'll get an error when you try to open the 164k vertex metric file. I'm sure there is a way to downsample the metric file, and there are also mapping features in Workbench's wb_command, if you want to map directly to 32k mesh surfaces. But we don't have a 32k version of Conte69 in caret5. On May 7, 2014, at 9:58 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Audrey-Anne, Erin and I tried to do that, but you can't see the menu picks very clearly in the video: https://www.youtube.com/watch?v=jED8sg9szdU But here are the steps: Download conte69 atlas: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8293720archive_name=Conte69_atlas_v2.LR.164k_fs_LR.c5.zip Unpack and cd to the Conte69_164k_fs_LR.c5 directory. Launch caret5. Cancel when spec file dialog comes up. Attributes: Map volume to surface Data mapping type: Metric; Next Add volumes from disk; select volume in MNI space; next Map to spec file with atlas Note: If you don't see this, then your caret installation is incomplete or confused about its parent directory. Launch from command line. Output spec file: select Conte69_atlas-v2.L.164k_fs_LR.c5.spec Space: FNIRT Atlas: Conte69 Map LEFT midthickness... Next Accept default metric filename Mapping Algorithm: Enclosing and interpolated are the most popular Next Close when Summary appears File: Open Spec File: Conte69_atlas-v2.L.164k_fs_LR.c5.spec Load scenes Double-click first scene (Conte69 midthickness and inflated...) Toolbar: Spec: Metric: map_data_0_Conte69... Erase all existing columns Toolbar: D/C: Page Selection: Overlay/underlay Surface Primary overlay Data type metric metric You should see it. Donna On May 6, 2014, at 7:36 PM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Hi Donna, As you suggested, I tried with the Conte69 atlas (164k and 74k), but same results. The metric file is recorded in the spec file, but the same error shows about different number of nodes. Thanks for paying attention to my problem. Would it be possible for you to make an online demonstration, with a screen sharing or a screen cast tool? In this way, we may find a way to solve the issue faster. Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Tue, May 6, 2014 at 9:50 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Audrey, I will look at this more closely later, but this is the step where you should be downloading the Conte69 atlas and using one of its visualization specs instead of this spec out of the distribution directory: 8. select in fmri_mapping_files Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you suggested The Conte69 atlas is here: http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas I wonder if your writing to the fmri_mapping_files that are intended to be read-only might cause trouble. Also, I would not expect to find a SPHERE or CMW configuration in that fmri_mapping_files spec. Will look more at this later, but here are some hints as to what looks amiss. Donna On May 5, 2014, at 10:28 AM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Here the attached image Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Mon, May 5, 2014 at 11:23 AM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Dear Donna, It is not a read-only issue since the spec files are modified when I do the mapping. Here is exactly what I did: 1. open CARET v5.65 2. Attributes Map volume(s) to surface(s) 3. chose Metric for Data mapping type 4. Enable entry of volume threshold 5. Add volumes from disk -- selected my ALE map, which is a nifti image, in Talairach format 6. Entered the volume thresholding in the pop-up window (positive: 0.028; negative: 0.00) 7. Map to spec file with Atlas 8. select in fmri_mapping_files
Re: [caret-users] mapping ALE on surface: error for number of nodes
I understand that the map I see is in fact the myelin smooting something. So, ine the spec file, when I go to metric open my metric file, I have a Choose Column to load window but no column has been loaded, and when I click ok, I receive the same error messag: Error PDHCEM_Conte69_LEFT_midthickness_164k_fs_LR_7_May_2014_14_58_48.metric: contains a different number of nodes than Conte69.L.midthickness.164k_fs_LR.coord.gii Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Wed, May 7, 2014 at 2:52 PM, Audrey-Anne Dubé audreyanned...@gmail.comwrote: Ok I see an overlay! I didn't know I had to use Scene. So that's good! But the problem now is that I the overlay is not related to my statistical data, as you can see with the screen shot of my file in Mango vs in Caret. Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Wed, May 7, 2014 at 2:20 PM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Hi, My volume is in Tal space. Is this a problem? Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Wed, May 7, 2014 at 11:30 AM, Donna Dierker do...@brainvis.wustl.eduwrote: Another thought occurred to me: If you select a 32k version of the Conte69 atlas as your spec file, then you'll get an error when you try to open the 164k vertex metric file. I'm sure there is a way to downsample the metric file, and there are also mapping features in Workbench's wb_command, if you want to map directly to 32k mesh surfaces. But we don't have a 32k version of Conte69 in caret5. On May 7, 2014, at 9:58 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Audrey-Anne, Erin and I tried to do that, but you can't see the menu picks very clearly in the video: https://www.youtube.com/watch?v=jED8sg9szdU But here are the steps: Download conte69 atlas: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8293720archive_name=Conte69_atlas_v2.LR.164k_fs_LR.c5.zip Unpack and cd to the Conte69_164k_fs_LR.c5 directory. Launch caret5. Cancel when spec file dialog comes up. Attributes: Map volume to surface Data mapping type: Metric; Next Add volumes from disk; select volume in MNI space; next Map to spec file with atlas Note: If you don't see this, then your caret installation is incomplete or confused about its parent directory. Launch from command line. Output spec file: select Conte69_atlas-v2.L.164k_fs_LR.c5.spec Space: FNIRT Atlas: Conte69 Map LEFT midthickness... Next Accept default metric filename Mapping Algorithm: Enclosing and interpolated are the most popular Next Close when Summary appears File: Open Spec File: Conte69_atlas-v2.L.164k_fs_LR.c5.spec Load scenes Double-click first scene (Conte69 midthickness and inflated...) Toolbar: Spec: Metric: map_data_0_Conte69... Erase all existing columns Toolbar: D/C: Page Selection: Overlay/underlay Surface Primary overlay Data type metric metric You should see it. Donna On May 6, 2014, at 7:36 PM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Hi Donna, As you suggested, I tried with the Conte69 atlas (164k and 74k), but same results. The metric file is recorded in the spec file, but the same error shows about different number of nodes. Thanks for paying attention to my problem. Would it be possible for you to make an online demonstration, with a screen sharing or a screen cast tool? In this way, we may find a way to solve the issue faster. Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Tue, May 6, 2014 at 9:50 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Audrey, I will look at this more closely later, but this is the step where you should be downloading the Conte69 atlas and using one of its visualization specs instead of this spec out of the distribution directory: 8. select in fmri_mapping_files Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you suggested The Conte69 atlas is here: http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas I wonder if your writing to the fmri_mapping_files that are intended to be read-only might cause trouble. Also, I would not expect to find a SPHERE or CMW configuration in that fmri_mapping_files spec. Will look more at this later, but here are some hints as to what looks amiss. Donna On May 5, 2014, at 10:28 AM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Here the attached image Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Mon, May 5, 2014 at 11:23 AM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Dear Donna, It is not a read-only issue since the spec files are modified when I do the mapping. Here is exactly what I
Re: [caret-users] mapping ALE on surface: error for number of nodes
Audrey, I will look at this more closely later, but this is the step where you should be downloading the Conte69 atlas and using one of its visualization specs instead of this spec out of the distribution directory: 8. select in fmri_mapping_files Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you suggested The Conte69 atlas is here: http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas I wonder if your writing to the fmri_mapping_files that are intended to be read-only might cause trouble. Also, I would not expect to find a SPHERE or CMW configuration in that fmri_mapping_files spec. Will look more at this later, but here are some hints as to what looks amiss. Donna On May 5, 2014, at 10:28 AM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Here the attached image Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Mon, May 5, 2014 at 11:23 AM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Dear Donna, It is not a read-only issue since the spec files are modified when I do the mapping. Here is exactly what I did: 1. open CARET v5.65 2. Attributes Map volume(s) to surface(s) 3. chose Metric for Data mapping type 4. Enable entry of volume threshold 5. Add volumes from disk -- selected my ALE map, which is a nifti image, in Talairach format 6. Entered the volume thresholding in the pop-up window (positive: 0.028; negative: 0.00) 7. Map to spec file with Atlas 8. select in fmri_mapping_files Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you suggested 9. Space : FNIRT; Atlas: Conte69 Map LEFT midthickness (164k_LR nodes) 10. idem 8 and 9, but with RIGHT 11. renamed by data files (L and R) 12. Mapping algorith: METRIC_ENCLOSING_VOXEL 13. ok (or next), heard a bip like there was an error, but the summary shows 14. Close 15. Open spec file Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec 16. check my metric file (please see joint image) load 17. Got this error message Error PDHCEM_Conte69_LEFT_midthickness_164k_fs_LR_5_May_2014_11_13_13.metric: Error PDHCEM_Conte69_LEFT_midthickness_164k_fs_LR_5_May_2014_11_13_13.metric: contains a different number of nodes than Conte69.L.midthickness.164k_fs_LR.coord.gii Pressed ok 18. The brain image is displayed, but without my data on it Can you see if I did something wrong? Thanks very much Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Wed, Apr 30, 2014 at 3:22 PM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Audrey, Hmmm. I wonder if this might be because the spec file you name below is part of the Caret distribution, and it might be read-only. In fact, it's a good idea for it to be read-only. The files under data_files are intended to be used by Caret without risk of users writing their analysis files there. Is this spec file under $CARET_HOME/data_files or has it been copied from there? And is the directory and spec file writeable? There are better choices for other visualization specs, e.g., like those in this tutorial spec: http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/CARET_TUTORIAL_SEPT06.zip login pub password download Also, depending on the constraints of your meta-analysis, you might consider moving from the PALS atlas to the Conte69 atlas: http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas Donna On Apr 30, 2014, at 1:19 PM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Dear Caret users, I want to map my meta-analysis results on an PALS surface. So I tried to map my ALE map (nifti format) to a surface atlas using this spec file Human.PALS_B12.LR.MULTI-FIDUCIAL_711-2C_fMRI-MAPPER.B1-12.RIGHT.align2.73730.spec I got this error message: Error PDHCEM_Mapped_to_PALS.RIGHT.73730.metric: Error PDHCEM_Mapped_to_PALS.RIGHT.73730.metric: contains a different number of nodes than Human_Buck_Case12.R.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align2.73730.coord I cannot figure how to resolve this problem. Help would be greatly appreciated! Thank! Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users Screen Shot 2014-05-05 at 11.18.18.jpg___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu
Re: [caret-users] mapping ALE on surface: error for number of nodes
Dear Donna, It is not a read-only issue since the spec files are modified when I do the mapping. Here is exactly what I did: 1. open CARET v5.65 2. Attributes Map volume(s) to surface(s) 3. chose Metric for Data mapping type 4. Enable entry of volume threshold 5. Add volumes from disk -- selected my ALE map, which is a nifti image, in Talairach format 6. Entered the volume thresholding in the pop-up window (positive: 0.028; negative: 0.00) 7. Map to spec file with Atlas 8. select in fmri_mapping_files Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you suggested 9. Space : FNIRT; Atlas: Conte69 Map LEFT midthickness (164k_LR nodes) 10. idem 8 and 9, but with RIGHT 11. renamed by data files (L and R) 12. Mapping algorith: METRIC_ENCLOSING_VOXEL 13. ok (or next), heard a bip like there was an error, but the summary shows 14. Close 15. Open spec file Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec 16. check my metric file (please see joint image) load 17. Got this error message Error PDHCEM_Conte69_LEFT_midthickness_164k_fs_LR_5_May_2014_11_13_13.metric: Error PDHCEM_Conte69_LEFT_midthickness_164k_fs_LR_5_May_2014_11_13_13.metric: contains a different number of nodes than Conte69.L.midthickness.164k_fs_LR.coord.gii Pressed ok 18. The brain image is displayed, but without my data on it Can you see if I did something wrong? Thanks very much Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Wed, Apr 30, 2014 at 3:22 PM, Donna Dierker do...@brainvis.wustl.eduwrote: Hi Audrey, Hmmm. I wonder if this might be because the spec file you name below is part of the Caret distribution, and it might be read-only. In fact, it's a good idea for it to be read-only. The files under data_files are intended to be used by Caret without risk of users writing their analysis files there. Is this spec file under $CARET_HOME/data_files or has it been copied from there? And is the directory and spec file writeable? There are better choices for other visualization specs, e.g., like those in this tutorial spec: http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/CARET_TUTORIAL_SEPT06.zip login pub password download Also, depending on the constraints of your meta-analysis, you might consider moving from the PALS atlas to the Conte69 atlas: http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas Donna On Apr 30, 2014, at 1:19 PM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Dear Caret users, I want to map my meta-analysis results on an PALS surface. So I tried to map my ALE map (nifti format) to a surface atlas using this spec file Human.PALS_B12.LR.MULTI-FIDUCIAL_711-2C_fMRI-MAPPER.B1-12.RIGHT.align2.73730.spec I got this error message: Error PDHCEM_Mapped_to_PALS.RIGHT.73730.metric: Error PDHCEM_Mapped_to_PALS.RIGHT.73730.metric: contains a different number of nodes than Human_Buck_Case12.R.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align2.73730.coord I cannot figure how to resolve this problem. Help would be greatly appreciated! Thank! Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] mapping ALE on surface: error for number of nodes
Hi Audrey, Hmmm. I wonder if this might be because the spec file you name below is part of the Caret distribution, and it might be read-only. In fact, it's a good idea for it to be read-only. The files under data_files are intended to be used by Caret without risk of users writing their analysis files there. Is this spec file under $CARET_HOME/data_files or has it been copied from there? And is the directory and spec file writeable? There are better choices for other visualization specs, e.g., like those in this tutorial spec: http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/CARET_TUTORIAL_SEPT06.zip login pub password download Also, depending on the constraints of your meta-analysis, you might consider moving from the PALS atlas to the Conte69 atlas: http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas Donna On Apr 30, 2014, at 1:19 PM, Audrey-Anne Dubé audreyanned...@gmail.com wrote: Dear Caret users, I want to map my meta-analysis results on an PALS surface. So I tried to map my ALE map (nifti format) to a surface atlas using this spec file Human.PALS_B12.LR.MULTI-FIDUCIAL_711-2C_fMRI-MAPPER.B1-12.RIGHT.align2.73730.spec I got this error message: Error PDHCEM_Mapped_to_PALS.RIGHT.73730.metric: Error PDHCEM_Mapped_to_PALS.RIGHT.73730.metric: contains a different number of nodes than Human_Buck_Case12.R.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align2.73730.coord I cannot figure how to resolve this problem. Help would be greatly appreciated! Thank! Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
