Re: [caret-users] medial wall override via caret_command
Dear Donna, Thanks! I am trying to map the functional volume in MNI152 (SPM99) space to the surface space (PALS) as metric. It is like the following: caret_command -volume-map-to-surface-pals \ \ $metric_filename \ SPM99 \ $hemisphere \ METRIC_AVERAGE_NODES \ $fMRI_vol_filename \ -metric-afm Could you please provide an example to use “select” in caret_command to select the medial wall paint column as an overlay on top of the functional overlay? Many thanks!!! Daniel On 8/19/15, 6:38 PM, caret-users-boun...@brainvis.wustl.edu on behalf of Donna Dierker caret-users-boun...@brainvis.wustl.edu on behalf of do...@brainvis.wustl.edu wrote: Could you elaborate on how you are using caret_command? The Enable Medial Wall Override affects display, which is not applicable using caret_command, unless you are using -show-scenes, in which case you would select the medial wall paint column as an overlay on top of your functional overlay, in order to gray out the medial wall. It gets more complicated if you want to exclude the medial wall from processing, but isn't too hard (search for select in the caret_command full help output). On Aug 19, 2015, at 3:13 PM, Yang, Daniel daniel.yj.y...@yale.edu wrote: Dear Caret Experts, In Paint Main, I can check “Enable Medial Wall Override” to gray out medial wall. Is it possible to do so via caret_command? Many thanks! Daniel ___ caret-users mailing list caret-users@brainvis.wustl.edu https://urldefense.proofpoint.com/v2/url?u=http-3A__brainvis.wustl.edu_ma ilman_listinfo_caret-2Dusersd=AwIF-gc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919 MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHYm=h5-YV_ETDHGYBcqGmBeefwlj-rjDZnlPAYp WTcIsjmIs=K1vKNA8KK-hNQ2Za8ncWGM47HbBDDXZwfOaGXikwyZYe= ___ caret-users mailing list caret-users@brainvis.wustl.edu https://urldefense.proofpoint.com/v2/url?u=http-3A__brainvis.wustl.edu_mai lman_listinfo_caret-2Dusersd=AwIF-gc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MO RXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHYm=h5-YV_ETDHGYBcqGmBeefwlj-rjDZnlPAYpWTc IsjmIs=K1vKNA8KK-hNQ2Za8ncWGM47HbBDDXZwfOaGXikwyZYe= ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] medial wall override via caret_command
Dear Donna, Thanks so much! Very helpful! Yes, I do want to primarily display the blacked-out medial wall, rather than analyze it. Could you please show how I can use caret_command to add/select AVERAGE-MED-WALL B1-12 RIGHT as the Display Column from the Paint file as a secondary overlay to an existing spec? I would like to avoid clicking in the caret UI if possible. Many thanks! Daniel On 8/20/15, 11:02 AM, caret-users-boun...@brainvis.wustl.edu on behalf of Donna Dierker caret-users-boun...@brainvis.wustl.edu on behalf of do...@brainvis.wustl.edu wrote: It depends on how critical it is the $metric_filename have zeroes in the medial wall, rather than just look gray when you view/capture it. For display/capture purposes, you can use the existing PALS paint file: Human.PALS_B12.BOTH.COMPOSITE_Areas_Functional_WS.73730.paint … which has these columns: AVERAGE-MED-WALL B1-12 RIGHT AVERAGE-MED-WALL B1-12 LEFT Then adjust your D/C: Surface Overlay/Underlay settings as shown here: https://urldefense.proofpoint.com/v2/url?u=http-3A__brainmap.wustl.edu_pub _donna_US_CT_YALE_medial-5Fwall-5Fgray.pngd=AwIF-gc=-dg2m7zWuuDZ0MUcV7Sd qwr=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHYm=u5j7Df9p95woZ9z0eTo3nv8 WhnplQZYwSn-D2Unh2Fcs=0ubFqD2d6iE4otxojW-Jv3VgMJLlcUYIOpV6mXdrNS0e= login pub password download That paint file is included in this archive: CARET_TUTORIAL_SEPT06.zip https://urldefense.proofpoint.com/v2/url?u=http-3A__sumsdb.wustl.edu_sums_ archivelist.do-3Farchive-5Fid-3D6595030d=AwIF-gc=-dg2m7zWuuDZ0MUcV7Sdqw r=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHYm=u5j7Df9p95woZ9z0eTo3nv8Whn plQZYwSn-D2Unh2Fcs=8OClUz8TulQVknEPxf1ukRvEn-YtXtwpKga-vaZ-wlce= If you are doing analysis with $metric_filename that needs the medial wall to be zeroed out, you can create an inverted mask like this: caret_command -surface-region-of-interest-selection my.coord my.topo cortical_mask_outside_medial_wall.roi -paint medial.wall.paint column-number MEDIAL.WALL NORMAL -invert-selection But then what you do next depends on your analysis, and I suspect you care more about the display. On Aug 20, 2015, at 8:27 AM, Yang, Daniel daniel.yj.y...@yale.edu wrote: Dear Donna, Thanks! I am trying to map the functional volume in MNI152 (SPM99) space to the surface space (PALS) as metric. It is like the following: caret_command -volume-map-to-surface-pals \ \ $metric_filename \ SPM99 \ $hemisphere \ METRIC_AVERAGE_NODES \ $fMRI_vol_filename \ -metric-afm Could you please provide an example to use “select” in caret_command to select the medial wall paint column as an overlay on top of the functional overlay? Many thanks!!! Daniel On 8/19/15, 6:38 PM, caret-users-boun...@brainvis.wustl.edu on behalf of Donna Dierker caret-users-boun...@brainvis.wustl.edu on behalf of do...@brainvis.wustl.edu wrote: Could you elaborate on how you are using caret_command? The Enable Medial Wall Override affects display, which is not applicable using caret_command, unless you are using -show-scenes, in which case you would select the medial wall paint column as an overlay on top of your functional overlay, in order to gray out the medial wall. It gets more complicated if you want to exclude the medial wall from processing, but isn't too hard (search for select in the caret_command full help output). On Aug 19, 2015, at 3:13 PM, Yang, Daniel daniel.yj.y...@yale.edu wrote: Dear Caret Experts, In Paint Main, I can check “Enable Medial Wall Override” to gray out medial wall. Is it possible to do so via caret_command? Many thanks! Daniel ___ caret-users mailing list caret-users@brainvis.wustl.edu https://urldefense.proofpoint.com/v2/url?u=http-3A__brainvis.wustl.edu_ ma ilman_listinfo_caret-2Dusersd=AwIF-gc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z9 19 MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHYm=h5-YV_ETDHGYBcqGmBeefwlj-rjDZnlPA Yp WTcIsjmIs=K1vKNA8KK-hNQ2Za8ncWGM47HbBDDXZwfOaGXikwyZYe= ___ caret-users mailing list caret-users@brainvis.wustl.edu https://urldefense.proofpoint.com/v2/url?u=http-3A__brainvis.wustl.edu_m ai lman_listinfo_caret-2Dusersd=AwIF-gc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919 MO RXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHYm=h5-YV_ETDHGYBcqGmBeefwlj-rjDZnlPAYpW Tc IsjmIs=K1vKNA8KK-hNQ2Za8ncWGM47HbBDDXZwfOaGXikwyZYe= ___ caret-users mailing list caret-users@brainvis.wustl.edu https://urldefense.proofpoint.com/v2/url?u=http-3A__brainvis.wustl.edu_ma ilman_listinfo_caret-2Dusersd=AwIF-gc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919 MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHYm=u5j7Df9p95woZ9z0eTo3nv8WhnplQZYwSn- D2Unh2Fcs=IYkkOT7fsaJ0JUphfRnuXu7nq8c2fD5YCiJvjFxBDwMe= ___ caret-users mailing list caret
[caret-users] how to specify palette using caret_command?
Hi Caret Experts and Users, I want to change the palette in mapping volume to surface pals. Do you know how I can do that using caret_command? Thanks! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
[caret-users] p-value color bar in the surface mapping?
Hi Donna, Thank you so much! That helps a lot! By the way, do you know how I can add a p-value bar in the surface mapping with metric? I want to show something like p .05 ~ .0001 for example. Thanks! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 4/8/14 2:19 PM, Donna Dierker do...@brainvis.wustl.edumailto:do...@brainvis.wustl.edu wrote: Hi Daniel, The palette isn't used in the mapping step (caret_command -volume-map-to-surface or -volume-map-to-surface-pals). Rather, it is used when visualizing the results of mapping (output metric), either interactively in caret5 or using a ready-made scene or caret_command -show-scene. The palette can be set on the Metric Settings menu. There is a drop-down menu, or you can make your own palette (http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#paletteFile). Donna On Apr 8, 2014, at 11:12 AM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Hi Caret Experts and Users, I want to change the palette in mapping volume to surface pals. Do you know how I can do that using caret_command? Thanks! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu ___ caret-users mailing list caret-users@brainvis.wustl.edumailto:caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edumailto: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] The INFLATED surface in the tutorial data
Dear Caret Developers and Users, I am trying to superimpose fMRI activation onto the INFLATED surface available in the tutorial data; however, I found that the tutorial data only provided the RIGHT hemisphere. Thus, I would like to inflate the surface on my own. Do you know the inflation and smoothing parameters that are used to create the INFLATED surface in the tutorial data? Thanks! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] The INFLATED surface in the tutorial data
Sorry, I just found that I can do that via caret_command -surface-generate-inflated … Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/30/14 9:16 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Dear Caret Developers and Users, I am trying to superimpose fMRI activation onto the INFLATED surface available in the tutorial data; however, I found that the tutorial data only provided the RIGHT hemisphere. Thus, I would like to inflate the surface on my own. Do you know the inflation and smoothing parameters that are used to create the INFLATED surface in the tutorial data? Thanks! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] newbie's question: how to add lobe
Hi Donna, Sure! As I said I'm a newbie to caret, so all I did is very basic. I basically downloaded the Apple Macintosh 64-bit version of Caret v5.65 for my Mac OS 10.8.4 and then I installed it in /Applications/caret there is a subdirectory called data_files/ there. within the subdirectory, it shows the following subdirectories: CONSTRUCT.SPHERE/ flat_registration/ flatten_borders/ flatten_landmarks/ fmri_mapping_file/ icons/ images/ REGISTER.LVD.SPHERE/ REGISTER.SPHERE/ segmentation/ segmentation_masks/ spherical_registration/ standard_mesh_atlases/ sulcal_identification/ within standard_mesh_atlases/, it shows the following file and subdirectories: atlases.csv Human.PALS.LEFT/ Human.PALS.RIGHT/ within the Human.PALS.RIGHT/ (for example), it shows the following files: ForSPHERICAL.REGISTRATION_Human.Class3.bordercolor Human.colin.RIGHT.RegToPALS_B12.CUTS.CartSTD.clean.73730.topo Human.colin.RIGHT.RegToPALS_B12.FLAT.CartSTD.clean.73730.coord Human.PALS_B12.B1-12.DEPTH_ANALYSES_RIGHT.73730.spec -- THIS is the one I opened and I cannot see Paint/lobes Human.PALS_B12.R.border_projection_file_94.borderproj Human.PALS_B12.R.preferences_file_0caret5_preferences Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL.clean.align.73730.coord Human.PALS_B12.SPHERE.73730.coord Human.sphere_6.RIGHT_HEM.73730.topo I hope this provides some diagnostic information (maybe?) I will take a look at the file you suggested soon. Thanks a lot for your help! Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 7/29/13 10:08 AM, Donna Dierker do...@brainvis.wustl.edumailto:do...@brainvis.wustl.edu wrote: Hi Daniel, Can you send a listing of the directory containing the surfaces you're using? This will tell us not only whether you're using PALS or fs_LR, but also whether you are using caret5-style files or workbench (GIFTI) style files. This file, for example, will work if you've got fs_LR mesh surfaces in caret5 format: parcels-from-pals_composite_29mar11.164k_fs_LR.label.gii.paint http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8288069 Donna On Jul 28, 2013, at 8:14 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Hi Caret Experts, After studying the QuickStart tutorials, I am able to display the lobe on the right hemisphere via Paint. However, when I load the standard meshes, there is no lobe information by default. May I ask how do I add lobe information perhaps via Paint? Specific directory / file locations and steps will be much appreciated! Thanks, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ caret-users mailing list caret-users@brainvis.wustl.edumailto:caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edumailto: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
