Re: [HCP-Users] from volume to gifti file to cifti roi
Thank you Timothy, I found your email very useful. I followed it and is done!! Also thanks to Donna and Jo! Best wishes always, Leah ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry Columbia University College of Physicians and Surgeons 1051 Riverside Dr., Unit 21 New York, NY 10032 phone: (646) 774-5428 email: mm4...@cumc.columbia.edu On Apr 21, 2015, at 5:04 PM, Timothy Coalson wrote: > You can always get help for an individual command by running it without any > arguments, and you can list the commands and only a short description with > -list-commands. You can also browse the commands here: > > http://www.humanconnectome.org/software/workbench-command.php > > In this case, you will want to start with -volume-to-surface-mapping and > -metric-label-import, then either -cifti-create-label if you have the > Atlas_ROIs.2.nii.gz file handy, or else -cifti-replace-structure (potentially > with -cifti-math, -cifti-merge, and -cifti-label-import commands to create an > empty single-map cifti label file from an existing cifti file). This will > get you a cifti label file, and you can then use -cifti-label-to-roi or > -cifti-all-labels-to-rois to get a label as an ROI. > > We are working on a way to make it easier to get volume and surface data into > cifti format, matching the brainordinate space of an existing file. > > Tim > > > On Tue, Apr 21, 2015 at 9:27 AM, wrote: > Hi Marta, > > You will probably end up using wb_command to do what you need to do. > There are a bunch of tools that might be able to help. The usage is huge, > so do something like this to write it to a text file: > > wb_command -all-commands-help > ~/Desktop/wb_command.help.txt > > Then open ~/Desktop/wb_command.help.txt in a text editor and have a look > at the help for these commands: > > -cifti-all-labels-to-rois > -cifti-create-label > -cifti-find-clusters > -cifti-label-import > -cifti-label-to-roi > -volume-to-surface-mapping > > You won't use all of them, but this will narrow the focus. > > Donna > > > > Dear Users, > > > > I am generating ROIs in subject volume space and need to know how to > > create a gifti label file when I map from volume to surface and how to > > convert that label gifti file to cifti roi? > > > > Best wishes always, > > > > Leah > > ___ > > Marta Moreno-Ortega, Ph.D. > > Postdoctoral Research Fellow > > Division of Experimental Therapeutics > > New York State Psychiatric Institute > > Department of Psychiatry > > Columbia University College of Physicians and Surgeons > > 1051 Riverside Dr., Unit 21 > > New York, NY 10032 > > > > phone: (646) 774-5428 > > email: mm4...@cumc.columbia.edu > > > > > > > > > > ___ > > 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] from volume to gifti file to cifti roi
You can always get help for an individual command by running it without any arguments, and you can list the commands and only a short description with -list-commands. You can also browse the commands here: http://www.humanconnectome.org/software/workbench-command.php In this case, you will want to start with -volume-to-surface-mapping and -metric-label-import, then either -cifti-create-label if you have the Atlas_ROIs.2.nii.gz file handy, or else -cifti-replace-structure (potentially with -cifti-math, -cifti-merge, and -cifti-label-import commands to create an empty single-map cifti label file from an existing cifti file). This will get you a cifti label file, and you can then use -cifti-label-to-roi or -cifti-all-labels-to-rois to get a label as an ROI. We are working on a way to make it easier to get volume and surface data into cifti format, matching the brainordinate space of an existing file. Tim On Tue, Apr 21, 2015 at 9:27 AM, wrote: > Hi Marta, > > You will probably end up using wb_command to do what you need to do. > There are a bunch of tools that might be able to help. The usage is huge, > so do something like this to write it to a text file: > > wb_command -all-commands-help > ~/Desktop/wb_command.help.txt > > Then open ~/Desktop/wb_command.help.txt in a text editor and have a look > at the help for these commands: > > -cifti-all-labels-to-rois > -cifti-create-label > -cifti-find-clusters > -cifti-label-import > -cifti-label-to-roi > -volume-to-surface-mapping > > You won't use all of them, but this will narrow the focus. > > Donna > > > > Dear Users, > > > > I am generating ROIs in subject volume space and need to know how to > > create a gifti label file when I map from volume to surface and how to > > convert that label gifti file to cifti roi? > > > > Best wishes always, > > > > Leah > > ___ > > Marta Moreno-Ortega, Ph.D. > > Postdoctoral Research Fellow > > Division of Experimental Therapeutics > > New York State Psychiatric Institute > > Department of Psychiatry > > Columbia University College of Physicians and Surgeons > > 1051 Riverside Dr., Unit 21 > > New York, NY 10032 > > > > phone: (646) 774-5428 > > email: mm4...@cumc.columbia.edu > > > > > > > > > > ___ > > 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] from volume to gifti file to cifti roi
Hi Marta, You will probably end up using wb_command to do what you need to do. There are a bunch of tools that might be able to help. The usage is huge, so do something like this to write it to a text file: wb_command -all-commands-help > ~/Desktop/wb_command.help.txt Then open ~/Desktop/wb_command.help.txt in a text editor and have a look at the help for these commands: -cifti-all-labels-to-rois -cifti-create-label -cifti-find-clusters -cifti-label-import -cifti-label-to-roi -volume-to-surface-mapping You won't use all of them, but this will narrow the focus. Donna > Dear Users, > > I am generating ROIs in subject volume space and need to know how to > create a gifti label file when I map from volume to surface and how to > convert that label gifti file to cifti roi? > > Best wishes always, > > Leah > ___ > Marta Moreno-Ortega, Ph.D. > Postdoctoral Research Fellow > Division of Experimental Therapeutics > New York State Psychiatric Institute > Department of Psychiatry > Columbia University College of Physicians and Surgeons > 1051 Riverside Dr., Unit 21 > New York, NY 10032 > > phone: (646) 774-5428 > email: mm4...@cumc.columbia.edu > > > > > ___ > 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] from volume to gifti file to cifti roi
Dear Users, I am generating ROIs in subject volume space and need to know how to create a gifti label file when I map from volume to surface and how to convert that label gifti file to cifti roi? Best wishes always, Leah ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry Columbia University College of Physicians and Surgeons 1051 Riverside Dr., Unit 21 New York, NY 10032 phone: (646) 774-5428 email: mm4...@cumc.columbia.edu ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
