If you are using CIFTI you don't need to mask the data/can use a CIFTI file of all ones.
Peace, Matt. Sent from my Verizon, Samsung Galaxy smartphone -------- Original message -------- From: nailin yao <[email protected]> Date: 11/29/16 11:33 AM (GMT-06:00) To: "Glasser, Matthew" <[email protected]> Cc: NEUROSCIENCE tim <[email protected]>, [email protected] Subject: Re: [HCP-Users] group comparison So how do I deal with the two hemispheres when comparing ${subj}.MyelinMap.32k_fs_LR.dscalar.nii if the mask is only for one hemisphere? Thank you! Nailin 2016-11-28 20:07 GMT-05:00 Glasser, Matthew <[email protected]<mailto:[email protected]>>: You can use the atlas ROI file: ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.atlasroi.32k_fs_LR.shape.gii. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of nailin yao <[email protected]<mailto:[email protected]>> Date: Monday, November 28, 2016 at 3:06 PM To: Timothy Coalson <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] group comparison Thank you Tim! I have now concatenated the myelin maps and going to do the permutation test with Palm. I plan to do a whole brain vertex level comparison, do you know which existing mask should I use to group level analysis? Thanks! Best, Nailin 2016-11-22 16:48 GMT-05:00 Timothy Coalson <[email protected]<mailto:[email protected]>>: wb_shortcuts comes with the latest release of workbench, v1.2.3 - however, there are a few bugs in the version that was released that way, and a newer version is available here: https://github.com/Washington-University/wb_shortcuts If you want just the script itself, use this link: https://raw.githubusercontent.com/Washington-University/wb_shortcuts/master/wb_shortcuts I noticed you used "./wb_command", suggesting that you don't have the workbench executables in your $PATH. They will need to be in your $PATH in order for wb_shortcuts to work. As a final note, there is also wb_command -metric-merge and wb_shortcuts -metric-concatenate, which do the same thing for .func.gii files, in case you actually do need to use the non-cifti files. Tim On Tue, Nov 22, 2016 at 2:57 PM, nailin yao <[email protected]<mailto:[email protected]>> wrote: where can I download wb_shortcuts command? Thanks! Best, Nailin 2016-11-22 15:28 GMT-05:00 Harms, Michael <[email protected]<mailto:[email protected]>>: Two things: 1) That is not the proper syntax for using -cifti-merge. You need to repeat the -cifti argument separately for *each* cifti file. I suggest that you use wb_shortcuts -cifti-concatenate instead to make it simpler. 2) A .func.gii is not a CIFTI file. Use the .dscalar.nii version of the myelin maps as input. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173<tel:314-747-6173> St. Louis, MO 63110Email: [email protected]<mailto:[email protected]> From: nailin yao <[email protected]<mailto:[email protected]>> Date: Tuesday, November 22, 2016 at 2:14 PM To: Michael Harms <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] group comparison Hi Michael, I tried the command: ./wb_command -cifti-merge L.SmoothedMyelinMap.32k_fs_LR.out.func.gii -cifti *.L.SmoothedMyelinMap.32k_fs_LR.func.gii, but comes the error: ERROR: error reading NIfTI file /gpfs/scratch60/fas/glahn/ny87/Connectivity_Study/myelinmap_analysis/S0009QPW.L.SmoothedMyelinMap.32k_fs_LR.func.gii: /gpfs/scratch60/fas/glahn/ny87/Connectivity_Study/myelinmap_analysis/S0009QPW.L.SmoothedMyelinMap.32k_fs_LR.func.gii is not a valid NIfTI file How can I solve this? Thank you ! Best, Nailin 2016-11-22 14:14 GMT-05:00 nailin yao <[email protected]<mailto:[email protected]>>: Thank you MH! Best, Nailin 2016-11-22 13:30 GMT-05:00 Harms, Michael <[email protected]<mailto:[email protected]>>: By “compress” do you mean merge into a single file? If so, you can use wb_command -cifti-merge, or wb_shortcuts -cifti-concatenate. (The latter is a wrapper that simplifies the merge call). And you can use FSL’s PALM to do a permutation test. If 164k is too dense a sampling, there are 32k versions of the myelin maps that you could use instead. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173<tel:314-747-6173> St. Louis, MO 63110Email: [email protected]<mailto:[email protected]> From: <[email protected]<mailto:[email protected]>> on behalf of nailin yao <[email protected]<mailto:[email protected]>> Date: Tuesday, November 22, 2016 at 12:07 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] group comparison Hi, I want to compare group difference of *L.SmoothedMyelinMap.164k_fs_LR.func.gii of each subjects. How can I compress the myelinmap of all the subjects and do the group level permutation test on them? Thank you very much! Best, Nailin -- Nailin Yao, PhD Postdoctoral Associate Department of Psychiatry, Yale University _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -- Nailin Yao, PhD Postdoctoral Associate Department of Psychiatry, Yale University -- Nailin Yao, PhD Postdoctoral Associate Department of Psychiatry, Yale University ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -- Nailin Yao, PhD Postdoctoral Associate Department of Psychiatry, Yale University _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- Nailin Yao, PhD Postdoctoral Associate Department of Psychiatry, Yale University _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -- Nailin Yao, PhD Postdoctoral Associate Department of Psychiatry, Yale University ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
