Certainly that can be done. Take the beta (cope) maps from the CIFTI data, load them into (e.g., matlab), and correlate those vectors across subjects. If you specifically want only the cortex, you’d need to exclude the subcortical voxels from the grayordinates.
There is no need to go back to voxels for what you are trying to do. Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Yassine Benhajali <yanama...@gmail.com> Date: Tuesday, March 27, 2018 at 11:05 AM To: "Harms, Michael" <mha...@wustl.edu> Cc: NEUROSCIENCE tim <tsc...@mst.edu>, hcp-users <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Convert activation cifti data to volume nifti Ok, here te hole story behind what I try to achieve: - What I did? The surface maps you see on the figure is originally a volume based activation maps that I mapped on surface. This map is generated from unprocessed HCP data with our lab software NIAK<http://niak.simexp-lab.org/>. My analysis consist of stacking volume activation maps as vector of voxels, then correlate each subject vector with the rest of the dataset to have a subject by subject correlation matrix. - What I'm trying to do? My aim is to repeat the same process above but now with already computed activation map from HCP pipeline. So i need a way to transform activation surface map to a vector of voxels in order to correlate thse vector between subjects. If you think that there is a way to correlate activation maps between subject directly from surface, I would be happy to know how. Thanks Yassine Le mar. 27 mars 2018 à 10:04, Harms, Michael <mha...@wustl.edu<mailto:mha...@wustl.edu>> a écrit : For the surfaces, why not quantify the activation via the surface area, rather than volume? Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave<https://maps.google.com/?q=660+South+Euclid+Ave&entry=gmail&source=g>. Tel: 314-747-6173<tel:(314)%20747-6173> St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Yassine Benhajali <yanama...@gmail.com<mailto:yanama...@gmail.com>> Date: Tuesday, March 27, 2018 at 8:58 AM To: NEUROSCIENCE tim <tsc...@mst.edu<mailto:tsc...@mst.edu>> Cc: hcp-users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Convert activation cifti data to volume nifti Thank you for your reply. I would like to extract the volume based activation maps from each subject and put it as vector and do the same for each subject then stack them all in one matrix like this figure. Then, I'll do some clustering on that stack. [age.png] If you have any hint on how to accomplish that without loosing the benefit of surface based registration. Best, Yassine Le lun. 26 mars 2018 à 17:20, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> a écrit : For subcortical structures, it is as simple as wb_command -cifti-separate using -volume-all. For surface data, you would need to map it back into volume, using that subject's surfaces, thereby losing the advantages of surface registration (for both analysis and display). You would need to use -cifti-separate with -metric, and then use -metric-to-volume-mapping. Why are you trying to do this? We might have suggestions of other ways to accomplish your task. Tim On Mon, Mar 26, 2018 at 12:37 PM, Yassine Benhajali <yanama...@gmail.com<mailto:yanama...@gmail.com>> wrote: Hi all, Any one knows how to extract activation volume in nifti from cifti file like this one : '139435/FMRI/fMRI_EMOTION/tfMRI_EMOTION_hp200_s4_level2.feat/139435_tfMRI_EMOTION_level2_hp200_s4.dscalar.nii' Best, Yassine -- Yassine Benhajali Doctorant en Neuroanthropologie au Laboratoire SIMEXP - http://www.simexp-lab.org/members/ Université de Montréal, Québec, Canada 514 839 0501<tel:(514)%20839-0501> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- Yassine Benhajali Doctorant en Neuroanthropologie au Laboratoire SIMEXP - http://www.simexp-lab.org/members/ Université de Montréal, Québec, Canada 514 839 0501<tel:(514)%20839-0501> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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. -- Yassine Benhajali Doctorant en Neuroanthropologie au Laboratoire SIMEXP - http://www.simexp-lab.org/members/ Université de Montréal, Québec, Canada 514 839 0501 ________________________________ 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
