Re: [HCP-Users] Convert activation cifti data to volume nifti

Here is how to read cifti into matlab: https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB? Side note, cifti files already use the concept of putting all the data elements into a 1-D vector, and use a second dimension for timeseries, or

Re: [HCP-Users] path to bbregister .dat file for REST call

Thanks for posting your solution. A few comments: while fsl's volume spaces don't respect the origin or some other aspects of the nifti header, they are at least consistent, so you can concatenate two fsl-format affines with convert_xfm (which does the obvious matrix math thing), so if you have

Re: [HCP-Users] Convert activation cifti data to volume nifti

Thank you! Le mar. 27 mars 2018 à 14:15, Harms, Michael a écrit : > > > That depends on which of the contrasts for the EMOTION you want to use. > You can find a listing of them in the Contrasts.txt file. > > > > > > -- > > Michael Harms, Ph.D. > >

Re: [HCP-Users] path to bbregister .dat file for REST call

Dear Michael and Timothy, first of all thanks for all the detailed help and suggestions. Apologies for the late reply, but in the end I opted for rerunning the HCP scripts myself, because I also wanted to adapt the “OneStepResampling" to resample the fMRI data into native T1 space instead of

Re: [HCP-Users] Convert activation cifti data to volume nifti

That depends on which of the contrasts for the EMOTION you want to use. You can find a listing of them in the Contrasts.txt file. -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine

Re: [HCP-Users] Convert activation cifti data to volume nifti

Thank you for the clarification. Here is a tree structure of one subject folder "tfMRI_EMOTION_hp200_s2_level2.feat" , could you tell me which cope folder you are talking about? there is six of them, and which file to be read on matlab? . ├── 139435_tfMRI_EMOTION_level2_hp200_s2.dscalar.nii ├──

Re: [HCP-Users] Convert activation cifti data to volume nifti

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