Re: [HCP-Users] Extract average time-course from cortical parcels

[Harms, Michael]

A .nii or .nii.gz is not a CIFTI file (it is a NIFTI file), and consequently ciftiopen doesn’t work with it. If you want to load a NIFTI file in matlab, there are a number of tools out there, including load_nifti.m that comes with FreeSurfer, and read_avw.m that comes with FSL.  I’m sure there are other dedicated NIFTI matlab readers as well. 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 St. Louis, MO  63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of Ferdaus Kawsar <ferdaus.kaw...@gmail.com> Date: Wednesday, August 24, 2016 at 10:46 AM To: Timothy Coalson <tsc...@mst.edu> Cc: "hcp-users@humanconnectome.org" <HCP-Users@humanconnectome.org> Subject: Re: [HCP-Users] Extract average time-course from cortical parcels Hi Tim,          I used -cifti-separate and created the files. However, even though I can load the data in Matlab for left_data.func.gii and right_data.func.gii, I cannot load the volume files in Matlab. I could not load out_vol.nii.gz and out_vol_structs.nii.gz , files in matlab.(I unzipped them first) I tried both ft_read_cifti and ciftiopen and none of them works. They can both be viewed by workbench.  Here is the error message I see when I use ciftiopen to load out_vol.nii out_vol_cft_open=ciftiopen('/home/fkawsar/HCP_Data/Experimental/MNI3.17/out_vol.nii','/home/fkawsar/Downloads/workbench/exe_linux64/wb_command'); While running: /home/fkawsar/Downloads/workbench/exe_linux64/wb_command -cifti-convert -to-gifti-ext /home/fkawsar/HCP_Data/Experimental/MNI3.17/out_vol.nii /tmp/tp5ece90ba_3f9e_4d81_aec6_2b19c0f950c2.gii ERROR: no cifti extension found in file '/home/fkawsar/HCP_Data/Experimental/MNI3.17/out_vol.nii' /home/fkawsar/Downloads/workbench/exe_linux64/wb_command -cifti-convert -to-gifti-ext /home/fkawsar/HCP_Data/Experimental/MNI3.17/out_vol.nii /tmp/tp5ece90ba_3f9e_4d81_aec6_2b19c0f950c2.gii: Signal 127 Error using read_gifti_file_standalone (line 20) [GIFTI] Loading of XML file /tmp/tp5ece90ba_3f9e_4d81_aec6_2b19c0f950c2.gii failed. Error in gifti (line 71)                 this = read_gifti_file_standalone(varargin{1},giftistruct); Error in ciftiopen (line 31) cifti = gifti([tmpfile '.gii']);​ Hope you can help. Best, -Ferdaus On Thu, Aug 11, 2016 at 5:39 PM, Timothy Coalson <tsc...@mst.edu> wrote: -cifti-separate creates nifti and gift files from parts of the cifti file.  That output is a volume file, and should have been named ending in .nii.gz, such that it would be compressed on-disk.  However, I would not recommend doing it this way for all subcortical structures, as that is a lot of volume files, all of which will have the full original FOV from the volume preprocessing output. If the only thing you want to do with them is average them into per-area timeseries, I suggest you try -cifti-parcellate before anything else.  You may need to first make a dlabel file that combines your chosen surface and subcortical parcellations. If you want all the individual timeseries separately, then you might try the -volume-all option of -cifti-separate, and possibly the -crop options, as well as the -roi options to tell you which voxels have data in them.  The -metric option will get you the surface data.  Note that you can specify these options simultaneously to a single command: wb_command -cifti-separate <input> COLUMN -volume-all out_vol.nii.gz -crop -label out_vol_structs.nii.gz -metric CORTEX_LEFT left_data.func.gii -roi left_roi.func.gii -metric CORTEX_RIGHT right_data.func.gii -roi right_roi.func.gii Tim On Thu, Aug 11, 2016 at 3:35 PM, Ferdaus Kawsar <ferdaus.kaw...@gmail.com> wrote: Hi Tim,          Thanks for your reply. I used  cifti-separate as you suggested to create volumes from *.dtseries.nii file I have. However, I am having difficulty to read the resultant file. Is it a cifti file? I cannot read this file using either ft_read_cifti() or ciftiopen(). Also the file is huge (1.8 GB). How do I extract time-course from this file? I created the file using following command: wb_command -cifti-separate  '*.dtseries.nii' COLUMN -volume PUTAMEN_RIGHT 'out_putament_right' Best -Ferdaus On Wed, Aug 10, 2016 at 5:42 PM, Timothy Coalson <tsc...@mst.edu> wrote: You might want to use "wb_command -cifti-parcellate" to do this for you, it has some extra options to do things like weighted means according to vertex area. Manually matching things up in matlab from loaded cifti files may be difficult, as some .dlabel.nii files don't exclude the medial wall, and may not include the subcortical voxels that the .dtseries.nii files do.  You can use -cifti-separate on cifti files to make simpler single-hemisphere full-surface gifti files, and a nifti volume file for the subcortical stuff (though doing this on the timeseries will result in a fairly large volume file when loaded in memory). Tim On Wed, Aug 10, 2016 at 2:48 PM, Ferdaus Kawsar <ferdaus.kaw...@gmail.com> wrote: Hi HCP Team,                     I was wondering if someone could help regarding a task I am trying to do. I need to extract average time-course for both cortical and sub-cortical parcels.  I was able to extract average time-courses for sub-cortical parcels.  After I loaded my *dtseries.nii cifti files (using ft_read_cifti()) in matlab, I could access all the time-courses for sub-cortical regions. There are 19 sub-cortical regions. After I got all the time -courses for a sub-cortical region, a simple mean() method in matlab gave me the average time-course. I am curious if this approach is right? Also, how do I get the time-courses for a cortical parcel? My eventual goal is to extract average time course for each of 180 parcels in each hemisphere. Best regards, -Ferdaus -- Ferdaus A. Kawsar, PhD Research Scientist II Department of Neurology Medical College of Wisconsin Milwaukee, WI _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- Ferdaus A. Kawsar, PhD Research Scientist II Department of Neurology Medical College of Wisconsin Milwaukee, WI -- Ferdaus A. Kawsar, PhD Research Scientist II Department of Neurology Medical College of Wisconsin Milwaukee, WI _______________________________________________ HCP-Users mailing list 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. 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