There is also the -cifti-separate command, which will pull out the different pieces of the cifti file as standard volume(nifti-1)/metric(gifti) files.
However, note that the cifti file doesn't use voxels for everything - the cortex is represented as surface data, not voxel data, so you will need to use surface-based analysis for that. Tim On Wed, Oct 15, 2014 at 8:27 AM, Harms, Michael <[email protected]> wrote: > > Hi, > Please keep replies to the HCP-User list, so that others can respond, and > others can benefit. > > You can use > wb_command -cifti-convert -to-nifti > which reshapes the cifti grayordinates into a standard nifti. > > HOWEVER, that only works if you will be using tools and subsequent > processing that is not dependent in some fashion on spatial neighbor > information, because once you reshape the CIFTI into NIFTI, all information > about which grayordinate is adjacent to another grayordinate is lost. > > 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: [email protected] > > From: Mahsa Alizade shalchy <[email protected]> > Reply-To: Mahsa Alizade shalchy <[email protected]> > Date: Wednesday, October 15, 2014 5:12 AM > To: "Harms, Michael" <[email protected]> > Subject: Re: [HCP-Users] ROI extraction of rest fmri data > > Dear MH > > How could I convert it to standard images? (i.e I could not use afni, > because afni does not recognize the data) > Many thanks in advance. > > Best, > mahsa > > > On Wednesday, October 15, 2014 1:51 AM, "Harms, Michael" < > [email protected]> wrote: > > > > Yes, to my knowledge, Workbench (wb_view) and wb_command are the only > tools that support reading CIFTI data currently, which is based on the > NIFTI-2 format (that's why the extension ends in .nii, but the part prior > to the .nii-- i.e., .dtseries.nii -- is the clue that it isn't standard > NIFTI-1 format). > > 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 63110Email: [email protected] > > From: Mahsa Alizade shalchy <[email protected]> > Reply-To: Mahsa Alizade shalchy <[email protected]> > Date: Tuesday, October 14, 2014 5:15 PM > To: "Harms, Michael" <[email protected]>, Hcp-users < > [email protected]> > Subject: Re: [HCP-Users] ROI extraction of rest fmri data > > Dear MH > > Thank you so much for your help.I have one more question if that's ok... > I am trying to work with compact data (gray ordinate time series data). > However,as I proceed to open them with mri cro(and mri cron) the following > error prompts: > > The header file is not in Analyze format [the first 4 bytes do not have > the value 348]. Assuming big-endian data. > > Header describes an unknown data type.Bit pixels=256 Data Type=0 > Could you please tell me what is wrong? > Many thanks in advance. > > Best, > mahsa > > > > > On Tuesday, October 14, 2014 11:43 PM, "Harms, Michael" < > [email protected]> wrote: > > > > Hi, > For Workbench and 'wb_command', I'd suggest that you start with the > documentation and tutorials available at: > http://humanconnectome.org/software/ > > If you are not familiar with CIFTI and the outputs we provide, it sounds > like you would also benefit by reviewing: > http://humanconnectome.org/documentation/ > > For FSL, they have their own extensive set of documentation and > tutorials that you can take advantage of. > > 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 63110Email: [email protected] > > From: Mahsa Alizade shalchy <[email protected]> > Reply-To: Mahsa Alizade shalchy <[email protected]> > Date: Tuesday, October 14, 2014 3:07 PM > To: "Harms, Michael" <[email protected]> > Subject: Re: [HCP-Users] ROI extraction of rest fmri data > > Sorry if my questions sound naive. I am a beginner in fmri(esp rfmri > )field. > Since I'm working on Q1 data, I do not remember any "CIFTI/grayordinate " > versions of the data (There were 3 kinds of rfmri data namely as > preprocessed,fix,fix extended and I utilized the 3rd one to skip any > preprocessing step). > I unfortunately have no idea about Workbench and wb_command... > Could I mask my data using FSL?Could you please explain a bit more? > Thank you in advance. > > Best, > mahsa > > > On Tuesday, October 14, 2014 11:27 PM, "Harms, Michael" < > [email protected]> wrote: > > > > Hi, > You are going to have a hard time working with the resting state volume > data in matlab. > I'd suggest using the CIFTI/grayordinate versions of the data (which are > much more compact) and starting to familiarize yourself with the > capabilities of Workbench and 'wb_command'. In my experience, the various > FSL tools work, although again, if you are working with the volume data, > just be prepared that some operations are going to be slow. > > 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 63110Email: [email protected] > > From: Mahsa Alizade shalchy <[email protected]> > Reply-To: Mahsa Alizade shalchy <[email protected]> > Date: Tuesday, October 14, 2014 2:49 PM > To: "Harms, Michael" <[email protected]> > Subject: Re: [HCP-Users] ROI extraction of rest fmri data > > Dear MH > > Thank you so much for replying. > My goal is to extract functional connectivity maps of my ROI. > For task fmri data I manually did " fmri data.*ROI " (using matlab). > However, for rest fmri data, due to large size this is not possible.I also > tried 3dcalc of afni but failed. > Please let me know if you need further information. > > Best, > mahsa > > > On Tuesday, October 14, 2014 11:04 PM, "Harms, Michael" < > [email protected]> wrote: > > > > Hi Mahsa, > I think you are going to have to be more specific for anyone to be able to > help you. What is your goal? And what tools are you using and how are > you trying to apply the masking. For example, if you are trying to work > with the resting state volume data in Matlab/SPM, you may find that the > file sizes are too large to work conveniently in Matlab. > > 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 63110Email: [email protected] > > From: Mahsa Alizade shalchy <[email protected]> > Reply-To: Mahsa Alizade shalchy <[email protected]> > Date: Tuesday, October 14, 2014 2:23 PM > To: Hcp-users <[email protected]> > Subject: [HCP-Users] ROI extraction of rest fmri data > > Dear all > Hi > > I'm working on the rest fmri data(fix extended) and I have a problem > regarding masking. Since the data is very large (4D image with 1200 > volumes), I could not apply masking.Could you please help me on this matter? > Many thanks in advance. > Ps:I have 8 G of RAM available. > > Best, > mahsa > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailma n/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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