Re: [HCP-Users] ROI extraction of rest fmri data

[Harms, Michael]

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: mha...@wustl.edu From: Mahsa Alizade shalchy <ma.shal...@yahoo.com> Reply-To: Mahsa Alizade shalchy <ma.shal...@yahoo.com> Date: Wednesday, October 15, 2014 5:12 AM To: "Harms, Michael" <mha...@wustl.edu> 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" <mha...@wustl.edu> 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: mha...@wustl.edu From: Mahsa Alizade shalchy <ma.shal...@yahoo.com> Reply-To: Mahsa Alizade shalchy <ma.shal...@yahoo.com> Date: Tuesday, October 14, 2014 5:15 PM To: "Harms, Michael" <mha...@wustl.edu>, Hcp-users <hcp-users@humanconnectome.org> 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" <mha...@wustl.edu> 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: mha...@wustl.edu From: Mahsa Alizade shalchy <ma.shal...@yahoo.com> Reply-To: Mahsa Alizade shalchy <ma.shal...@yahoo.com> Date: Tuesday, October 14, 2014 3:07 PM To: "Harms, Michael" <mha...@wustl.edu> 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" <mha...@wustl.edu> 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: mha...@wustl.edu From: Mahsa Alizade shalchy <ma.shal...@yahoo.com> Reply-To: Mahsa Alizade shalchy <ma.shal...@yahoo.com> Date: Tuesday, October 14, 2014 2:49 PM To: "Harms, Michael" <mha...@wustl.edu> 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" <mha...@wustl.edu> 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: mha...@wustl.edu From: Mahsa Alizade shalchy <ma.shal...@yahoo.com> Reply-To: Mahsa Alizade shalchy <ma.shal...@yahoo.com> Date: Tuesday, October 14, 2014 2:23 PM To: Hcp-users <hcp-users@humanconnectome.org> 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 HCP-Users@humanconnectome.org 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. If you have received this email in error, please immediately notify the sender via telephone or return mail.   The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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