Re: [HCP-Users] FW: HCP Scripts

Please use the launcher scripts in ${GitRepo}/Examples and don’t modify the pipelines themselves unless you know what you are doing (i.e. have read and understood the code).  Only the code in examples is intended for you to modify.   Peace, Matt. From: Jennifer Elam

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

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

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 b

[HCP-Users] FW: HCP Scripts

From: hcp-announce-boun...@humanconnectome.org [mailto:hcp-announce-boun...@humanconnectome.org] Sent: Monday, October 13, 2014 9:39 AM To: e...@wustl.edu Subject: Forward of moderated message Hello, thank you all for publishing this extensive set of image processing scripts. I've go

Re: [HCP-Users] B-values for DWI data

Hi Sam, The HCP diffusion data was collected with the b-values interleaved throughout each run. You might want to search the HCP-Users archive for more information/answers to questions on this. Specifically, here’s a relevant thread with a link to the reference with details on the data: http:/

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

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.o

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

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,

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

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 f

[HCP-Users] ROI extraction of rest fmri data

Dear allHi 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 _

Re: [HCP-Users] REST_fix and REST_preproc

Hi Priyank, If you go more deep into the folders inside MNINonLinear, you will arrive at compressed (.gz) files having size of around 1GB. It will be evident from the filename that it is the resting state data. Unzip it and use. You can refer to the HCP500 reference manual for complete details: h

Re: [HCP-Users] REST_fix and REST_preproc

Hi Priyank, If you go more deep into the folders inside MNINonLinear, you will arrive at compressed (.gz) files having size of around 1GB. It will be evident from the filename that it is the resting state data. Unzip it and use. You can refer to the HCP500 reference manual for complete details: h

[HCP-Users] REST_fix and REST_preproc

Hi, I just downloaded 100 subject data for resting state analysis (part of 500 data set). After extracting the compressed files, I get 3 folders in each subject. Str REST_fix REST_preproc Each of these folders contain MNINonLinear and release-notes subfolders and Str has T1w subfolder too.