Hi - no we do not (in general for resting-state) ever recommend temporal contatenation like this before further analyses - for the reason you're seeing here. For example, for the HCP released netmats, we take the 4 runs, one at a time, estimate the 4 (zstat) netmats, and average those. Cheers.
> On 12 Jul 2016, at 09:43, David Hofmann <davidhofma...@gmail.com> wrote: > > Hi Michael, > > thanks for the reply, using a different routine works and shows 1200 volumes. > But now it seems that in some data (extracted ROI mean) there is a huge > difference between LR and RL phase encoding in the signal (see attached > picture). Is this "normal" and can I just concatenate LR and RL together or > is this not possible? > > greetings > > David > > 2016-07-11 19:43 GMT+02:00 Harms, Michael <mha...@wustl.edu > <mailto:mha...@wustl.edu>>: > > Hi, > Can you check the number of volumes/frames of the unpacked > REST1_{LR,RL}.nii.gz files using something other than your Matlab/SPM tools? > e.g., FSL’s ‘fslhd’ or ‘fslnvols’ commands. > > 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 <tel:314-747-6173> > St. Louis, MO 63110 Email: mha...@wustl.edu <mailto:mha...@wustl.edu> > > From: <hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of David Hofmann > <davidhofma...@gmail.com <mailto:davidhofma...@gmail.com>> > Date: Monday, July 11, 2016 at 3:15 AM > To: "Dierker, Donna" <do...@wustl.edu <mailto:do...@wustl.edu>> > Cc: hcp-users <hcp-users@humanconnectome.org > <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] Extracting ROI data from HCP resting state data - > 2400 data points instead of 1200 ? > > Hi Donna and others, > > thanks for your answer. I'm facing a difficulty with extracting data from the > preprocessed files, that is they seems to each contain 2400 data points > rather than 1200 like described in the documentation. > > I downloaded the 10 subjects data set and used the following files: > subjectcode_3T_rfMRI_REST1_preproc.zip, from which I assume that these are > the preprocessed files. > > It contains two datasets LR and RL: > > \MNINonLinear\Results\rfMRI_REST1_LR > \MNINonLinear\Results\rfMRI_REST1_RL > > I unpacked these files: > > rfMRI_REST1_LR.nii.gz > rfMRI_REST1_RL.nii.gz > > and read them as 4D NIFTI with Matlab and an SPM function. Afterwards they > each contain 2400 data points (dimension: 91 109 91 2400), but in the > documention it says they each should contain only 1200 data points. So I'm > not sure if I did something wrong. > > greetings > > David > > > 2016-06-30 18:30 GMT+02:00 Dierker, Donna <do...@wustl.edu > <mailto:do...@wustl.edu>>: > Hi David, > > I hope this publication answers your questions about HCP rfMRI preprocessing: > > Resting-state fMRI in the Human Connectome Project. > Smith SM1, Beckmann CF, Andersson J, Auerbach EJ, Bijsterbosch J, Douaud G, > Duff E, Feinberg DA, Griffanti L, Harms MP, Kelly M, Laumann T, Miller KL, > Moeller S, Petersen S, Power J, Salimi-Khorshidi G, Snyder AZ, Vu AT, > Woolrich MW, Xu J, Yacoub E, Uğurbil K, Van Essen DC, Glasser MF; WU-Minn HCP > Consortium. > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3720828/ > <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3720828/> > > I am only used to seeing what it is in the fix extended packages, so I'm not > sure all these volumes are in the basic fix packages, but here are NIFTI > volumes in a sample subject's rfMRI subdirectories: > > 177645/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000.ica/filtered_func_data.ica/mask.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000.ica/filtered_func_data.ica/melodic_IC.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000.ica/filtered_func_data.ica/melodic_oIC.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000.ica/filtered_func_data.ica/mask.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000.ica/filtered_func_data.ica/melodic_IC.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000.ica/filtered_func_data.ica/melodic_oIC.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000_clean.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000.ica/filtered_func_data.ica/mask.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000.ica/filtered_func_data.ica/melodic_IC.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000.ica/filtered_func_data.ica/melodic_oIC.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000_clean.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000.ica/filtered_func_data.ica/mask.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000.ica/filtered_func_data.ica/melodic_IC.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000.ica/filtered_func_data.ica/melodic_oIC.nii.gz > 177645/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL.nii.gz > > Maybe this page will help explain those: > > http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/rfMRIconnectivity/ > <http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/rfMRIconnectivity/> > > But keep in mind that for neocortex, you can take advantage of the surface > data the HCP provides (e.g., fsaverage_32k/*surf.gii, *dscalar.nii and > *dtseries.nii). You can get better inter-subject registration/alignment on > the surface, if that will be a factor in your study. > > Donna > > > On Jun 28, 2016, at 6:30 PM, David Hofmann <davidhofma...@gmail.com > <mailto:davidhofma...@gmail.com>> wrote: > > > Hi all, > > > > I would like to extract ROI data (only neocortex) 'manually' e.g. using a > > ROI from Harvard-Oxford atlas from HCP resting state data, but I'm not sure > > which (nifti) files to use and where to find them. I'm also looking for > > some information about the preprocessing steps applied to the resting state > > data that is, if some additional steps (e.g. filtering) have to be carried > > out before ROI extraction or if this has already been done. > > > > Any help on this appreciated! > > > > Thanks > > > > David > > _______________________________________________ > > HCP-Users mailing list > > HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> > > > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <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. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > <timecourse.png> --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet <http://smithinks.net/> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
