Hi Matthew, thank you for the help!
I did the following: 1. I used the "clean" datasets now and extracted my ROI data from the LR and RL phase encodings (first two sessions) 2. I calculated the mean across time for every ROI and substracted it, i.e. I have a 1200 by 112 matrix and calculated the row mean (over time) and substracted it from each column (ROIs). 3. I did this for LR and RL seperately and then concatenated them together Can you confirm that this is the correct? thanks again! David 2016-07-13 0:55 GMT+02:00 Glasser, Matthew <[email protected]>: > I would recommend using the data with _hp2000_clean in the name. I a > referring to taking the mean across time at each point in space and > subtracting that from the data. > > Peace, > > Matt. > > From: David Hofmann <[email protected]> > Date: Tuesday, July 12, 2016 at 6:56 AM > To: Matt Glasser <[email protected]> > Cc: Stephen Smith <[email protected]>, "Dierker, Donna" < > [email protected]>, hcp-users <[email protected]> > > Subject: Re: [HCP-Users] Extracting ROI data from HCP resting state data > - 2400 data points instead of 1200 ? > > Hi all, > > Regarding Stephen's answer: I thought it is necessary to concatenate the > LR/RL phase encoding directions together somehow or can I just treat every > run seperately? What I basically want is the timecourse from a voxel or a > region (from preprocessed data) which I can use for further analysis. > > Regarding Matthew's answer: I'm afraid I'm not exactly sure what you mean > by cleaning or removing the mean image from the data. Mean centering? > > I used the preprocessed datasets: > > > > *subjectcode_3T_rfMRI_REST1_preproc.zip * > \MNINonLinear\Results\rfMRI_REST1_LR > \MNINonLinear\Results\rfMRI_REST1_RL > > Is this the correct data or is it necessary to use some different datasets > for my specific purposes? (Normally I'd use the netmats datasets, but in > I'm especially interested in the amygdala which I'm trying to extract from > the Harvard-Oxford Atlas ROI). > > Thanks for your answers! > > David > > 2016-07-12 12:47 GMT+02:00 Glasser, Matthew <[email protected]>: > >> Also it appears you haven’t either cleaned or removed the mean image from >> the data. >> >> Matt. >> >> From: <[email protected]> on behalf of Stephen Smith >> <[email protected]> >> Date: Tuesday, July 12, 2016 at 3:48 AM >> To: David Hofmann <[email protected]> >> Cc: "Dierker, Donna" <[email protected]>, hcp-users < >> [email protected]> >> >> Subject: Re: [HCP-Users] Extracting ROI data from HCP resting state data >> - 2400 data points instead of 1200 ? >> >> 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 <[email protected]> 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 <[email protected]>: >> >>> >>> 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 >>> St. Louis, MO 63110 Email: [email protected] >>> >>> From: <[email protected]> on behalf of David >>> Hofmann <[email protected]> >>> Date: Monday, July 11, 2016 at 3:15 AM >>> To: "Dierker, Donna" <[email protected]> >>> Cc: hcp-users <[email protected]> >>> 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 <[email protected]>: >>> >>>> 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/ >>>> >>>> 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/ >>>> >>>> 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 <[email protected]> >>>> 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 >>>> > [email protected] >>>> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> > >>>> >>>> >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] >>> 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 >> [email protected] >> 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) >> [email protected] http://www.fmrib.ox.ac.uk/~steve >> >> --------------------------------------------------------------------------- >> >> Stop the cultural destruction of Tibet <http://smithinks.net> >> >> >> >> >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> 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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