I see, thanks again :). David
2016-07-15 13:05 GMT+02:00 Glasser, Matthew <[email protected]>: > You can, or you can compute on individual rows and average as Steve > suggested. It depends on what you are doing with the data where one or > another is preferred. > > Matt. > > From: David Hofmann <[email protected]> > Date: Friday, July 15, 2016 at 3:52 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 Matthew, > > one last clarification: After doing this for LR and RL seperately, I can > (or have to!) concatenate them together, is this correct? > > Thanks so much for the support :) > > David > > 2016-07-15 4:50 GMT+02:00 Glasser, Matthew <[email protected]>: > >> That’s fine, I usually have time along rows for better or for worse… >> >> Peace, >> >> Matt. >> >> From: David Hofmann <[email protected]> >> Date: Thursday, July 14, 2016 at 12:14 PM >> >> 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 Matthew, >> >> I'm sorry I made a mistake. I meant that I calculated the column mean and >> subtracted it from each column. For example given a 3 by 2 matrix with 3 >> time points and 2 ROIs >> >> Time | ROI 1 | ROI 2 >> 1 3 4 >> 2 2 2 >> 3 1 3 >> ------------------------ >> mean 2 3 >> >> Substracting 2 from ROI 1 and 3 from ROI 2 gives me >> >> Time | ROI 1 | ROI 2 >> 1 1 1 >> 2 0 -1 >> 3 -1 0 >> >> hope this clarifies it and this is what you meant. Sorry again for this >> mistake! >> >> David >> >> >> 2016-07-13 22:53 GMT+02:00 Glasser, Matthew <[email protected]>: >> >>> 2) Did you subtract the row mean from each row? >>> >>> Peace, >>> >>> Matt. >>> >>> From: David Hofmann <[email protected]> >>> Date: Wednesday, July 13, 2016 at 9:56 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 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. 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