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 <glass...@wustl.edu>:
> That’s fine, I usually have time along rows for better or for worse…
>
> Peace,
>
> Matt.
>
> From: David Hofmann <davidhofma...@gmail.com>
> Date: Thursday, July 14, 2016 at 12:14 PM
>
> To: Matt Glasser <glass...@wustl.edu>
> Cc: Stephen Smith <st...@fmrib.ox.ac.uk>, "Dierker, Donna" <
> do...@wustl.edu>, hcp-users <hcp-users@humanconnectome.org>
> 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 <glass...@wustl.edu>:
>
>> 2) Did you subtract the row mean from each row?
>>
>> Peace,
>>
>> Matt.
>>
>> From: David Hofmann <davidhofma...@gmail.com>
>> Date: Wednesday, July 13, 2016 at 9:56 AM
>>
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: Stephen Smith <st...@fmrib.ox.ac.uk>, "Dierker, Donna" <
>> do...@wustl.edu>, hcp-users <hcp-users@humanconnectome.org>
>> 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 <glass...@wustl.edu>:
>>
>>> 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 <davidhofma...@gmail.com>
>>> Date: Tuesday, July 12, 2016 at 6:56 AM
>>> To: Matt Glasser <glass...@wustl.edu>
>>> Cc: Stephen Smith <st...@fmrib.ox.ac.uk>, "Dierker, Donna" <
>>> do...@wustl.edu>, hcp-users <hcp-users@humanconnectome.org>
>>>
>>> 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 <glass...@wustl.edu>:
>>>
>>>> Also it appears you haven’t either cleaned or removed the mean image
>>>> from the data.
>>>>
>>>> Matt.
>>>>
>>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Stephen
>>>> Smith <st...@fmrib.ox.ac.uk>
>>>> Date: Tuesday, July 12, 2016 at 3:48 AM
>>>> To: David Hofmann <davidhofma...@gmail.com>
>>>> Cc: "Dierker, Donna" <do...@wustl.edu>, hcp-users <
>>>> hcp-users@humanconnectome.org>
>>>>
>>>> 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 <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>:
>>>>
>>>>>
>>>>> 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: mha...@wustl.edu
>>>>>
>>>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of David
>>>>> Hofmann <davidhofma...@gmail.com>
>>>>> Date: Monday, July 11, 2016 at 3:15 AM
>>>>> To: "Dierker, Donna" <do...@wustl.edu>
>>>>> Cc: hcp-users <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>:
>>>>>
>>>>>> 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 <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
>>>>>> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>>> >
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> HCP-Users mailing list
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>>>>>
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>>>>
>>>>
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>>>> <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
>>>>
>>>> ---------------------------------------------------------------------------
>>>>
>>>> Stop the cultural destruction of Tibet <http://smithinks.net>
>>>>
>>>>
>>>>
>>>>
>>>>
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--
David Hofmann (M.Sc.)
Institut für Medizinische Psychologie und Systemneurowissenschaften
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Tel: 0251/ 8352794
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