Thanks! Matt!
I have one more following-up question. In order to run the script
"hcp_fix_multi_run", we have to concatenate all the data temporally, right?
I combined the data using following command: fslmerge -t <rfMRI_REST_Concat>
<rfMRI_REST1_AP> …<rfMRI_REST4_PA>.
Then, I ran the hcp_fix_multi_run script as follow: hcp_fix_multi_run
<rfMRI_REST_Concat.nii.gz> 2000 rfMRI_REST_Concat
${FSL_FIXDIR}/training_files/HCP_hp2000.RData
I also tried to input the data as a list file, but the script didn’t work with
error. It seems to get only one 4D rfMRI data set as input.
That’s why I concatenated each run of rfMRI data set.
Could you please confirm whether the above procedures are correct or not?
Thanks again.
Sang-Young
> On Oct 6, 2017, at 3:57 PM, Glasser, Matthew <[email protected]> wrote:
>
> I would not do #2 as you need to do some preprocessing prior to running
> ICA+FIX when concatenating across runs and this is all that the multi-run
> ICA+FIX pipeline does differently from regular ICA+FIX.
>
> I’ll let Steve answer that other question.
>
> Matt.
>
> From: Sang-Young Kim <[email protected] <mailto:[email protected]>>
> Date: Friday, October 6, 2017 at 11:06 AM
> To: Matt Glasser <[email protected] <mailto:[email protected]>>, Stephen
> Smith <[email protected] <mailto:[email protected]>>
> Cc: "[email protected] <mailto:[email protected]>"
> <[email protected] <mailto:[email protected]>>
> Subject: Re: [HCP-Users] Combining rfMRI data for different phase encoding
> directions
>
> Hi, Matt and Stephen:
>
> Thanks for your responses. So I will try below three options to see which one
> is better.
>
> 1. ICA+FIX on each 5 min run separately
> 2. Concatenate each pair of scans from each session and then ICA+FIX on each
> session
> 3. Use multi-run ICA+FIX to combine across runs
>
> I have another simple question. In the paper published in NeuroImage (Smith
> et al., 2013, rfMRI in the HCP), the Figure 9 shows functional connectivity
> in the default mode network; one is from 15 min run from single subject,
> another one is from 4*15 min runs from single subject, and the other one is
> from all subjects concatenated.
>
> How did you process the data to present those figures (second and third one)?
> The third one should be processed with group ICA, right?
> What about the second one? This is processed with method 3 on above list?
>
> Thanks.
>
> Sang-Young
>
>
>> On Oct 6, 2017, at 5:40 AM, Glasser, Matthew <[email protected]
>> <mailto:[email protected]>> wrote:
>>
>> There is a beta version of a multi-run ICA+FIX pipeline available in the HCP
>> Pipeline’s repository. For 5 minute runs, I would expect combining across
>> runs to be best. We haven’t tested combining across sessions yet, so you
>> would have to check that that was working okay if you wanted to try that.
>>
>> Peace,
>>
>> Matt.
>>
>> From: <[email protected]
>> <mailto:[email protected]>> on behalf of Stephen Smith
>> <[email protected] <mailto:[email protected]>>
>> Date: Friday, October 6, 2017 at 1:49 AM
>> To: Sang-Young Kim <[email protected] <mailto:[email protected]>>
>> Cc: "[email protected] <mailto:[email protected]>"
>> <[email protected] <mailto:[email protected]>>
>> Subject: Re: [HCP-Users] Combining rfMRI data for different phase encoding
>> directions
>>
>> Hi - I think your main two choices are whether to run FIX on each 5min run
>> separately, or to preprocess and concatenate each pair of scans from each
>> session and run FIX for each of the 4 paired datasets. You could try FIX
>> both ways on a few subjects and decide which is working better.
>>
>> Cheers.
>>
>>
>>
>>> On 5 Oct 2017, at 22:53, Sang-Young Kim <[email protected]
>>> <mailto:[email protected]>> wrote:
>>>
>>> Dear Experts:
>>>
>>> We have acquired rfMRI dataset with A-P and P-A phase encoding direction
>>> and the data was acquired in eight 5-minute runs split across four imaging
>>> sessions. We have processed the data using HCP pipelines (e.g.,
>>> PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface and
>>> ICA+FIX). So we have results for each run of rfMRI data.
>>>
>>> I’m just curious about what is recommended way to combine each run of data
>>> (e.g., rfMRI_REST1_AP, rfMRI_REST1_PA, …, rfMRI_REST4_AP, rfMRI_REST4_PA).
>>>
>>> Can we just temporally concatenate each run of data before running ICA+FIX?
>>> Or can we do group ICA using each data processed with ICA+FIX?
>>> What is the optimal way to do combining analysis across each run?
>>>
>>> Any insights would be greatly appreciated.
>>>
>>> Thanks.
>>>
>>> Sang-Young Kim
>>> ***********************************************************
>>> Postdoctoral Research Fellow
>>> Department of Radiology at University of Pittsburgh
>>> email: [email protected] <mailto:[email protected]>
>>> ***********************************************************
>>>
>>>
>>> _______________________________________________
>>> HCP-Users mailing list
>>> [email protected] <mailto:[email protected]>
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>
>>
>>
>> ---------------------------------------------------------------------------
>> 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] <mailto:[email protected]>
>> http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve>
>> ---------------------------------------------------------------------------
>>
>> Stop the cultural destruction of Tibet <http://smithinks.net/>
>>
>>
>>
>>
>>
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