Dear Matt:
I ran the multi-run ICA+FIX according to your guideline. But at the last stage
of cleaning the data (e.g., fix_3_clean), I got an error message in the file of
.fix.log. Please see below:
Could you please help me how to handle this issue?
Thanks.
Sang-Young
TR =
0.8000
Elapsed time is 24.545680 seconds.
Elapsed time is 2.739398 seconds.
{^HError using '
Requested 902629x3360 (22.6GB) array exceeds maximum array size preference.
Creation of arrays greater than this limit may take a long time and cause
MATLAB to become unresponsive. See <a href="matlab: helpview([docroot
'/matlab/helptargets.map'], 'matlab_env_workspace_prefs')">array size limit</a>
or preference panel for more information.
Error in fix_3_clean (line 67)
cts=reshape(cts,ctsX*ctsY*ctsZ,ctsT)’;
> On Oct 6, 2017, at 4:40 PM, Glasser, Matthew <[email protected]> wrote:
>
> No multi-run ICA+FIX handles the concatenation for you so you specify the
> separate runs. That is the whole point. Have a look at this bioRvix paper
> in the methods about multi-run ICA+FIX so you understand why it is
> implemented the way it is:
>
> https://www.biorxiv.org/content/early/2017/09/27/193862
> <https://www.biorxiv.org/content/early/2017/09/27/193862>
>
> Here is an example call to multi-run ICA+FIX:
>
> ${FSL_FIXDIR}/hcp_fix_multi_run
> ${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}.nii.gz@${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}.nii.gz@${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}.nii.gz@${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}.nii.gz
> 2000
> ${StudyFolder}/${Subject}/MNINonLinear/Results/${ConcatName}/${ConcatName}.nii.gz
>
> Peace,
>
> Matt.
>
> From: Sang-Young Kim <[email protected] <mailto:[email protected]>>
> Date: Friday, October 6, 2017 at 4:17 PM
> To: Matt Glasser <[email protected] <mailto:[email protected]>>
> Cc: Stephen Smith <[email protected] <mailto:[email protected]>>,
> "[email protected] <mailto:[email protected]>"
> <[email protected] <mailto:[email protected]>>
> Subject: Re: [HCP-Users] Combining rfMRI data for different phase encoding
> directions
>
> 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]
>> <mailto:[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]>
>>>> ***********************************************************
>>>>
>>>>
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>>>
>>>
>>> ---------------------------------------------------------------------------
>>> 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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>
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