Dear Matt:
I turned off the array size limit in Matlab, then ran again hcp_fix_multi_run.
I cannot see any error in .fix.log file but cleaned data was not generated. One
thing I can notice in the terminal is that some process is killed
automatically.
Please see below:
FIX Applying cleanup using cleanup file:
rfMRI_REST_All_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup
set to 1
sh: line 1: 7063 Killed: 9
/Applications/MATLAB_R2015b.app/bin/matlab -nojvm -nodisplay -nodesktop
-nosplash -r "restoredefaultpath; addpath('/usr/local/fsl/etc/matlab');
addpath('/Users/sang-young/projects/Pipelines/global/matlab');
addpath('/usr/local/fix'); fix_3_clean('.fix',0,1,-1)" >> .fix.log 2>&1
Start=1 Stop=420
Do you have any idea why this happen and how to fix it?
Many thanks.
Sang-Young
> On Oct 9, 2017, at 6:19 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
>
> I think you will need to go in the matlab preferences and fix that. I don’t
> recall exactly where it is, but it should be easy to find on google.
> Basically you need to turn off the array size limit. Alternatively you need
> to run the job on a machine with more RAM.
>
> Peace,
>
> Matt.
>
> From: Sang-Young Kim <sykim...@gmail.com <mailto:sykim...@gmail.com>>
> Date: Monday, October 9, 2017 at 9:58 AM
> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>
> Cc: Stephen Smith <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>>,
> "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>"
> <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] Combining rfMRI data for different phase encoding
> directions
>
> 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 <glass...@wustl.edu
>> <mailto:glass...@wustl.edu>> 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 <sykim...@gmail.com <mailto:sykim...@gmail.com>>
>> Date: Friday, October 6, 2017 at 4:17 PM
>> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>
>> Cc: Stephen Smith <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>>,
>> "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>"
>> <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>>
>> 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 <glass...@wustl.edu
>>> <mailto:glass...@wustl.edu>> 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 <sykim...@gmail.com <mailto:sykim...@gmail.com>>
>>> Date: Friday, October 6, 2017 at 11:06 AM
>>> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>, Stephen
>>> Smith <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>>
>>> Cc: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>"
>>> <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>>
>>> 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 <glass...@wustl.edu
>>>> <mailto:glass...@wustl.edu>> 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: <hcp-users-boun...@humanconnectome.org
>>>> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Stephen Smith
>>>> <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>>
>>>> Date: Friday, October 6, 2017 at 1:49 AM
>>>> To: Sang-Young Kim <sykim...@gmail.com <mailto:sykim...@gmail.com>>
>>>> Cc: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>"
>>>> <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>>
>>>> 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 <sykim...@gmail.com
>>>>> <mailto:sykim...@gmail.com>> 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: sykim...@gmail.com <mailto:sykim...@gmail.com>
>>>>> ***********************************************************
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> HCP-Users mailing list
>>>>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
>>>>> 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)
>>>> st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>
>>>> 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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