Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-11 Thread Timothy Coalson 
It was probably killed because it ran out of memory.  The best solution is
to use a machine with more memory.

A workaround, but one that will take a LOT more time to run on each subject
(unless you happen to already have fast SSDs), is to add swap space to your
system, which will allow it to pretend that it has more memory than it
really does, by writing some data that should be in RAM onto a storage
device (which is orders of magnitude slower than RAM).

Tim


On Wed, Oct 11, 2017 at 10:40 AM, Sang-Young Kim <sykim...@gmail.com> wrote:

> 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>
> Date: Monday, October 9, 2017 at 9:58 AM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: Stephen Smith <st...@fmrib.ox.ac.uk>, "hcp-users@humanconnectome.org"
> <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 array size
> limit
> 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> 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
>
> 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>
> Date: Friday, October 6, 2017 at 4:17 PM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: Stephen Smith <st...@fmrib.ox.ac.uk>, "hcp-users@humanconnectome.org"
> <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
>   ….
>
> Then, I ran the hcp_fix_multi_run script as follow: hcp_fix_multi_run
>  2000 rfMRI_REST_Concat
> ${FSL_FIXDIR}/training_files/HCP_hp2000.RData
> I also tried to

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-11 Thread Sang-Young Kim 
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 array size 
> limit
> 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  
>>  …. 
>> 
>> Then, I ran the hcp_fix_multi_run script as follow: hcp_fix_multi_run 
>>  2000 rfMRI_REST_Concat 
>> ${FSL_FIXDIR}/training_files

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-09 Thread Glasser, Matthew 
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 array size limit
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

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  
 ….

Then, I ran the hcp_fix_multi_run script as follow: hcp_fix_multi_run 
 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

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-09 Thread Timothy Coalson 
That looks like a generic matlab error related to the amount of memory the
computer has.  The memory requirements for some of these scripts are fairly
high (the machines we often use have 64GB of memory).

Tim


On Mon, Oct 9, 2017 at 9:58 AM, Sang-Young Kim <sykim...@gmail.com> wrote:

> 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 array size
> limit
> 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> 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
>
> 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>
> Date: Friday, October 6, 2017 at 4:17 PM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: Stephen Smith <st...@fmrib.ox.ac.uk>, "hcp-users@humanconnectome.org"
> <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
>   ….
>
> Then, I ran the hcp_fix_multi_run script as follow: hcp_fix_multi_run
>  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> 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>
> Date: Friday, October 6, 2017 at 11:06 AM
> To: Matt Glasser <glass...@wustl.edu>, Stephen Smith <st...@fmrib.ox.ac.uk
> >
> Cc: "hcp-users@humanconnectome.org" <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?

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-09 Thread Sang-Young Kim 
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 array size limit
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> 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  
>  …. 
> 
> Then, I ran the hcp_fix_multi_run script as follow: hcp_fix_multi_run 
>  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. 
>>

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-06 Thread Sang-Young Kim 
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  
 …. 

Then, I ran the hcp_fix_multi_run script as follow: hcp_fix_multi_run 
 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> 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 
>>>

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-06 Thread Glasser, Matthew 
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

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  
 ….

Then, I ran the hcp_fix_multi_run script as follow: hcp_fix_multi_run 
 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

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-06 Thread Glasser, Matthew 
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>
***


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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)
st...@fmrib.ox.ac.uk<mailto: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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Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-06 Thread Sang-Young Kim 
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> 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/>
> 
> 
> 
> 
> 
> ___
> 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>

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Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-06 Thread Glasser, Matthew 
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>
***


___
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HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
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
---

Stop the cultural destruction of Tibet<http://smithinks.net>






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Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-05 Thread Stephen Smith 
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  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
> ***  
> 
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> 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.ukhttp://www.fmrib.ox.ac.uk/~steve 

---

Stop the cultural destruction of Tibet 






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[HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-05 Thread Sang-Young Kim 
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
***  


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