Re: [HCP-Users] hcp_fix.for_fix1.06a

2017-07-20 Thread Glasser, Matthew 
Hi Yeun,

How long are your scans in frames and minutes.  What is your acquisition 
resolution and TR?  Using hcp_fix_multi_run might be helpful.

Matt.

From: Yeun Kim >
Date: Thursday, July 20, 2017 at 4:33 PM
To: Matt Glasser >
Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] hcp_fix.for_fix1.06a

I've been creating the preprocessing pipeline for CRHD Perturbation of the 
Treatment of Resistant Depression Connectome by Fast-Acting Therapies. Since it 
is a longitudinal study, I need all the versions to be consistent for optimal 
reproducibility. All preprocessing workflows so far have used FSL 
5.0.9-3~nd14.04+1. I would like to know if an installation of a newer version 
is necessary to obtain the modified version of melodic, because this will 
require re-processing of all data to ensure consistency in data processing. Or, 
if I can find the modified melodic in another repository separately.

Also, we have multiple fMRI scans (2 sets of rs-fMRIs and 2 sets of 
task-fMRIs). Should we use hcp_fix_multi_run?

Thank you,
Yeun

On Wed, Jul 19, 2017 at 5:21 PM, Glasser, Matthew 
> wrote:
The latest of everything will work for most applications.

Peace,

Matt.

From: Yeun Kim >
Date: Wednesday, July 19, 2017 at 7:20 PM

To: Matt Glasser >
Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] hcp_fix.for_fix1.06a

Latest release meaning 5.0.10? Or were the modifications implemented in 
previous releases/patches (in 5.0.9)?

Is the hcp_fix script in http://www.fmrib.ox.ac.uk/~steve/ftp/fix.tar.gz (the 
latest release - version 1.065) the correct one to use, then?


On Wed, Jul 19, 2017 at 5:15 PM, Glasser, Matthew 
> wrote:
I wouldn’t worry about that.  Those modifications should be in the latest FSL 
release.

Peace,

Matt.

From: Yeun Kim >
Date: Wednesday, July 19, 2017 at 7:14 PM
To: Matt Glasser >
Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] hcp_fix.for_fix1.06a

In the script ICAFIX/hcp_fix.for_fix1.06a, it uses the modified version of 
melodic:

Debug "Modified version of melodic in use"
Debug "melodic located at: ${HOME}/pipeline_tools/fix1.06a/melodic used"
Debug "instead of melodic located at: ${FSLDIR}/bin/melodic"
Debug "Beginning of melodic version log"
if [ "${DEBUG}" = "TRUE" ] ; then
${HOME}/pipeline_tools/fix1.06a/melodic --version
fi
Debug "End of melodic version log"

# "old" melodic command
#$FSLDIR/bin/melodic -i $fmri -o ${fmri}.ica/filtered_func_data.ica -d -250 
--nobet --report --Oall --tr=$tr
#

${HOME}/pipeline_tools/fix1.06a/melodic -i $fmri -o 
${fmri}.ica/filtered_func_data.ica -d -250 --nobet --report --Oall --tr=$tr

---
Or should I be using the old melodic?

On Wed, Jul 19, 2017 at 5:05 PM, Glasser, Matthew 
> wrote:
What is this in reference to?

Peace,

Matt.

From: 
>
 on behalf of Yeun Kim >
Date: Wednesday, July 19, 2017 at 7:04 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] hcp_fix.for_fix1.06a

Hi,

I cannot find the modified version of melodic in 
http://www.fmrib.ox.ac.uk/~steve/ftp/fix.tar.gz.

Where is the modified melodic?

Thank you,
Yeun

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Re: [HCP-Users] hcp_fix.for_fix1.06a

2017-07-20 Thread Yeun Kim 
I've been creating the preprocessing pipeline for CRHD Perturbation of the
Treatment of Resistant Depression Connectome by Fast-Acting Therapies.
Since it is a longitudinal study, I need all the versions to be consistent
for optimal reproducibility. All preprocessing workflows so far have used
FSL 5.0.9-3~nd14.04+1. I would like to know if an installation of a newer
version is necessary to obtain the modified version of melodic, because
this will require re-processing of all data to ensure consistency in data
processing. Or, if I can find the modified melodic in another repository
separately.

Also, we have multiple fMRI scans (2 sets of rs-fMRIs and 2 sets of
task-fMRIs). Should we use hcp_fix_multi_run?

Thank you,
Yeun

On Wed, Jul 19, 2017 at 5:21 PM, Glasser, Matthew 
wrote:

> The latest of everything will work for most applications.
>
> Peace,
>
> Matt.
>
> From: Yeun Kim 
> Date: Wednesday, July 19, 2017 at 7:20 PM
>
> To: Matt Glasser 
> Cc: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] hcp_fix.for_fix1.06a
>
> Latest release meaning 5.0.10? Or were the modifications implemented in
> previous releases/patches (in 5.0.9)?
>
> Is the hcp_fix script in http://www.fmrib.ox.ac.uk/~steve/ftp/fix.tar.gz (the
> latest release - version 1.065) the correct one to use, then?
>
>
> On Wed, Jul 19, 2017 at 5:15 PM, Glasser, Matthew 
> wrote:
>
>> I wouldn’t worry about that.  Those modifications should be in the latest
>> FSL release.
>>
>> Peace,
>>
>> Matt.
>>
>> From: Yeun Kim 
>> Date: Wednesday, July 19, 2017 at 7:14 PM
>> To: Matt Glasser 
>> Cc: "hcp-users@humanconnectome.org" 
>> Subject: Re: [HCP-Users] hcp_fix.for_fix1.06a
>>
>> In the script ICAFIX/hcp_fix.for_fix1.06a, it uses the modified version
>> of melodic:
>>
>> Debug "Modified version of melodic in use"
>> Debug "melodic located at: ${HOME}/pipeline_tools/fix1.06a/melodic used"
>> Debug "instead of melodic located at: ${FSLDIR}/bin/melodic"
>> Debug "Beginning of melodic version log"
>> if [ "${DEBUG}" = "TRUE" ] ; then
>> ${HOME}/pipeline_tools/fix1.06a/melodic --version
>> fi
>> Debug "End of melodic version log"
>>
>> # "old" melodic command
>> #$FSLDIR/bin/melodic -i $fmri -o ${fmri}.ica/filtered_func_data.ica -d
>> -250 --nobet --report --Oall --tr=$tr
>> #
>>
>> ${HOME}/pipeline_tools/fix1.06a/melodic -i $fmri -o
>> ${fmri}.ica/filtered_func_data.ica -d -250 --nobet --report --Oall
>> --tr=$tr
>>
>> ---
>> Or should I be using the old melodic?
>>
>> On Wed, Jul 19, 2017 at 5:05 PM, Glasser, Matthew 
>> wrote:
>>
>>> What is this in reference to?
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From:  on behalf of Yeun Kim <
>>> yeun...@gmail.com>
>>> Date: Wednesday, July 19, 2017 at 7:04 PM
>>> To: "hcp-users@humanconnectome.org" 
>>> Subject: [HCP-Users] hcp_fix.for_fix1.06a
>>>
>>> Hi,
>>>
>>> I cannot find the modified version of melodic in
>>> http://www.fmrib.ox.ac.uk/~steve/ftp/fix.tar.gz.
>>>
>>> Where is the modified melodic?
>>>
>>> Thank you,
>>> Yeun
>>>
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>
>>
>

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