Re: [HCP-Users] hcp_fix.for_fix1.06a
Hi Matt, Great, thanks. I was able to use the multi-run ICA+FIX with MELODIC from FSL 5.0.9-3~nd14.04+1. Is it correct to use MELODIC from this FSL release (5.0.9-3~nd14.04+1) for HCP multi-run ICA+FIX? We would like to lock down the software versions for our pipelines very soon. According to their change logs, the 5.0.10 version of MELODIC has the following updates: MELODIC can run on CIFTI files; temporal concatenation in MELODIC now defaults to using MIGP. Thank you, Yeun On Fri, Jul 21, 2017 at 1:19 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > Hi Yeun, > > I think you should use multi-run ICA+FIX given the relatively short runs > you have. If your data are all from the same session, I would recommend > cleaning all fMRI runs together (resting state and task). > > As for which version to use, I think using the original is fine, as the > other may have modifications specific to the HCP computer system. I’ve > CCed Tim Brown who made the additional changes in case he has further > comment. > > Matt. > > From: Yeun Kim <yeun...@gmail.com> > Date: Friday, July 21, 2017 at 1:38 PM > > To: Matt Glasser <glass...@wustl.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] hcp_fix.for_fix1.06a > > To follow up, which script should I work with? hcp_fix_multi_run > or hcp_fix_multi_run.original? > > Thanks, > Yeun > > On Fri, Jul 21, 2017 at 11:13 AM, Yeun Kim <yeun...@gmail.com> wrote: > >> Hi Matt, >> >> We're a Depression-HCP site, using nearly identical sequences as ongoing >> HCP Aging projects. For rs-fMRI: TR = 800ms, 488 volumes, voxel size 2mm^3, >> for 2 runs (one AP, one PA phase encoding). Total time when concatenating >> the two runs is about 13 minutes. Task fMRI runs are the same but shorter >> (300 volumes for CARIT; 338 vol x 2 runs for an in-house task). >> >> On Thu, Jul 20, 2017 at 5:38 PM, Glasser, Matthew <glass...@wustl.edu> >> wrote: >> >>> 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 <yeun...@gmail.com> >>> Date: Thursday, July 20, 2017 at 4:33 PM >>> >>> To: Matt Glasser <glass...@wustl.edu> >>> Cc: "hcp-users@humanconnectome.org" <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 <glass...@wustl.edu> >>> wrote: >>> >>>> The latest of everything will work for most applications. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: Yeun Kim <yeun...@gmail.com> >>>> Date: Wednesday, July 19, 2017 at 7:20 PM >>>> >>>> To: Matt Glasser <glass...@wustl.edu> >>>> Cc: "hcp-users@humanconnectome.org" <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 <glass...@wustl.edu> >>>> wrote: >>>> >>>>> I wouldn’t worry about that. Those modifications should be in the >>>>> latest FSL release.
Re: [HCP-Users] hcp_fix.for_fix1.06a
To follow up, which script should I work with? hcp_fix_multi_run
or hcp_fix_multi_run.original?
Thanks,
Yeun
On Fri, Jul 21, 2017 at 11:13 AM, Yeun Kim <yeun...@gmail.com> wrote:
> Hi Matt,
>
> We're a Depression-HCP site, using nearly identical sequences as ongoing
> HCP Aging projects. For rs-fMRI: TR = 800ms, 488 volumes, voxel size 2mm^3,
> for 2 runs (one AP, one PA phase encoding). Total time when concatenating
> the two runs is about 13 minutes. Task fMRI runs are the same but shorter
> (300 volumes for CARIT; 338 vol x 2 runs for an in-house task).
>
> On Thu, Jul 20, 2017 at 5:38 PM, Glasser, Matthew <glass...@wustl.edu>
> wrote:
>
>> 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 <yeun...@gmail.com>
>> Date: Thursday, July 20, 2017 at 4:33 PM
>>
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <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 <glass...@wustl.edu>
>> wrote:
>>
>>> The latest of everything will work for most applications.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: Yeun Kim <yeun...@gmail.com>
>>> Date: Wednesday, July 19, 2017 at 7:20 PM
>>>
>>> To: Matt Glasser <glass...@wustl.edu>
>>> Cc: "hcp-users@humanconnectome.org" <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 <glass...@wustl.edu>
>>> wrote:
>>>
>>>> I wouldn’t worry about that. Those modifications should be in the
>>>> latest FSL release.
>>>>
>>>> Peace,
>>>>
>>>> Matt.
>>>>
>>>> From: Yeun Kim <yeun...@gmail.com>
>>>> Date: Wednesday, July 19, 2017 at 7:14 PM
>>>> To: Matt Glasser <glass...@wustl.edu>
>>>> Cc: "hcp-users@humanconnectome.org" <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 <glass...@wustl.edu>
>>>> wrote:
>>>>
>>>>> What is this in reference to?
>>>>>
>>>>> Peace,
>>>>>
>>>>> Matt.
>>>>>
>>>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Yeun Kim <
>>>>> yeun...@gmail.com>
>>>>> Date: Wednesday, July 19, 2017 at 7:04 PM
>>>>> To: "hcp-users@humanconnectome.org" <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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Re: [HCP-Users] hcp_fix.for_fix1.06a
Hi Matt,
We're a Depression-HCP site, using nearly identical sequences as ongoing
HCP Aging projects. For rs-fMRI: TR = 800ms, 488 volumes, voxel size 2mm^3,
for 2 runs (one AP, one PA phase encoding). Total time when concatenating
the two runs is about 13 minutes. Task fMRI runs are the same but shorter
(300 volumes for CARIT; 338 vol x 2 runs for an in-house task).
On Thu, Jul 20, 2017 at 5:38 PM, Glasser, Matthew <glass...@wustl.edu>
wrote:
> 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 <yeun...@gmail.com>
> Date: Thursday, July 20, 2017 at 4:33 PM
>
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <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 <glass...@wustl.edu>
> wrote:
>
>> The latest of everything will work for most applications.
>>
>> Peace,
>>
>> Matt.
>>
>> From: Yeun Kim <yeun...@gmail.com>
>> Date: Wednesday, July 19, 2017 at 7:20 PM
>>
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <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 <glass...@wustl.edu>
>> wrote:
>>
>>> I wouldn’t worry about that. Those modifications should be in the
>>> latest FSL release.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: Yeun Kim <yeun...@gmail.com>
>>> Date: Wednesday, July 19, 2017 at 7:14 PM
>>> To: Matt Glasser <glass...@wustl.edu>
>>> Cc: "hcp-users@humanconnectome.org" <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 <glass...@wustl.edu>
>>> wrote:
>>>
>>>> What is this in reference to?
>>>>
>>>> Peace,
>>>>
>>>> Matt.
>>>>
>>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Yeun Kim <
>>>> yeun...@gmail.com>
>>>> Date: Wednesday, July 19, 2017 at 7:04 PM
>>>> To: "hcp-users@humanconnectome.org" <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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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 <glass...@wustl.edu>
wrote:
> The latest of everything will work for most applications.
>
> Peace,
>
> Matt.
>
> From: Yeun Kim <yeun...@gmail.com>
> Date: Wednesday, July 19, 2017 at 7:20 PM
>
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <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 <glass...@wustl.edu>
> wrote:
>
>> I wouldn’t worry about that. Those modifications should be in the latest
>> FSL release.
>>
>> Peace,
>>
>> Matt.
>>
>> From: Yeun Kim <yeun...@gmail.com>
>> Date: Wednesday, July 19, 2017 at 7:14 PM
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <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 <glass...@wustl.edu>
>> wrote:
>>
>>> What is this in reference to?
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Yeun Kim <
>>> yeun...@gmail.com>
>>> Date: Wednesday, July 19, 2017 at 7:04 PM
>>> To: "hcp-users@humanconnectome.org" <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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Re: [HCP-Users] diffusion data merge pipeline
Don't recommend the parallel processing or the eddy_cuda?
On Tue, Jul 18, 2017 at 2:13 PM, Glasser, Matthew <glass...@wustl.edu>
wrote:
> We really don’t recommend you do that. I would ask about the eddy_cuda on
> the FSL or neurodebian lists.
>
> Peace,
>
> Matt.
>
> From: Yeun Kim <yeun...@gmail.com>
> Date: Tuesday, July 18, 2017 at 4:11 PM
> To: "Harms, Michael" <mha...@wustl.edu>
> Cc: Matt Glasser <glass...@wustl.edu>, "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] diffusion data merge pipeline
>
> Thanks for the reply.
> I would like to reduce the computing time for DiffusionPreprocessing;
> feeding in both sets of dMRIs takes about 24.16 hours to run, while
> parallel processing takes 10.72 hours.
> I've been trying to retrieve the eddy_cuda version, but I can't find it in
> the neurodebian packages. Where can I find pre-compiled binaries of
> eddy_cuda?
> The platform I am using in my Docker is Ubuntu 14.04 LTS.
>
> Thank you again,
> Yeun
>
> On Mon, Jul 17, 2017 at 11:57 AM, Harms, Michael <mha...@wustl.edu> wrote:
>
>>
>> Hi,
>> Is there a particular reason that you can’t provide all the dMRI scans at
>> once, and let the pipeline handle the merging for you?
>> If you process each dMRI run separately, then the individual runs will
>> not be in optimal alignment. (You would be relying on the registration of
>> each run to the T1, rather than registering the dMRI directly to each other
>> as part of ‘eddy’).
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave.Tel: 314-747-6173 <(314)%20747-6173>
>> St. Louis, MO 63110Email: mha...@wustl.edu
>>
>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Yeun Kim <
>> yeun...@gmail.com>
>> Date: Monday, July 17, 2017 at 1:32 PM
>> To: "Glasser, Matthew" <glass...@wustl.edu>
>>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] diffusion data merge pipeline
>>
>> I am using the following function (and is looped through the pairs of
>> unique sets of gradient tables (i.e. loops twice for dir99 and dir98):
>> ${HCPPIPEDIR}/DiffusionPreprocessing/DiffPreprocPipeline.sh \
>> --posData="{posData}" \
>> --negData="{negData}" \
>> --path="{path}" \
>> --subject="{subject}" \
>> --echospacing="{echospacing}" \
>> --PEdir={PEdir} \
>> --gdcoeffs="NONE" \
>> --dwiname="{dwiname}" \
>> --printcom=""'
>>
>> Where:
>> $posData = diffusion data in the positive direction
>> $negData = diffusion data in the negative direction
>> $path = output directory path
>> $echospacing = echospacing
>> $PEdir = 2
>> $dwiname = i.e. Diffusion_dir-98_run-01
>>
>>
>> FYI: I'm using HCPPipelines v3.17.
>>
>> -
>>
>> Technical details:
>>
>> I run ${HCPPIPEDIR}/DiffusionPreprocessing/DiffPreprocPipeline.sh in a
>> Docker container with the following python code. It is looped through the
>> pairs of unique sets of gradient tables (i.e. loops twice for dir99 and
>> dir98) and set to process in parallel:
>>
>> dwi_stage_dict = OrderedDict([("DiffusionPreprocessing",
>> partial(run_diffusion_processsing,
>>
>>*posData*=pos,
>>
>>*negData*=neg,
>>
>>*path*=args.output_dir,
>>
>>*subject*="sub-%s" % subject_label,
>>
>>*echospacing*=echospacing,
>>
>>*PEdir*=PEdir,
>>
>>*gdcoeffs*="NONE",
>>
>>*dwiname*=dwiname,
>>
>>*n_cpus*=args.n_cpus))])
>> for stage, stage_func in
>> dwi_stage_dict.iteritems():
>> if stage in args.stages:
>> Process(target=stage_func).start()
>>
>> On Mon, Jul 17, 2017 at 11:15 AM, Glasser, Matthew <glass...@wustl.edu>
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 <glass...@wustl.edu>
wrote:
> I wouldn’t worry about that. Those modifications should be in the latest
> FSL release.
>
> Peace,
>
> Matt.
>
> From: Yeun Kim <yeun...@gmail.com>
> Date: Wednesday, July 19, 2017 at 7:14 PM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <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 <glass...@wustl.edu>
> wrote:
>
>> What is this in reference to?
>>
>> Peace,
>>
>> Matt.
>>
>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Yeun Kim <
>> yeun...@gmail.com>
>> Date: Wednesday, July 19, 2017 at 7:04 PM
>> To: "hcp-users@humanconnectome.org" <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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HCP-Users@humanconnectome.org
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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 <glass...@wustl.edu>
wrote:
> What is this in reference to?
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Yeun Kim <
> yeun...@gmail.com>
> Date: Wednesday, July 19, 2017 at 7:04 PM
> To: "hcp-users@humanconnectome.org" <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
>
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[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
Re: [HCP-Users] diffusion data merge pipeline
Thanks for the reply.
I would like to reduce the computing time for DiffusionPreprocessing;
feeding in both sets of dMRIs takes about 24.16 hours to run, while
parallel processing takes 10.72 hours.
I've been trying to retrieve the eddy_cuda version, but I can't find it in
the neurodebian packages. Where can I find pre-compiled binaries of
eddy_cuda?
The platform I am using in my Docker is Ubuntu 14.04 LTS.
Thank you again,
Yeun
On Mon, Jul 17, 2017 at 11:57 AM, Harms, Michael <mha...@wustl.edu> wrote:
>
> Hi,
> Is there a particular reason that you can’t provide all the dMRI scans at
> once, and let the pipeline handle the merging for you?
> If you process each dMRI run separately, then the individual runs will not
> be in optimal alignment. (You would be relying on the registration of each
> run to the T1, rather than registering the dMRI directly to each other as
> part of ‘eddy’).
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173 <(314)%20747-6173>
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Yeun Kim <
> yeun...@gmail.com>
> Date: Monday, July 17, 2017 at 1:32 PM
> To: "Glasser, Matthew" <glass...@wustl.edu>
>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] diffusion data merge pipeline
>
> I am using the following function (and is looped through the pairs of
> unique sets of gradient tables (i.e. loops twice for dir99 and dir98):
> ${HCPPIPEDIR}/DiffusionPreprocessing/DiffPreprocPipeline.sh \
> --posData="{posData}" \
> --negData="{negData}" \
> --path="{path}" \
> --subject="{subject}" \
> --echospacing="{echospacing}" \
> --PEdir={PEdir} \
> --gdcoeffs="NONE" \
> --dwiname="{dwiname}" \
> --printcom=""'
>
> Where:
> $posData = diffusion data in the positive direction
> $negData = diffusion data in the negative direction
> $path = output directory path
> $echospacing = echospacing
> $PEdir = 2
> $dwiname = i.e. Diffusion_dir-98_run-01
>
>
> FYI: I'm using HCPPipelines v3.17.
>
> -
>
> Technical details:
>
> I run ${HCPPIPEDIR}/DiffusionPreprocessing/DiffPreprocPipeline.sh in a
> Docker container with the following python code. It is looped through the
> pairs of unique sets of gradient tables (i.e. loops twice for dir99 and
> dir98) and set to process in parallel:
>
> dwi_stage_dict = OrderedDict([("DiffusionPreprocessing",
> partial(run_diffusion_processsing,
>
>*posData*=pos,
>
>*negData*=neg,
>
>*path*=args.output_dir,
>
>*subject*="sub-%s" % subject_label,
>
>*echospacing*=echospacing,
>
>*PEdir*=PEdir,
>
>*gdcoeffs*="NONE",
>
>*dwiname*=dwiname,
>
>*n_cpus*=args.n_cpus))])
> for stage, stage_func in
> dwi_stage_dict.iteritems():
> if stage in args.stages:
> Process(target=stage_func).start()
>
> On Mon, Jul 17, 2017 at 11:15 AM, Glasser, Matthew <glass...@wustl.edu>
> wrote:
>
>> The pipeline is capable of doing the merge for you if you want. Can you
>> post how you called the diffusion pipeline?
>>
>> Peace,
>>
>> Matt.
>>
>> From: Yeun Kim <yeun...@gmail.com>
>> Date: Monday, July 17, 2017 at 1:12 PM
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] diffusion data merge pipeline
>>
>> When I run DiffusionPreprocessing, I make the --dwiname=DWIName specific
>> to the diffusion scan (i.e. DWIName= Diffusion_dir-98_run-01) to prevent
>> files from being overwritten.
>> I end up with:
>> ${StudyFolder}/${Subject}/T1w/Diffusion_dir-98_run-01/data.nii.gz
>> ${StudyFolder}/${Subject}/T1w/Diffusion_dir-99_run-01/data.nii.gz
>>
>> I would like to combine the two data.nii.gz files.
>>
>> On Mon, Jul 17, 2017 at 10:58 AM, Glasser, Matthew <glass...@wustl.edu>
>>
Re: [HCP-Users] diffusion data merge pipeline
I am using the following function (and is looped through the pairs of
unique sets of gradient tables (i.e. loops twice for dir99 and dir98):
${HCPPIPEDIR}/DiffusionPreprocessing/DiffPreprocPipeline.sh \
--posData="{posData}" \
--negData="{negData}" \
--path="{path}" \
--subject="{subject}" \
--echospacing="{echospacing}" \
--PEdir={PEdir} \
--gdcoeffs="NONE" \
--dwiname="{dwiname}" \
--printcom=""'
Where:
$posData = diffusion data in the positive direction
$negData = diffusion data in the negative direction
$path = output directory path
$echospacing = echospacing
$PEdir = 2
$dwiname = i.e. Diffusion_dir-98_run-01
FYI: I'm using HCPPipelines v3.17.
-
Technical details:
I run ${HCPPIPEDIR}/DiffusionPreprocessing/DiffPreprocPipeline.sh in a
Docker container with the following python code. It is looped through the
pairs of unique sets of gradient tables (i.e. loops twice for dir99 and
dir98) and set to process in parallel:
dwi_stage_dict = OrderedDict([("DiffusionPreprocessing",
partial(run_diffusion_processsing,
*posData*=pos,
*negData*=neg,
*path*=args.output_dir,
*subject*="sub-%s" % subject_label,
*echospacing*=echospacing,
*PEdir*=PEdir,
*gdcoeffs*="NONE",
*dwiname*=dwiname,
*n_cpus*=args.n_cpus))])
for stage, stage_func in
dwi_stage_dict.iteritems():
if stage in args.stages:
Process(target=stage_func).start()
On Mon, Jul 17, 2017 at 11:15 AM, Glasser, Matthew <glass...@wustl.edu>
wrote:
> The pipeline is capable of doing the merge for you if you want. Can you
> post how you called the diffusion pipeline?
>
> Peace,
>
> Matt.
>
> From: Yeun Kim <yeun...@gmail.com>
> Date: Monday, July 17, 2017 at 1:12 PM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] diffusion data merge pipeline
>
> When I run DiffusionPreprocessing, I make the --dwiname=DWIName specific
> to the diffusion scan (i.e. DWIName= Diffusion_dir-98_run-01) to prevent
> files from being overwritten.
> I end up with:
> ${StudyFolder}/${Subject}/T1w/Diffusion_dir-98_run-01/data.nii.gz
> ${StudyFolder}/${Subject}/T1w/Diffusion_dir-99_run-01/data.nii.gz
>
> I would like to combine the two data.nii.gz files.
>
> On Mon, Jul 17, 2017 at 10:58 AM, Glasser, Matthew <glass...@wustl.edu>
> wrote:
>
>> Look for the ${StudyFolder}/${Subject}/T1w/Diffusion/data.nii.gz file.
>>
>> Peace,
>>
>> Matt.
>>
>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Yeun Kim <
>> yeun...@gmail.com>
>> Date: Monday, July 17, 2017 at 12:56 PM
>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: [HCP-Users] diffusion data merge pipeline
>>
>> Hi,
>>
>> We have the diffusion scans:
>> dMRI_dir98_AP, dMRI_dir98_PA
>> dMRI_dir99_AP, dMRI_dir99_PA
>>
>> in which there is a pair of phase encoding directions (AP,PA) and two
>> sets of different diffusion weighting directions (dir98 and dir99).
>>
>> After running the DiffusionPreprocessing module of the HCP minimal
>> preprocessing pipeline, I would like to merge the processed dMRI_dir98 and
>> dMRI_dir99 data. Do you have any suggestions on how to perform this step?
>> Also, are there any workflows developed by HCP for
>> post-DiffusionPreprocessing?
>>
>> Thank you,
>> Yeun
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>
>
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] diffusion data merge pipeline
When I run DiffusionPreprocessing, I make the --dwiname=DWIName specific to
the diffusion scan (i.e. DWIName= Diffusion_dir-98_run-01) to prevent files
from being overwritten.
I end up with:
${StudyFolder}/${Subject}/T1w/Diffusion_dir-98_run-01/data.nii.gz
${StudyFolder}/${Subject}/T1w/Diffusion_dir-99_run-01/data.nii.gz
I would like to combine the two data.nii.gz files.
On Mon, Jul 17, 2017 at 10:58 AM, Glasser, Matthew <glass...@wustl.edu>
wrote:
> Look for the ${StudyFolder}/${Subject}/T1w/Diffusion/data.nii.gz file.
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Yeun Kim <
> yeun...@gmail.com>
> Date: Monday, July 17, 2017 at 12:56 PM
> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: [HCP-Users] diffusion data merge pipeline
>
> Hi,
>
> We have the diffusion scans:
> dMRI_dir98_AP, dMRI_dir98_PA
> dMRI_dir99_AP, dMRI_dir99_PA
>
> in which there is a pair of phase encoding directions (AP,PA) and two sets
> of different diffusion weighting directions (dir98 and dir99).
>
> After running the DiffusionPreprocessing module of the HCP minimal
> preprocessing pipeline, I would like to merge the processed dMRI_dir98 and
> dMRI_dir99 data. Do you have any suggestions on how to perform this step?
> Also, are there any workflows developed by HCP for
> post-DiffusionPreprocessing?
>
> Thank you,
> Yeun
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
___
HCP-Users mailing list
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Re: [HCP-Users] task fMRI analysis
Hi, After I run the fMRIVolume and and fMRISurface using 2 runs of tfMRI data with (AP and PA), should I expect two output directories (i.e. emotion_AP and emotion_PA)? Does the fmri preprocessing combine the two runs at a certain point? Thank you, Yeun On Tue, Nov 29, 2016 at 10:31 AM, Harms, Michael <mha...@wustl.edu> wrote: > > Hi, > The TaskfMRIAnalysis Pipeline, as currently written, assumes two or more > runs of each task. You could comment out the last part of > TaskfMRIAnalysis.v2.0.sh where it calls TaskfMRILevel2.v2.0.sh, so that > the TaskfMRIAnalysis.v2.0.sh script would run without error. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > --- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 <(314)%20747-6173> > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Yeun Kim < > yeun...@gmail.com> > Date: Tuesday, November 29, 2016 at 12:05 PM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] task fMRI analysis > > Hi, > > For task fMRI analysis in the minimal processing pipeline, do I need the > separated outputs of fmri data of each phase encoding direction? (i.e. > tFMRI_EMOTION_LR_* and tFMRI_EMOTION_RL_*). I just want to perform level > one analysis. > > Thank you, > Yeun > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] task fMRI analysis
Hi, For task fMRI analysis in the minimal processing pipeline, do I need the separated outputs of fmri data of each phase encoding direction? (i.e. tFMRI_EMOTION_LR_* and tFMRI_EMOTION_RL_*). I just want to perform level one analysis. Thank you, Yeun ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Diffusion Preprocessing
Hi, For the HCP diffusion processing pipeline, do you have the option to use the single-band reference images for registration purposes? Thank you in advance, Yeun ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] 7T (full resolution structural) data download
Hello, I would like to download some 7T structural data from HCP (at full resolution). Are there any available? Thank you, Yeun Kim ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
