Well, in this case, I will be using your toolbox now as it is just to get
familiar with it. I am really looking forward to the update then!
Thank you so much for the support.
Pedro
2018-03-16 21:40 GMT+01:00 Erin W. E. Dickie <erin.w.dic...@gmail.com>:
> In cases where you don't have a T2w image. You would run freesurfer's
> `*recon_all`
> *on your T1w scans and then *`ciftify_recon_all` * to essentially mimic
> the HCPPipelines Anatomical. * `ciftify_recon_all` *contains a little bit
> of PreFreesurfer.sh and all of PostFreesurfer.sh and is meant to be run
> after freesurfer.
>
> In the next release (i.e. next week), ciftify_recon_all will use the
> MSMSulc surface based registration (matching the HCP outputs) instead of
> the freesurfer registration. I would recommend waiting for that.
>
> For fMRI, the current workflow will be fMRIprep followed by
> ciftify_subject_fmri.
>
> We will also try to clarify this more in the documentation over the next
> few weeks.
>
> Thanks,
> Erin
>
> On Fri, Mar 16, 2018 at 11:12 AM, Pedro Costa Klein <pedrockl...@gmail.com
> > wrote:
>
>> Thank you Matt for the indication and thank you Erin for such a quick
>> response!
>>
>> Erin, this toolbox seems to be exactly what I was looking for!
>>
>> Does this toolbox replaces all the stages of the pipeline or should I use
>> it at some point of the HCP pipeline (e.g. after running the
>> PreFressurfer.sh)?
>>
>> Best regards,
>>
>> 2018-03-16 15:56 GMT+01:00 Erin W. E. Dickie <erin.w.dic...@gmail.com>:
>>
>>> Thanks for the recommendation Matt!
>>>
>>> Pedro, the ciftify toolbox link is here (https://edickie.github.io/cif
>>> tify). The toolbox started with exactly with what you are suggesting
>>> (modifying the .sh files to make them run without T2w images). Over time we
>>> ended up translating the key parts to python and adding more detailed
>>> logging and less intermediate output files.
>>>
>>> The current state of the package is a little unstable as I'm currently
>>> working in a few final changes. I'm aiming to publish a more stable release
>>> within the next two weeks.
>>>
>>> Let me know if you have any questions.
>>>
>>> Thanks,
>>> Erin
>>>
>>>
>>>
>>> On Fri, Mar 16, 2018 at 10:28 AM, Glasser, Matthew <glass...@wustl.edu>
>>> wrote:
>>>
>>>> I would recommend the ciftify toolbox if your data do not meet HCP
>>>> Pipelines acquisition requirements (lacking highres T2w scan and or
>>>> Fieldmap). The ciftify toolbox is currently beta, but should be fully
>>>> available in the very near future (Erin Dickie the author is CCed and can
>>>> give more details).
>>>>
>>>> Peace,
>>>>
>>>> Matt.
>>>>
>>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Pedro Costa
>>>> Klein <pedrockl...@gmail.com>
>>>> Date: Friday, March 16, 2018 at 3:49 AM
>>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>>> Subject: [HCP-Users] HCP Pipeline without T2w
>>>>
>>>> Dear all,
>>>>
>>>> I have a dataset that I wish to use with the HCP pipeline scripts from
>>>> the repository in https://github.com/Washington-University/Pipelines,
>>>> but I don't have the T2w images for the subjects. Is it possible (perhaps
>>>> with some modification on the .sh files) to use pipeline without the T2w?
>>>> If so, what would be the impact on the outputs and what are the most
>>>> "critical" steps that I must pay attention to while changing the scripts?
>>>>
>>>> Another idea would be to replace the T2w images by a synthetic image
>>>> (e.g. a T2w atlas, like the MNI). Is this option acceptable? If so, what
>>>> would be the best approach for using a atlas replacing the T2w?
>>>>
>>>> Thank you very much for your insights.
>>>>
>>>> --
>>>> *Pedro Costa Klein **(*https://scholar.google.
>>>> com.br/citations?user=ll3ukqMJ)
>>>> *PhD Student*
>>>> *Klinik und Poliklink für Psychiatrie und Psychotherapie
>>>> - Ludwig-Maximilians Universität*
>>>> pedrockl...@gmail.com
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ___
>>>> HCP-Users mailing list
>>>> HCP-Users@humanconnectome.org
>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>
>>>
>>>
>>
>>
>> --
>> *Pedro Costa Klein **(*https://scholar.google.
>> com.br/citations?user=ll3ukqMJ)
>> *PhD Student*
>> *Klinik und Poliklink für Psychiatrie und Psychotherapie
>> - Ludwig-Maximilians Universität*
>> pedrockl...@gmail.com
>>
>>
>>
>>
>>
>>
>
--
*Pedro Costa Klein **(*
https://scholar.google.com.br/citations?user=ll3ukqMJ)
*PhD Student*
*Klinik und Poliklink für Psychiatrie und Psychotherapie
- Ludwig-Maximilians Universität*
pedrockl...@gmail.com
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