[HCP-Users] Request for DTIV1_to_Workbench.sh

[Durgerian, Sally]

Dear Experts,

I'm interested in using the script DTIV1_to_Workbench.sh as described in the 
HCP course materials, but I don't want to have to download the entire course VM 
to get it. Is there a way of making that script available on GitHub or on the 
HCP web site? Note that it also requires Whole_Brain_Trajectory_1.25.nii.gz 
which I haven't been able to find outside the VM either.

I saw a thread in the past (Tue, 01 Mar 
2016)
 requesting this script, but when I clicked that link my browser removed the 
attachment saying it was a security hazard.

Thanks for your help.

Sally

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Re: [HCP-Users] Forbidden to download

[Timothy Coalson]

Did you agree to the "open access" data use terms before trying to
download?  The tutorial dataset is covered by these terms, but maybe it
doesn't make this obvious.

Tim


On Wed, Feb 6, 2019 at 5:31 PM Rosalia Dacosta Aguayo 
wrote:

> Dear HCP users,
>
> I registered to the HCP web. I installed what was needed following the pdf
> documentation. I also have firefox as my browser but when I tried to
> download the tutprial dataset it says me "forbidden"
>
> Any idea why this is happening and how to solve it?
>
> Yours sincerely,
> Rosalia
>
> ___
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> HCP-Users@humanconnectome.org
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>

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Re: [HCP-Users] FreeSurfer6 subcortical segmentation

[Glasser, Matthew]

I don’t see these being generated in our current test FreeSurfer 6.0 runs.  How 
are they generated?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Sanchez, Juan (NYSPI)" 
mailto:juan.sanc...@nyspi.columbia.edu>>
Date: Wednesday, February 6, 2019 at 12:56 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] FreeSurfer6 subcortical segmentation


Hey HCP community

When Freesurfer 6.0  is implemented into the HCP Pipeline, are there plans to 
use the subcortical segmentation script outputs (amygdala and thalamus mgz 
files) into cifti space (column 3)?

If so will they be an addition to the current ROI atlas or will they be 
separate?


Thanks so much

Juan



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[HCP-Users] Forbidden to download

[Rosalia Dacosta Aguayo]

Dear HCP users,

I registered to the HCP web. I installed what was needed following the pdf
documentation. I also have firefox as my browser but when I tried to
download the tutprial dataset it says me "forbidden"

Any idea why this is happening and how to solve it?

Yours sincerely,
Rosalia

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Re: [HCP-Users] Bandpass filtering ICA-FIX resting data

[Glasser, Matthew]

It’s better to remove structured noise with ICA-based techniques, and we really 
essentially are only detrending HCP data.  For unstructured noise, this will 
not affect regression-based analyses much, but will affect correlation 
analyses.  I’d recommend parcellating your data to reduce unstructured noise.  
Temporal filtering will remove higher frequency BOLD signal.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Anita Sinha mailto:amsi...@wisc.edu>>
Date: Wednesday, February 6, 2019 at 2:43 PM
To: Steve Smith mailto:st...@fmrib.ox.ac.uk>>
Cc: "hcp-users@humanconnectome.org" 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] Bandpass filtering ICA-FIX resting data


Others in the literature have looked into how slow-4 (0.027-0.073 Hz) and 
slow-5 (0.01-0.027 Hz) oscillations in rs-fMRI data change between populations. 
Would you then recommend that unless we are looking at specific frequency bins 
within resting-state, we should not bandpass filter the rs-fMRI data that has 
gone through ICA-FIX?


From: Steve Smith mailto:st...@fmrib.ox.ac.uk>>
Sent: Wednesday, February 6, 2019 12:34:55 PM
To: Anita Sinha
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Bandpass filtering ICA-FIX resting data

Hi


On 6 Feb 2019, at 18:08, Anita Sinha 
mailto:amsi...@wisc.edu>> wrote:

To Whom It May Concern,

I am interested in using ICA-FIX resting-fMRI data from HCP. Given that ICA-FIX 
functions to denoise the data by removing high frequency noise,

It's not explicitly doing this.   The pre-filtering removes just the *very* 
lowest frequencies.   But yes in practice FIX will remove a lot of high 
frequency components if they are deemed artefact.

do you recommend bandpass filtering the rs-fMRI data (0.01- 0.1 Hz) that has 
already gone through ICA-FIX before running any analysis?

No - I would almost never recommend doing lowpass filtering (removing high 
frequency signal).

Cheers.




Thank you for your time. I look forward to hearing from you soon.

Regards,

Anita

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---
Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  WIN (FMRIB) Oxford

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 610470
st...@fmrib.ox.ac.uk
http://www.fmrib.ox.ac.uk/~steve
---

Stop the cultural destruction of Tibet









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The materials in this message are private and may contain Protected Healthcare 
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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.

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Re: [HCP-Users] Bandpass filtering ICA-FIX resting data

[Anita Sinha]

Others in the literature have looked into how slow-4 (0.027-0.073 Hz) and 
slow-5 (0.01-0.027 Hz) oscillations in rs-fMRI data change between populations. 
Would you then recommend that unless we are looking at specific frequency bins 
within resting-state, we should not bandpass filter the rs-fMRI data that has 
gone through ICA-FIX?


From: Steve Smith 
Sent: Wednesday, February 6, 2019 12:34:55 PM
To: Anita Sinha
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Bandpass filtering ICA-FIX resting data

Hi


On 6 Feb 2019, at 18:08, Anita Sinha 
mailto:amsi...@wisc.edu>> wrote:

To Whom It May Concern,

I am interested in using ICA-FIX resting-fMRI data from HCP. Given that ICA-FIX 
functions to denoise the data by removing high frequency noise,

It's not explicitly doing this.   The pre-filtering removes just the *very* 
lowest frequencies.   But yes in practice FIX will remove a lot of high 
frequency components if they are deemed artefact.

do you recommend bandpass filtering the rs-fMRI data (0.01- 0.1 Hz) that has 
already gone through ICA-FIX before running any analysis?

No - I would almost never recommend doing lowpass filtering (removing high 
frequency signal).

Cheers.




Thank you for your time. I look forward to hearing from you soon.

Regards,

Anita

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---
Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  WIN (FMRIB) Oxford

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 610470
st...@fmrib.ox.ac.uk
http://www.fmrib.ox.ac.uk/~steve
---

Stop the cultural destruction of Tibet









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[HCP-Users] FreeSurfer6 subcortical segmentation

[Sanchez, Juan (NYSPI)]

Hey HCP community

When Freesurfer 6.0  is implemented into the HCP Pipeline, are there plans to 
use the subcortical segmentation script outputs (amygdala and thalamus mgz 
files) into cifti space (column 3)?

If so will they be an addition to the current ROI atlas or will they be 
separate?


Thanks so much

Juan



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Re: [HCP-Users] Bandpass filtering ICA-FIX resting data

[Steve Smith]

Hi


> On 6 Feb 2019, at 18:08, Anita Sinha  wrote:
> 
> To Whom It May Concern,
> 
> I am interested in using ICA-FIX resting-fMRI data from HCP. Given that 
> ICA-FIX functions to denoise the data by removing high frequency noise,

It's not explicitly doing this.   The pre-filtering removes just the *very* 
lowest frequencies.   But yes in practice FIX will remove a lot of high 
frequency components if they are deemed artefact.

> do you recommend bandpass filtering the rs-fMRI data (0.01- 0.1 Hz) that has 
> already gone through ICA-FIX before running any analysis?

No - I would almost never recommend doing lowpass filtering (removing high 
frequency signal).

Cheers.



> 
> Thank you for your time. I look forward to hearing from you soon.
> 
> Regards,
> 
> Anita
> ___
> 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,  WIN (FMRIB) Oxford

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 610470
st...@fmrib.ox.ac.ukhttp://www.fmrib.ox.ac.uk/~steve 

---

Stop the cultural destruction of Tibet 









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[HCP-Users] Bandpass filtering ICA-FIX resting data

[Anita Sinha]

To Whom It May Concern,


I am interested in using ICA-FIX resting-fMRI data from HCP. Given that ICA-FIX 
functions to denoise the data by removing high frequency noise, do you 
recommend bandpass filtering the rs-fMRI data (0.01- 0.1 Hz) that has already 
gone through ICA-FIX before running any analysis?


Thank you for your time. I look forward to hearing from you soon.


Regards,


Anita

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