mixing parameters up (new segment + Dartel)

Submitted by Ham on Thu, 08/28/2014 - 14:17

Hello again!

Firs of all, congratulations! The new tool "dpabi" looks amazing! Another step forward!

It could be a silly question, but if run an analysis, with New segmentation + Dartel and then I Normalized to EPI template. Is this a bad processing criteria?

How it can affect to my analysis?

Or if I want to normalize to EPI templates I need to run the old segmentation?

Thank you!

Hi Ham,

Why do you want to normalize to EPI template if you New Segment + DARTEL done?

Software wise, you can. Paper wise, you may need to rethink.

Best,

Chao-Gan

That's right, it has no sense

That's right, it has no sense. Just wondering to try different parameters.

So, you recommend to try New segmentation + Dartel and and Normalize by Dartel?

And old Segment with normalize to epi?

Thank you so much!

Re: [RFMRI] mixing parameters

Normalize to EPI, you don't need T1 image.

If you have T1 image, just go to New Segment + DARTEL. Old Segment only if you have 3 subjects.

Best,

Chao-Gan

On Thu, Aug 28, 2014 at 11:05 AM, The R-fMRI Network <rfmri.org@gmail.com> wrote:

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Commented by Joan (Ham)
That's right, it has no sense. Just wondering to try different parameters.
So, you recommend to try New segmentation + Dartel and and Normalize by Dartel?
And old Segment with normalize to epi?

Thank you so much!

Online version of this post: http://rfmri.org/comment/3186#comment-3186

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The problem when I perform

The problem when I perform with New segment + Dartel and then I normalize with Dartel are the black spots.

I know that I can avoid this doing smoothing after normalization. But, I'm not sure about this step. So, in this case would you recommend to perform without segmentation and then normalize to the template?

What do you think?

best,

Re: [RFMRI] mixing parameters

No, I would still use DARTEL.

I have asked, and Dr. John Ashburner has replied that issue for several times. So I choose to trust him. :)

Best,

Chao-Gan

On Thu, Aug 28, 2014 at 11:35 AM, The R-fMRI Network <rfmri.org@gmail.com> wrote:

[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

Commented by Joan (Ham)
The problem when I perform with New segment + Dartel and then I normalize with Dartel are the black spots.
I know that I can avoid this doing smoothing after normalization. But, I'm not sure about this step. So, in this case would you recommend to perform without segmentation and then normalize to the template?

What do you think?

best,

Online version of this post: http://rfmri.org/comment/3188#comment-3188

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In Dr. John Ashburner We Trust

Thank you again,

Cheers!

mixing parameters up

Hi Chao-Gan,

I had the same issues, if you recall. In my own experience, I had to use EPI normalizations to get good registrations. But that might be because I had data from two magnets with different scan parameters (thickness, voxel size, etc).

Best,

Matt

Re: [RFMRI] mixing parameters

Hi Matt,

I think those mis-registration issues can be fixed by "bet" in DPARSF V3.0 Advanced Edition.

Best,

Chao-Gan

On Thu, Aug 28, 2014 at 2:49 PM, The R-fMRI Network <rfmri.org@gmail.com> wrote:

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Commented by Matthew Hoptman (hoptman)
Hi Chao-Gan,
I had the same issues, if you recall. In my own experience, I had to use EPI normalizations to get good registrations. But that might be because I had data from two magnets with different scan parameters (thickness, voxel size, etc).

Best,
Matt

Online version of this post: http://rfmri.org/comment/3191#comment-3191

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Dear Yan Chao-Gan,

As you correctly pointed out, even with an apparently bad normalization using DARTEL, the results after smoothing looks good and quite similars (i.e; using EPI template).

Could you please tell me if these parameters, which I used to perform with Dartel were properly used? Please realize, that to obtain better results I need to filter before W and S, and put a FWHM of 8.

http://s28.postimg.org/vu3zuxbjx/Captura_de_pantalla_2014_08_29_a_la_s_14_50_16.png

What do you think?

PS: I've already contributed, just a little bit sorry! hope you get more contributions soon!

Best,

Hi, I can't see the image,

Hi, I can't see the image, becaused my institute banned postimg.org.

Actually, you can post images here, just click

Best,

Chao-Gan

Thank you!

How do you determine your

How do you determine your normalization results are better if you put filter before W and S?

I know it sounds weird, but

I know it sounds weird, but when I was trying to replicate different hypothesis, just filtering before normalized & smoothed, I obtained similar aproximations. In the other case, If I put the filter after W/S I can't see nothing interesting, just a few significative clusters (from a list of 34 rois).

This I don't know well. This

This I don't know well. This is not a QC issue but a research issue, deserve a paper to study it.

For QC issue, I am thinking the normalization effects.

Best,

Chao-Gan

But do you think it could be

But do you think it could be a problem to submit a paper with data filtered before the normalization?

Best,

Juan Gea.

Re: [RFMRI] mixing parameters

If I am the reviewer, I don't think filter before spacial normalization is an issue.

Actually, DPARSFA, and my previous papers, have done some work "Calculate in original space". The spacial normalization only happens after the derivatives (e.g., FC maps, ALFF maps, ReHo maps) were calculated.

Best,

Chao-Gan

On Fri, Aug 29, 2014 at 10:23 AM, The R-fMRI Network <rfmri.org@gmail.com> wrote:

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Commented by Joan (Ham)
But do you think it could be a problem to submit a paper with data filtered before the normalization?
Best,
Juan Gea.

Online version of this post: http://rfmri.org/comment/3205#comment-3205

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Pefect! Thank you so much!

Cheers!

Mixing parameters up

Hi Chao-Gan,

Alas, this did not help in my case (see attached picture).

Best,

Matt

Hi Matt,

It's weird! You did "interactive reorienting" and "bet", right?

I don't know the cause, I suspect this is caused by that you still didn't make a contribution at http://rfmri.org/HelpUs.

;) I am teasing, Matt and I are good friends and know each other well.

Best,

Chao-Gan

RE: [RFMRI] mixing parameters

Hi Chao-Gan,

I forgot to do the interactive reorienting (DOH). Will try again. And will contribute even if you are kidding.

-M

From: RFMRI.ORG [mailto:rfmri.org-bounces@rnet.co] On Behalf Of The R-fMRI Network Sent: Friday, August 29, 2014 9:49 AM
To: rfmri.org@rnet.co
Subject: Re: [RFMRI] mixing parameters up (new segment + Dartel)

[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi Matt,

It's weird! You did "interactive reorienting" and "bet", right?

I don't know the cause, I suspect this is caused by that you still didn't make a contribution at http://rfmri.org/HelpUs.

;) I am teasing, Matt and I are good friends and know each other well.

Best,

Chao-Gan

Online version of this post: http://rfmri.org/comment/3198#comment-3198

Many a little makes a mickle -- your kind contributions shall make our efforts not perish from the earth. Please help The R-fMRI Network at http://rfmri.org/#overlay=HelpUs
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