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?
YAN Chao-Gan
Thu, 08/28/2014 - 14:39
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Hi Ham,
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
Ham
Thu, 08/28/2014 - 15:05
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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!
YAN Chao-Gan
Thu, 08/28/2014 - 15:10
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Re: [RFMRI] mixing parameters
Ham
Thu, 08/28/2014 - 15:35
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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,
YAN Chao-Gan
Thu, 08/28/2014 - 15:50
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Re: [RFMRI] mixing parameters
Ham
Thu, 08/28/2014 - 16:05
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In Dr. John Ashburner We Trust
Thank you again,
Cheers!
hoptman
Thu, 08/28/2014 - 18:49
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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
YAN Chao-Gan
Thu, 08/28/2014 - 19:00
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Re: [RFMRI] mixing parameters
Ham
Fri, 08/29/2014 - 12:58
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Dear Yan Chao-Gan,
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?
YAN Chao-Gan
Fri, 08/29/2014 - 13:30
Permalink
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
Ham
Fri, 08/29/2014 - 13:54
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Thank you!
Thank you!
YAN Chao-Gan
Fri, 08/29/2014 - 13:57
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How do you determine your
How do you determine your normalization results are better if you put filter before W and S?
Ham
Fri, 08/29/2014 - 14:08
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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).
YAN Chao-Gan
Fri, 08/29/2014 - 14:13
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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
Ham
Fri, 08/29/2014 - 14:23
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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.
YAN Chao-Gan
Fri, 08/29/2014 - 14:30
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Re: [RFMRI] mixing parameters
Ham
Fri, 08/29/2014 - 14:38
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Pefect! Thank you so much!
Pefect! Thank you so much!
Cheers!
hoptman
Fri, 08/29/2014 - 13:45
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Mixing parameters up
Hi Chao-Gan,
Alas, this did not help in my case (see attached picture).
Best,
Matt
YAN Chao-Gan
Fri, 08/29/2014 - 13:49
Permalink
Hi 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
hoptman
Fri, 08/29/2014 - 14:00
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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:
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