Strange effect on ReOh and ALFF maps

Submitted by dbd18 on

Dear experts,

 

I am trying to compute ALFF and ReOH maps with DPARSFA (for parametres see attached file. In case of ALFF I have only smoothed before and leave all the rest the same). The pipeline runs smoothly but I got a strange effect on the resulting maps (see attached figure).

 

Could you please advice on what to do?

 

Thank you very much in advance,

 

Kind regards,

Bianca

Juergen Haenggi

Fri, 01/06/2017 - 08:15

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Dear Bianca
I recommend not using DARTEL for spatial normalization. 
you can instead use T1 unified segmentation.
please have a look at the images in the folder PicturesForChkNormalization.
if the artefacts are also on this pictures, it is definitively DARTEL that have introduced these artefacts.

Cheers
Jürgen

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Am 06.01.2017 um 08:13 schrieb The R-fMRI Network:

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

By Bianca De Blasi (dbd18)

Dear experts,

 

I am trying to compute ALFF and ReOH maps with DPARSFA (for parametres see attached file. In case of ALFF I have only smoothed before and leave all the rest the same). The pipeline runs smoothly but I got a strange effect on the resulting maps (see attached figure).

 

Could you please advice on what to do?

 

Thank you very much in advance,

 

Kind regards,

Bianca


Online version of this post: http://rfmri.org/content/strange-effect-reoh-and-alff-maps-0


Thank you for this.
I got an error when I try using t1 unified segmentation (matrix index do not agree and I am not sure why). On the other hand the normalisation works fine when the epi template option is selected. Would this be good enough?

Thanks for your help,
Kind regards,
Bianca
From: RFMRI.ORG <rfmri.org-bounces@rnet.co> on behalf of The R-fMRI Network <rfmri.org@gmail.com>
Sent: 06 January 2017 08:15:07
To: rfmri.org@rnet.co
Subject: Re: [RFMRI] Strange effect on ReOh and ALFF maps
 

Dear all,

thank you for this. I read this post and tried what was suggested (smooth with DARTEL after or selecting MNI warp by DARTEL) but I still get the same effect. Also, in my case I have more than a black dot. Anything else you suggest to try?


Thank you,

Best regards,

Bianca 

From: RFMRI.ORG <rfmri.org-bounces@rnet.co> on behalf of The R-fMRI Network <rfmri.org@gmail.com>
Sent: 07 January 2017 01:12:12
To: rfmri.org@rnet.co
Subject: Re: [RFMRI] Strange effect on ReOh and ALFF maps
 

Just wanted to clarify that by using smooth by DARTEL after normalisation or MNI (warp by DARTEL), the obtained maps seem not to show the streak effect even if the CheckNorm images show this. On the other hand, if you use DARTEL and normal smoothing there is a streak effect on the resulting maps as well.

Please advise on what to do: I really would like to use DARTEL, but I am worried as the streak effects on the CheckNorm pictures makes me think this normalisation is not reliable and it would affect the results.

So far, the only way I got no error in the normalisation and normal appearing maps is by using EPI template for the normalisation.

Please let me know what you think,

Thank you,

Kind regards,

Bianca

With "smooth", the maps have a strike effect (parallel black lines). 

Please advise on what to do: I have tried many different options with DARTEL but I still get the streak effect on the CheckNormPics. The ALFF maps have different values every time and in most cases they have strikes similar to the normalisation picture.

Thanks, 

Kind regards,

Bianca

 

 

 
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