JISCMail - SPM Archives

Thanks for your reply chris. Following are my answers to the questions

What you can try to do is create a mask (perhaps just using c1 & c2 TPMs), and see what you get.

I tried doing that to cut off those activations, but it does leave some voxels between skull n brain 'gap'

The contrast with the light blue overlay looks pretty noisy;

yes,

what's the task?

semantic feature. where the patient sees a picture and answers y/n with button box

What p-value threshold do you use? FWE correction?

activations are showing up only at 0.001 uncorrected. Nothing at FWE.

Thanks for your helpful reply

Kushal J Kapse

Aphasia Research Laboratory
Boston University

From: Chris Watson [[log in to unmask]]
Sent: Wednesday, January 08, 2014 1:26 PM
To: Kapse, Kushal Janardan
Cc: [log in to unmask]
Subject: Re: [SPM] Activation on skull

Actually the EPI's don't have whole brain coverage; the top of the brain is cut off. If you aren't interested in that part of the brain then it might not be the end of the world. However I don't have experience with partial coverage.
I doubt that is what's causing you to see "activation" in the skull, though. What you can try to do is create a mask (perhaps just using c1 & c2 TPMs), and see what you get.
The contrast with the light blue overlay looks pretty noisy; what's the task? What p-value threshold do you use? FWE correction?

Chris

On 01/08/2014 01:35 PM, Kapse, Kushal Janardan wrote:

Thanks for the reply chris. Last page of the attachment contains TPMs and Coreg. Please take a look and let me know your words on this

There was whole brain coverage. The TPM after Segmentation look good. 


Please take a look and any words on this would be helpful
Kushal J Kapse

Aphasia Research Laboratory
Boston University


________________________________________
From: Chris Watson [[log in to unmask]]
Sent: Wednesday, January 08, 2014 1:00 PM
To: Kapse, Kushal Janardan
Cc: [log in to unmask]
Subject: Re: [SPM] Activation on skull

So the EPI's are like that after normalization? What do they look like
before? Was there not whole brain coverage?
Can you post screenshots of the EPI/T1 coregistration (using Check Reg)?
Do the TPM's look correct?

On 01/08/2014 11:24 AM, Kapse, Kushal Janardan wrote:

file attached.


Thanks
Kushal J Kapse

Aphasia Research Laboratory
Boston University


________________________________________
From: Watson, Christopher [[log in to unmask]]
Sent: Wednesday, January 08, 2014 11:23 AM
To: Kapse, Kushal Janardan; [log in to unmask]
Subject: RE: [SPM] Activation on skull

I think you forgot the attachment. Please post a png or other image file if you can.
________________________________________
From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of Kapse, Kushal Janardan [[log in to unmask]]
Sent: Wednesday, January 08, 2014 8:56 AM
To: [log in to unmask]
Subject: Re: [SPM] Activation on skull

Hi Donald,

I checked the EPI to T1 registration. Seems the top few slices of the EPI brain is getting chopped. No issues with T1. This happens in the step of normalization. I checked the slicetiming, realigned files and they looked. Its in mean realigned image and thereafter which seems to cutoff the top brain. I have attached a word file which has a axial/sagittal   snapshot of the EPI image. If you can take a look and give me a feedback of possible ways this issue happening, that would be helpful.


Thanks

Kushal J Kapse

Aphasia Research Laboratory
Boston University

________________________________
From: MCLAREN, Donald [[log in to unmask]]
Sent: Tuesday, January 07, 2014 5:14 PM
To: Kapse, Kushal Janardan
Subject: Re: [SPM] Activation on skull

Have you checked the EPI to T1 registration? If its not properly registered, could this be the source of activation in the skull?

Best Regards, Donald McLaren
=================
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Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Tue, Jan 7, 2014 at 5:08 PM, Kushal Kapse <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi SPM users,

I am analyzing data for stroke patient and we have been having issue for two of our patients with abnormal activation maps. There is large amount of activation on the skull and area between skull and gray matter. I have been reading and have been trying to change various parameters in SPM to find a solution for this issue, but havent been successful yet. Hence, i thought of sharing this with SPM users expecting a suggestion which might help me solve this problem.


Also, following pipeline was used to analyze the data

Slice timing
Realign Est & Reslice
Coreg- estimate (ref imge-mean resliced function; source image- T1, other image-masked image)
Segment
Normalise:write (T1 image)
Normalise:write
Smooth

GLM
units of design-secs
Canonical HRF
No derivatives
Classical estimation

Please provide me a thought on where i need to expect changes or source of these abnormal activations


Thanks
Kushal