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Then I think looking at 0.001 uncorrected is the reason you're seeing activation in the skull. It's a very liberal threshold. One option: you may want to look only at a few regions, based on the literature, and use explicit masks. (as long as you don't go "fishing" for results) Chris On 01/08/2014 01:57 PM, Kapse, Kushal Janardan wrote: > 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 >>> ================= >>> D.G. McLaren, Ph.D. >>> 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 >>> ===================== >>> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED >>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >>> intended only for the use of the individual or entity named above. If the >>> reader of the e-mail is not the intended recipient or the employee or agent >>> responsible for delivering it to the intended recipient, you are hereby >>> notified that you are in possession of confidential and privileged >>> information. Any unauthorized use, disclosure, copying or the taking of any >>> action in reliance on the contents of this information is strictly >>> prohibited and may be unlawful. If you have received this e-mail >>> unintentionally, please immediately notify the sender via telephone at (773) >>> 406-2464 or email. >>> >>> >>> 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 >>> >