 |
 |
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