 |
 |
Dear McLaren, I tried the method Marko mentioned and MRIcron worked partially well. Yes, we can makes it inversely, i.e., set the activation map as background, the template as overlay. Only in that case, the template is not bright, as I need to set the transparency like 50%. Alternatively, other methods work as well, like make the original spmT map clean before overlay using xjview (which i am familiar with) or spm_bwlabel, orthoview. Going back to MRIcro is also ok, only sometimes it will ask you to reslice the activation map before overlay. Thank you all for the information! Best wishes, Gao The University of Hong Kong On 17 April 2012 00:21, MCLAREN, Donald <[log in to unmask]> wrote: > Another alternative would be OrthoView > (http://nmr.mgh.harvard.edu/harvardagingbrain/People/AaronSchultz/OrthoView.html). > It can apply several different thresholds and has the ability to save > thresholded images. > > Best Regards, Donald McLaren > ================= > D.G. McLaren, Ph.D. > Postdoctoral Research Fellow, GRECC, Bedford VA > Research Fellow, Department of Neurology, Massachusetts General Hospital and > Harvard Medical School > 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 Mon, Apr 16, 2012 at 12:07 PM, Franziska Korb > <[log in to unmask]> wrote: >> Hi Gao, >> >> in case Marko's solution doesn't work for you, here's another >> workaround... ;-) : >> You could use the xjview toolbox (http://www.alivelearn.net/xjview8/) to >> threshold the T-maps (or whatever maps you have) and then save the >> thresholded image which you can display in MRIcron. You might have to >> convert it from *.img to *.nii, but that's a quick step (in case you are >> not familiar with it), especially if you use the batch editor. >> >> Good luck, >> Franziska >> >> >> On 4/16/2012 11:51 AM, Marko Wilke wrote: >>> >>> Hi Gao, >>> >>> I only saw this today myself, so don't know how well it works, but you >>> can try Draw, Advanced, Apply Cluster Threshold. You may then have to >>> load the background image as an overlay, but hey ;) Otherwise, you can >>> of course manipulate your image using spm_bwlabel and then use that >>> "cleaned" result for overlays. >>> >>> Cheers, >>> Marko >>> >>> >>> Gao wrote: >>>> >>>> Sorry if this is not very relevant to SPM. >>>> But anyone here know if it's possible to set a minimum cluster size >>>> (# of >>>> voxels) for overlays in MRIcron? >>>> This was possible in MRIcro, yet I can't seem to find a similarly >>>> functioning button (or command line reference) for it in MRIcron. >>>> Thanks in Advance! >>>> Gao >>>> >>> >> >> -- >> Franziska M. Korb, Ph.D. >> >> Postdoctoral Associate (Egner Lab) >> >> Center for Cognitive Neuroscience >> LSRC Building, Room C03D, Research Dr >> Box 90999 >> Duke University >> Durham, NC 27708 >> >> phone: ++1-919-684.1034 >> >> http://sites.google.com/site/egnerlab/