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The plotting function plots the data that went into generating the spm T map. So if you have a two-sample t-test of con_ values, then the plot function plots the con_ values for each subject by group for either the peak or the cluster. Otherwise, you'd just have a single value on the plots. 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 Wed, Apr 29, 2015 at 9:49 PM, Andy Yeung <[log in to unmask]> wrote: > Dear Donald, > > Thank you very much for your clarification. If I overlay a spm T map onto > FIVE, then I assume the Y axis is T value as I plot at peak voxel? > What if I plot cluster, does that mean averaged T value of that cluster > (sum of T values of each suprathreshold voxels in a cluster divided by no. > of suprathreshold voxels)? > > Best, > Andy > > On Thu, Apr 30, 2015 at 4:47 AM, MCLAREN, Donald <[log in to unmask] > > wrote: > >> There is no label because the program can not determine what the units >> should be. FIVE is a general plotting program and the Y values are the >> values of the input images. No where is the units of the input images >> specified, thus there can be no unit label. Values could be BOLD units, >> arbitrary units, FA, MD, grey matter volume, etc. It all depends on the >> input image unit. If you know the units of the input image, then you know >> the units for the Y axis. >> >> Hope this helps. >> >> 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 Wed, Apr 29, 2015 at 4:41 AM, Andy Yeung <[log in to unmask]> >> wrote: >> >>> Sorry, I mean no labels on Y axis. >>> >>> On Wed, Apr 29, 2015 at 4:40 PM, Andy Yeung <[log in to unmask]> >>> wrote: >>> >>>> Dear Lingfei and others, >>>> >>>> May I ask one more question? What does the plot mean if I click 'plot >>>> voxel' after putting crosshair at a peak voxel? >>>> I don't see values on the Y axis. Thanks for your help. >>>> >>>> Best, >>>> Andy >>>> >>>> On Wed, Apr 29, 2015 at 4:07 PM, Andy Yeung <[log in to unmask]> >>>> wrote: >>>> >>>>> Dear Lingfei, >>>>> >>>>> Thank you very much for your help. I figured out that when both >>>>> 'Thresh' and 'Color limits' are having the same values, the discrepancy >>>>> will surely go. >>>>> >>>>> Best, >>>>> Andy >>>>> >>>>> On Wed, Apr 29, 2015 at 3:53 PM, Lingfei Tang <[log in to unmask]> >>>>> wrote: >>>>> >>>>>> Hi Andy, >>>>>> >>>>>> This is a refresh problem. There could be other ways, but just make >>>>>> the program refresh the color bar. >>>>>> For that you can just click on the dropdown menu where you have your >>>>>> .img file and choose "overlay" and then choose that .img file again. >>>>>> >>>>>> >>>>>> Lingfei Tang >>>>>> >>>>>> Lingfei Tang >>>>>> >>>>>> On 29 April 2015 at 03:47, Andy Yeung <[log in to unmask]> wrote: >>>>>> >>>>>>> Dear all, >>>>>>> >>>>>>> I would like to ask for the meaning of 'Thresh' and 'Color limits' >>>>>>> in the image viewer FIVE. >>>>>>> As seen from attached picture, I understand the crosshair position >>>>>>> voxel has T value of 3.49 (red in color). But it doesn't match with the >>>>>>> color bar. This discrepancy occurs when I started to change the values in >>>>>>> 'Thresh' and 'Color limits'. >>>>>>> >>>>>>> It was OK at the beginning when I set 'P-value' = 1.0 and changed >>>>>>> 'Color limits' from '0, Inf' to '0, 6'. Because I wanted to show only blobs >>>>>>> with higher T-values, I changed the 'Thresh' and 'Color limits' and >>>>>>> discrepancy came out. >>>>>>> >>>>>>> Best, >>>>>>> Andy >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >> >