Try --tfce_C=26
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: [log in to unmask]
On 11/19/12 1:35 PM, "Anders Eklund" <[log in to unmask]> wrote:
>Is it possible to apply FDR instead of FWE with randomise?
>
>When I try to change the connectivity from 6 to 26 (--tfce_C 26 ) I get
>an error
>
>--tfce_C: Missing non-optional argument!
>try: randomise --help
>
>Has anyone encountered this?
>
>/Anders
>
>
>________________________________________
>Från: FSL - FMRIB's Software Library [[log in to unmask]] för Mark
>Jenkinson [[log in to unmask]]
>Skickat: den 19 november 2012 11:36
>Till: [log in to unmask]
>Ämne: Re: [FSL] SV: [FSL] SV: [FSL] Paired t-test with randomise
>
>Or, even easier, make an F-test across the +1 and -1 contrast.
>The result is then a two-sided test and you use the standard p-value
>thresholds.
>
>All the best,
>Mark
>
>
>On 19 Nov 2012, at 16:22, "David V. Smith"
><[log in to unmask]<mailto:[log in to unmask]>> wrote:
>
>Yes -- do two contrasts [1] and [-1] and look for voxels exceeding
>1-(.05/2) in the corrp map.
>
>David
>
>
>On Nov 19, 2012, at 11:17 AM, Anders Eklund wrote:
>
>OK thanks, is it possible to get a two sided test somehow?
>
>/Anders
>
>________________________________________
>Från: FSL - FMRIB's Software Library
>[[log in to unmask]<mailto:[log in to unmask]>] för David V. Smith
>[[log in to unmask]<mailto:[log in to unmask]>]
>Skickat: den 19 november 2012 10:59
>Till: [log in to unmask]<mailto:[log in to unmask]>
>Ämne: Re: [FSL] SV: [FSL] Paired t-test with randomise
>
>Neither of those are used for TFCE, hence the "threshold-free" part of
>the name. See the documentation and Steve's paper for further details.
>
>Cheers,
>David
>
>On Nov 19, 2012, at 10:47 AM, Anders Eklund wrote:
>
>Thanks. If I use threshold free cluster enhancement, is cluster size or
>cluster mass used?
>
>/Anders
>
>________________________________________
>Från: FSL - FMRIB's Software Library
>[[log in to unmask]<mailto:[log in to unmask]>] för David V. Smith
>[[log in to unmask]<mailto:[log in to unmask]>]
>Skickat: den 19 november 2012 10:06
>Till:
>[log in to unmask]<mailto:[log in to unmask]><mailto:[log in to unmask]>
>Ämne: Re: [FSL] Paired t-test with randomise
>
>Hi Anders,
>
>Yes -- I would recommend computing the difference between the two time
>points with fslmaths (cope_T1 - cope_T2), merging those difference
>images, and then running a one sample t-test with randomise. If you've
>already run a group analysis on each time point using FEAT, then you
>could just use the filtered_func_data files
>
>fslmaths groupT1.gfeat/cope1.feat/filtered_func_data -sub
>groupT2.gfeat/cope1.feat/filtered_func_data T1minusT2
>
>Hope this helps.
>
>Cheers,
>David
>
>
>
>
>On Nov 19, 2012, at 9:37 AM, Anders Eklund wrote:
>
>Dear FSL-experts,
>
>I am analyzing data collected from N subjects at two different
>timepoints. I wish to investigate, for each voxel, if there is any
>significant difference in the mean activity between these two timepoints.
>There is no information about paired t-tests in the randomise user guide,
>I suppose that the reason is that data from the same subject are not
>independent and complicates permutatation.
>
>http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Randomise/UserGuide?highlight=%28%5C
>bCategoryRandomise%5Cb%29
>
>Is the best solution to calculate the mean difference for each voxel and
>then simply run a one sample t-test with randomise?
>
>Regards,
>Anders
>
>--------------------------------------------
>David V. Smith, Ph.D.
>Postdoctoral Fellow, Delgado Lab
>Department of Psychology
>Rutgers University
>Newark, NJ 07102
>--------------------------------------------
>
>--------------------------------------------
>David V. Smith, Ph.D.
>Postdoctoral Fellow, Delgado Lab
>Department of Psychology
>Rutgers University
>Newark, NJ 07102
>--------------------------------------------
>
>--------------------------------------------
>David V. Smith, Ph.D.
>Postdoctoral Fellow, Delgado Lab
>Department of Psychology
>Rutgers University
>Newark, NJ 07102
>--------------------------------------------
|