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Hi - the output can be 0 if the data doesn't appear to have FDR-corrected significance….. Cheers. On 20 Sep 2010, at 09:56, Woodman, Sandra wrote: > Hello, > > Does anyone know if it looks like we are using FDR correctly. For a mask, we > used a non inverted image to make sure that we are using the same voxels as in > our inverted image. > > > [purkinje:Left-Pallidum] (nmr-std-env) fdr -i > FDRtest_contrast_CTRLaPATa_vox_vox_p_tstat2.nii.gz -m > contrast_CTRLaPATa_vox_vox_p_tstat2.nii.gz -q 0.05 -v > p-value image:: Size = (182,218,182,1) > p-value image:: ROI Size = (182,218,182,1) > p-value image:: Dims = (1,1,1,1) > p-value image:: Minimum and maximum intensities are: 0.000199974 and 1 > Calculating FDR values > Probability Threshold is: > 0 > > It looked like we had some good uncorrected p-values, but it doesn't make sense > that we would get a probability threshold of 0. Does anyone have any advice to > check to see if we're doing anything wrong? Or if there is something else we > could be doing/ using (flags etc.)? > > Thank you! > > Sandra > > > > -----Original Message----- > From: FSL - FMRIB's Software Library on behalf of Eugene Duff > Sent: Thu 9/16/2010 5:06 AM > To: [log in to unmask] > Subject: Re: [FSL] Making a mask > > Hi Sandra, > > You're right, your mask is empty. But following the instructions > exactly, I could create a mask on your image, save it, and view it > again in a new instance of fslview. I guess you're not quite doing > something right in creating the mask. Do you see the mask when you are > drawing it? > > Eugene > > -- > > Centre for Functional MRI of the Brain (FMRIB) | University of Oxford > John Radcliffe Hospital | Headington > OX3 9DU | Oxford | UK > > Ph: +44 (0) 1865 222 523 | Mob: +44 (0) 7946 362 059 | Fax: +44 (0) 1865 222 717 > > -- > > > > On 15 September 2010 22:27, Woodman, Sandra <[log in to unmask]> wrote: >> Hello, >> >> I have uploaded the image I wish to base the mask on: >> FDRtest_contrast_CTRLaPATa_vox_vox_p_tstat2.nii.gz >> >> And the image of the mask that I created: >> FDRtest_contrast_CTRLaPATa_vox_vox_p_tstat2-mask.nii.gz >> >> Refernce #: 987079 >> >> I know this mask was not created properly because when I used the paint bucket >> tool to fill the mask with color to check that the mask was created...It > filled >> in the entire square. What I'm thinking is that FSL is creating a mask that >> includes the white space that surrounds the ROI in >> FDRtest_contrast_CTRLaPATa_vox_vox_p_tstat2.nii.gz. I also assume the mask >> isn't working because when I feed it into fdr command I get a threshold= 0. >> >> [purkinje:Left-Pallidum] (nmr-std-env) fdr -i >> FDRtest_contrast_CTRLaPATa_vox_vox_p_tstat2.nii.gz -m >> FDRtest_contrast_CTRLaPATa_vox_vox_p_tstat2-mask.nii.gz -q 0.05 >> Probability Threshold is: >> 0 >> >> >> How do I specify in fslview to make a mask of just the ROI? Do I need to cut >> away the white space using another program? >> >> This is what I have been using as directions for creating a mask: >> http://fsl.fmrib.ox.ac.uk/fsl/fslview/masking.html >> >> I appreciate you help! >> >> Thank you, >> >> -Sandra >> >> Sandra Woodman >> Mood and Motor Control Laboratory >> Athinoula Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> 120 6th St. >> Charlestown, MA 02129 >> Tel: 617-643-6245 >> Fax: 617-726-1351 >> Email: [log in to unmask] >> >> >> >> -----Original Message----- >> From: FSL - FMRIB's Software Library on behalf of Eugene Duff >> Sent: Tue 9/14/2010 4:30 AM >> To: [log in to unmask] >> Subject: Re: [FSL] Making a mask >> >> It's still a bit hard to tell. Could you give more details, and/or >> upload the mask and background image to >> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi >> and send me the id.. >> >> Eugene >> >> On 13 September 2010 21:09, Woodman, Sandra <[log in to unmask]> wrote: >>> Hi Eugene, >>> >>> When I load both the mask and the image, the mask is transparent even when we >>> change the colors. Why can't we see the mask? >>> >>> Thank you! >>> >>> -Sandra >>> >>> Sandra Woodman >>> Mood and Motor Control Laboratory >>> Athinoula Martinos Center for Biomedical Imaging >>> Massachusetts General Hospital >>> 120 6th St. >>> Charlestown, MA 02129 >>> Tel: 617-643-6245 >>> Fax: 617-726-1351 >>> Email: [log in to unmask] >>> >>> >>> >>> -----Original Message----- >>> From: FSL - FMRIB's Software Library on behalf of Eugene Duff >>> Sent: Mon 9/13/2010 3:58 PM >>> To: [log in to unmask] >>> Subject: Re: [FSL] Making a mask >>> >>> Hi Sandra - >>> >>> I'm not exactly sure where the difficulty is, but once you've saved >>> the mask as an image file, you can then load it as an overlay to any >>> like-sized image. >>> >>> Does that help? >>> >>> Eugene >>> >>> -- >>> >>> >>> On 13 September 2010 20:35, Woodman, Sandra <[log in to unmask]> wrote: >>>> Hello! >>>> >>>> I'm working on creating a mask and was wondering if anyone knew how to view >>> the >>>> mask once it had been created? >>>> >>>> I used the steps in the following web page to create the mask: >>>> >>>> http://fsl.fmrib.ox.ac.uk/fsl/fslview/masking.html >>>> >>>> Now I want to make sure it is actually masking the correct area. >>>> >>>> Thanks for you help! >>>> >>>> -Sandra >>>> >>>> Sandra Woodman >>>> Mood and Motor Control Laboratory >>>> Athinoula Martinos Center for Biomedical Imaging >>>> Massachusetts General Hospital >>>> 120 6th St. >>>> Charlestown, MA 02129 >>>> Tel: 617-643-6245 >>>> Fax: 617-726-1351 >>>> Email: [log in to unmask] >>>> >>>> >>>> >>>> -----Original Message----- >>>> From: FSL - FMRIB's Software Library on behalf of Aditya Kumar Kasinadhuni >>>> Sent: Mon 9/13/2010 2:34 PM >>>> To: [log in to unmask] >>>> Subject: [FSL] Thresholding in Post-stats of FEAT >>>> >>>> Hi all, >>>> >>>> I was wondering if there was some documentation that I can go through >>> regarding >>>> the various thresholding options enlisted in the post-stats section. In >>>> particular I would like to know the difference between voxel and cluster >>>> thresholding, and also I understand it makes cluster indices based on the >>>> z-statistic threshold but how does FSL calculate this? >>>> >>>> Thank you. >>>> >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom it is >>>> addressed. If you believe this e-mail was sent to you in error and the > e-mail >>>> contains patient information, please contact the Partners Compliance > HelpLine >>> at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>>> but does not contain patient information, please contact the sender and >>> properly >>>> dispose of the e-mail. >>>> >>>> >>> >>> >> >> > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------