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.
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