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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>> contains patient information, please contact the Partners Compliance HelpLine
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>>
>
>
