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