Hi Mark,
Thank for the tip!
By calculating the intersection, I can indeed use fslmeants (it is all in MNI space, so that shouldn't be a problem)! Thanks!
Best
Heidi
================================================
Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
[log in to unmask]
www.maastrichtuniversity.nl
www.heidijacobs.nl
Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092
================================================
________________________________________
Van: FSL - FMRIB's Software Library [[log in to unmask]] namens Mark Jenkinson [[log in to unmask]]
Verzonden: donderdag 15 mei 2014 9:21
Aan: [log in to unmask]
Onderwerp: Re: [FSL] DTI ROI results
Hi,
Alternatively you can use the -m option in fslmeants and just pass it a mask.
You may need to transform your atlas from a different space (depending on what spaces this atlas and your data are in) and you may want to combine this with your thresholded FA_map using fslmaths (form the intersection by multiplying the binary masks).
All the best,
Mark
On 15 May 2014, at 01:08, Chou Paul <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear Heidi
Have a try for "fslstats -M" ?
Best
Paul
> Date: Wed, 14 May 2014 13:15:33 +0200
> From: [log in to unmask]<mailto:[log in to unmask]>
> Subject: [FSL] DTI ROI results
> To: [log in to unmask]<mailto:[log in to unmask]>
>
> Dear FSL members,
>
> I have preprocessed my DTI data (eddy-current correction, motion correction,...) and thresholded my diffusion maps to exclude grey matter (or partial volume effects).
> The thresholded FA_map served as a threshold for the other diffusion indices.
> I now have an ROI from an atlas that I want to overlay on these maps and extract the mean diffusion values.
>
> However, if I use fslmeants, it gives me the mean of all these voxels, including the zero-voxels.
> I think that fslstats could do the trick, but then it would probably not write the results to a text file (and I have more than 900 files).
>
> Is there a way to calculate the mean diffusivity in a ROI excluding zero-voxels?
>
> Thanks!
> Heidi
>
>
> ================================================
> Dr. Heidi Jacobs
> Postdoc researcher
> Faculty of Health, Medicine and Life Sciences
> School for Mental Health and Neurosciences
> Division Cognitive Neuropsychiatry and Clinical Neurosciences
> Alzheimer Center Limburg
> [log in to unmask]<mailto:[log in to unmask]>
> www.maastrichtuniversity.nl<http://www.maastrichtuniversity.nl>
> www.heidijacobs.nl<http://www.heidijacobs.nl>
>
> Dr. Tanslaan 12, 6229 ET Maastricht
> P.O. Box 616, 6200 MD Maastricht, The Netherlands
> T +31 43 38 84 090 F +31 43 38 84 092
> ================================================
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