Hi Paul and Niels,

           This is the code for WINSORIZATION  with I have pulled up from initial comments and later write up. Thanks all for the help.

Please see the code and write your feedback. Is this look ok?

#############extracting the mean and STD##############

fslmaths all_OD_skeletonised.nii.gz -mas ROI_01_mas.nii.gz -thr 0 all_OD_skeletonised_ROI_01.nii.gz

fslstats all_OD_skeletonised_ROI_01.nii.gz -M > ROI_01_OD_M.txt

fslstats all_OD_skeletonised_ROI_01.nii.gz -S > ROI_01_OD_S.txt

mu=`more ROI_01_OD_M.txt`
sd=`more ROI_01_OD_S.txt`

3sd_low=`echo "mu - 3*(sd)" | bc -l`
3sd_high=`echo "mu + 3*(sd)" | bc -l`

#######generation of WINSORIZED ROI ################

fslmaths all_OD_skeletonised_ROI_01.nii.gz -thr 3sd_low -uthr 3sd_high all_OD_skeletonised_ROI_01_thr.nii.gz

fslmaths all_OD_skeletonised_ROI_01.nii.gz -uthr 3sd_low all_OD_skeletonised_ROI_01_lthr.nii.gz -bin -mul 3sd_low all_OD_skeletonised_ROI_01_lthr.nii.gz

fslmaths all_OD_skeletonised_ROI_01.nii.gz -thr 3sd_high all_OD_skeletonised_ROI_01_lthr.nii.gz -bin -mul 3sd_high all_OD_skeletonised_ROI_01_uthr.nii.gz

fslmaths 3sd_high all_OD_skeletonised_ROI_01_thr.nii.gz -add all_OD_skeletonised_ROI_01_lthr.nii.gz -add all_OD_skeletonised_ROI_01_uthr.nii.gz all_OD_skeletonised_ROI_01_win.nii.gz

########################Extracting mean and std from WINSORIZED ROI

fslstats all_OD_skeletonised_ROI_01_win.nii.gz -M > ROI_01_OD_M_win.txt

fslstats all_OD_skeletonised_ROI_01_win.nii.gz -M > ROI_01_OD_S_win.txt

###################END#####################

Please see to it, and give your comments

Kind regards

sourajit

On Thu, Sep 29, 2016 at 3:18 PM, Niels Bergsland <[log in to unmask]> wrote:

You could alternatively modify your previous command and use -min and -max options instead. 

On Thursday, September 29, 2016, Paul Robinson <[log in to unmask]> wrote:

'lo again.

Sorry, it occurs to me that the code above simply truncates your roi which is not really Winsorization. However, it should remove those voxels which are 3 sds more or less than the mean, which is an okay first step. I would use fslmaths to create separate images of those voxels which exceed mu+/-3sd (-thr/-uthr), binarize them (-bin), and then multiply them by the appropriate constraint (-mul). Then you can simply add these three rois together.

Best,

Paul

On Thu, Sep 29, 2016 at 9:57 AM, Paul Robinson <[log in to unmask]> wrote:

Hi, Sourajit

Something like this?

### Or however you want to get the mean and sd

mu=`more ROI_01_OD_M.txt`

sd=`more ROI_01_OD_S.txt`

3sd_low=`echo "mu - 3*(sd)" | bc -l`

3sd_high=`echo "mu + 3*(sd)" | bc -l`

fslmaths all_OD_skeletonised_ROI_01.nii.gz -thr 3sd_low -uthr 3sd_high all_OD_skeletonised_ROI_01_win.nii.gz

Hope this helps,

Paul

On Thu, Sep 29, 2016 at 9:44 AM, Sourajit Mitra Mustafi <[log in to unmask]> wrote:

Dear admin,
                                   I have extracted an ROI image in FSL and computed its mean, median and standard deviation for non-zero voxel using
the following option.

fslmaths all_OD_skeletonised.nii.gz -mas ROI_01_mas.nii.gz -thr 0 all_OD_skeletonised_ROI_01.nii.gz

fslstats -t all_OD_skeletonised_ROI_01.nii.gz -M > ROI_01_OD_M.txt

fslstats -t all_OD_skeletonised_ROI_01.nii.gz -S > ROI_01_OD_S.txt

fslstats -t all_OD_skeletonised_ROI_01.nii.gz -P 50 > ROI_01_OD_P.txt

Is there is any way to WINSORIZE an image for non-zero voxel in FSL. I am trying a method based on ROI analysis and for that reason winsorization of image is important. fslstats doesn't provide that option. Please help me out.

Kind regards
sourajit

--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
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