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Dear Mark, Thank you very much for your suggestions. Ramesh On Wed, Nov 9, 2016 at 4:13 AM, Mark Jenkinson <[log in to unmask] > wrote: > Hi, > > Only the second option will be forming a binary mask for fslmeants, as > when flirt performs a transformation it will use trilinear interpolation > and hence the mask will no longer be binary. > > All the best, > Mark > > > On 7 Nov 2016, at 14:17, Ramesh Babu <[log in to unmask]> wrote: > > Dear Mark > > Thank you very much for your suggestions. I have included -init > highres2example_func.mat command in flirt call. I got time series data by > following two steps given below. Both the steps are giving different time > series data. Please see the attached file. I would like to confirm which > step should I follow? step-1 or 2? > > *Step-1 [fslmaths (erode-threshold-binarize) > transform > extract time > series]* > > fslmaths N5_T1_brain_pve_0.nii.gz -ero -thr .9 -bin csf_m -odt float > > flirt -in csf_m.nii.gz -ref filtered_func_data.nii.gz -out csf_m_fl > -applyxfm -init highres2example_func.mat > > fslmeants -i filtered_func_data.nii.gz -o csf_m.txt -m csf_m_fl.nii.gz > > > *Step-2 [transform > fslmaths (erode-threshold-binarize) > extract time > series]* > > flirt -in N5_T1_brain_pve_0.nii.gz -ref filtered_func_data.nii.gz -out > csf_fl -applyxfm -init highres2example_func.mat > > fslmaths csf_fl.nii.gz -ero -thr .9 -bin csf_m_fl_m -odt float > > fslmeants -i filtered_func_data.nii.gz -o csf_ts.txt -m csf_fl_m.nii.gz > > > Thanks > Ramesh > > On Mon, Nov 7, 2016 at 4:18 PM, Mark Jenkinson < > [log in to unmask]> wrote: > >> Hi, >> >> This looks generally fine to me, except that I think you've left off >> "-init highres2example_func.mat" in the flirt call (as otherwise the >> output, csf_m_fl, won't be registered to your filtered_func_data). Did you >> look at that? >> I would also threshold and binarise the output from flirt before using it >> as a mask in fslmeants. >> >> All the best, >> Mark >> >> >> On 5 Nov 2016, at 02:02, Ramesh Babu <[log in to unmask] >> <[log in to unmask]>> wrote: >> >> Dear Mark, >> >> I got the time series data by following the steps given below. >> >> fslmaths N5_T1_brain_pve_0.nii.gz -ero -thr .9 -bin csf_m -odt float >> flirt -in csf_m.nii.gz -ref filtered_func_data.nii.gz -out csf_m_fl >> -applyxfm >> fslmeants -i filtered_func_data.nii.gz -o csf_m.txt -m csf_m_fl.nii.gz >> >> Please see the attached file and give your suggestion. >> >> Thanks >> Ramesh >> >> On Fri, Nov 4, 2016 at 8:35 PM, Ramesh Babu <[log in to unmask]> >> wrote: >> >>> Dear Mark, >>> >>> Thank you for your prompt reply. >>> >>> I am going to use it into regression model. What are the steps should I >>> follow to extract time series? >>> >>> Thanks >>> Ramesh >>> >>> >>> >>> On Fri, Nov 4, 2016 at 3:34 AM, Mark Jenkinson < >>> [log in to unmask]> wrote: >>> >>>> Hi, >>>> >>>> The answer to this depends on what you are going to do with the >>>> extracted time series. >>>> If you are going to enter it into a regression then you should extract >>>> it from the same data that is going into the regression (so after whatever >>>> preprocessing is done to that data). >>>> >>>> If you are using it for some other purpose (e.g., as a QC measure for >>>> your data) then you might need to extract it from something else like the >>>> raw data. It all depends on your application. >>>> >>>> All the best, >>>> Mark >>>> >>>> >>>> >>>> On 3 Nov 2016, at 09:26, Ramesh Babu <[log in to unmask] >>>> <[log in to unmask]>> wrote: >>>> >>>> Dear Expert, >>>> >>>> By using FAST segmentation tool I obtained segmented GM, WM and CSF. I >>>> want extract time series of WM, and CSF by using fsl meants. >>>> >>>> I would like to know Is there any steps before extracting time series >>>> from these segmented images? >>>> >>>> To extract time series should I use raw BOLD sequence or >>>> filtered..image produced by FEAT preprocessing steps? >>>> >>>> Please provide the steps to extract time series from WM and CSF. >>>> >>>> Thanks in advance >>>> Ramesh >>>> >>>> >>>> >>> >> <csf_m.txt><csf_mask.png> >> >> >> > <step-1_csf.txt><step-2_csf.txt> > > >