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Dear sir, You can check the files at https://oxfile.ox.ac.uk/oxfile/work/extBox;jsessionid=9ABE0EB588FE568360877C8A7696FCE2?execution=e1s1 . Thanks Vasudev On Thu, Aug 22, 2019 at 5:09 PM paul mccarthy <[log in to unmask]> wrote: > Hi Vasudev, > > On the surface, your commands seem correct, although you are using the > same name (Amygdala_L.nii.gz) for your MNI-space input as for your > functional-space output - is there a chance you have overwritten the > original input? > > Would you be able to upload the files listed below to this url so I can > take a look: > https://oxfile.ox.ac.uk/oxfile/work/extBox?id=771963AC5AF6AD77F1 > > T1w.nii.gz > highres2standard.mat > highres2standard_warp.nii.gz > highres2standard_warp_inv.nii.gz > Amygdala_L.nii.gz > Amygdala_L_Hres.nii.gz > highres2example_func.mat > example_func.nii.gz > > Cheers, > > Paul > > On Wed, 21 Aug 2019 at 22:37, Dev vasu < > [log in to unmask]> wrote: > >> Dear all, >> >> I am trying to transform the Label file ( In this case Amygdala_Left >> hemisphere ) into functional space and i am encountering problems >> >> Following are the steps i have followed >> >> # Nonlinear transform highres to standard-where T1w.nii.gz is structural image >> >> >> 1. fnirt --in= T1w.nii.gz' --aff=reg/highres2standard.mat >> --cout=reg/highres2standard_warp >> --config=/usr/share/fsl/5.0/etc/flirtsch/T1_2_MNI152_2mm >> >> # Inverse of Non linear transform >> >> 2. inwarp --ref=T1w.nii.gz' --warp=reg/highres2standard_warp >> --out=reg/highres2standard_warp_inv >> >> # Now i am warping ROI ( Amygdala_L) to subject T1w.nii.gz space >> >> 3.applywarp --ref=T1w.nii.gz' --in=Amygdala_L.nii.gz >> --warp=reg/highres2standard_warp_inv --out=reg/Amygdala_L_Hres.nii.gz >> --interp=nn >> >> >> # Applying affine transform to move warped ROI (Amygdala_L_Hres.nii.gz) >> into functional space >> >> flirt -in reg/Amygdala_L_Hres.nii.gz -applyxfm -init >> reg/highres2example_func.mat -out Amygdala_L.nii.gz -datatype float >> -paddingsize 0.0 -interp nearestneighbour -ref reg/example_func.nii.gz >> >> and the result of this transformation is attached for your reference >> >> Could you please let me know why the ROI is completely misplaced here, >> and where i am doing wrong. >> >> Thanks >> Vasudev >> >> >> ------------------------------ >> >> To unsubscribe from the FSL list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1