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Dear Sir, I have redone the FEAT for few subjects without nonlinear registration. (see design.fsf attached) 1. Links to registrations https://www.dropbox.com/s/w946cnrqm3mtbnp/example_func2highres.png?dl=0 https://www.dropbox.com/s/ae8bv5da6ppmhpn/example_func2standard.png?dl=0 https://www.dropbox.com/s/tgle3p6tbukayjv/example_func2standard1.png?dl=0 https://www.dropbox.com/s/4ykuclydzbnpa73/highres2standard.png?dl=0 - The process you used to generate highres2standard_warp_inv is valid This is the process that i have used to generate highres2standard_warp_inv convert_xfm -omat highres2example_func.mat -inverse example_func2highres.mat invwarp --ref==highres --warp=highres2standard_warp --out=highres2standard_warp_inv and the output mask still has problem. [image: Visual_mask.png] On Thu, Feb 20, 2020 at 11:00 AM paul mccarthy <[log in to unmask]> wrote: > Hi Vasudev, > > No - your functional and structural data should be in the resolution they > were acquired in respectively, and should match the resolution of the > images you used in the registration process. The dimensions you have > quoted look like reasonable values for T1/functional EPI data. > > To solve your problem, you need to identify the specific point of failure, > and focus on fixing that. Refer to the list of steps in my previous email. > > In your other email thread, it looked to me like the non-linear > registration was not ideal - this could be caused by a poor brain > extraction, or an atypical brain. In your most recent screenshot it looks > like something more fundamental has gone wrong - I would hazard a guess > that one of the files you have used is incorrect. > > Paul > On Feb 20 2020, at 9:43 am, Dev vasu <[log in to unmask]> > wrote: > > Dear Sir, > > - that all of the input files have the correct dimensions , is it > necessary that dimensions of all functional and structural files should be > same ? > > The Dimensions of all structural files is > sizeof_hdr 348 > data_type FLOAT32 > dim0 3 > dim1 160 > dim2 256 > dim3 256 > dim4 1 > dim5 1 > dim6 1 > dim7 1 > vox_units mm > time_units s > datatype 16 > nbyper 4 > bitpix 32 > pixdim0 0.000000 > pixdim1 1.000000 > pixdim2 1.000000 > pixdim3 1.000000 > pixdim4 1.000000 > pixdim5 0.000000 > pixdim6 0.000000 > pixdim7 0.000000 > vox_offset 352 > > Dimensions of all Functional files > > sizeof_hdr 348 > data_type INT16 > dim0 4 > dim1 64 > dim2 64 > dim3 46 > dim4 300 > dim5 1 > dim6 1 > dim7 1 > vox_units mm > time_units s > datatype 4 > nbyper 2 > bitpix 16 > pixdim0 0.000000 > pixdim1 3.000000 > pixdim2 3.000000 > pixdim3 3.000000 > pixdim4 2.500000 > pixdim5 1.000000 > pixdim6 0.253332 > pixdim7 47455.246094 > vox_offset 352 > cal_max 0.0000 > cal_min 0.0000 > scl_slope 1.000000 > scl_inter 0.000000 > phase_dim 0 > freq_dim 0 > slice_dim 3 > slice_name alternating_increasing_2 > slice_code 5 > slice_start 0 > slice_end 45 > slice_duration 0.000000 > time_offset 0.000000 > intent Unknown > intent_code 0 > intent_name > intent_p1 0.000000 > intent_p2 0.000000 > intent_p3 0.000000 > qform_name Scanner Anat > qform_code 1 > > > > > > On Thu, Feb 20, 2020 at 10:26 AM paul mccarthy <[log in to unmask]> > wrote: > > Hi Vasudev, > > As I said in your other thread, this is due to a poor registration. Double > check the following: > > - that all of the input files have the correct dimensions > - The structural brain extraction is good > - The func-struc registration is good > - The struc-standard registration is good > - The process you used to generate highres2standard_warp_inv is valid > > Paul > > > On Feb 19 2020, at 8:09 pm, Dev vasu <[log in to unmask]> > wrote: > > Dear all, > > I have done functional preprocessing using FEAT and i would like to > perform seed based correlation for visual cortex seed regions, my seed is > defined in MNI152 space. > > The seed and example_func.nii.gz are completely mismatched ( see picture ) > , I have used Visual_thr_mask.nii.gz as seed ( see attachment) and tried to > transform by doing > > applywarp -i Visual_thr_mask.nii.gz -r reg/example_func.nii.gz -o Visual_func > --postmat=reg/highres2example_func.mat -w reg/highres2standard_warp_inv > > I dont understand what is the problem with my approach-could you please provide > > me some input. > > > > > > 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 > > > ------------------------------ > > 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