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Hi Vasudev, FEAT scales the functional data as part of its preparation for model fitting. The magnitude of the fMRI signal is arbitrary - what is important is how the signal changes over time. Paul On Feb 21 2020, at 1:00 pm, Dev vasu <[log in to unmask]> wrote: > Dear Sir, > > Thanks for your reply, Now i found out the issue, my mask is actually made out of > ICBM 2009c Nonlinear Symmetric - 1×1x1mm template > > > Now i have transformed my mask into MNI152 2mm template, I have a question, i extracted time series using > > fslmeants -i filtered_func_data.nii.gz -o Visual.txt -m Visual_thr_func.nii.gz > > the Visual_thr_func.nii.gz is generated after transforming Visual_thr_mask.nii.gz into functional space. > > The time series file that i am getting ( see attachment) is huge, can such high values for time series are possible ?. > > Thanks > Vasudev > > > > On Fri, Feb 21, 2020 at 1:31 PM paul mccarthy <[log in to unmask] (mailto:[log in to unmask])> wrote: > > Hi Vasudev, > > > > You may have missed my most recent email: > > Actually, I was slightly wrong - your mask image is aligned to the MNI152 template. However, it does not have the same resoluion as the MNI152 template you used in registration (2mm I presume). > > Your mask needs to have the same dimensions and orientation as the standard space image you used for registration. > > Paul > > On Feb 21 2020, at 12:24 pm, Dev vasu <[log in to unmask] (mailto:[log in to unmask])> wrote: > > > Dear Sir, > > > > > > I am annexing Visual_thr_mask.nii.gz file,it is actually in MNI152 space. > > > > > > Thanks > > > Vasudev > > > > > > > > > > > > On Fri, Feb 21, 2020 at 1:01 PM paul mccarthy <[log in to unmask] (mailto:[log in to unmask])> wrote: > > > > Hi Vasudev, > > > > > > > > I've just noticed that the file you attached to the beginning of this email thread (Visual_thr_mask.nii.gz ) is not in MNI space - I'm guessing it is in the space of your structural image. This command: > > > > 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 > > > > assumes that the input file is in MNI152 space. > > > > Paul > > > > On Feb 21 2020, at 9:41 am, Dev vasu <[log in to unmask] (mailto:[log in to unmask])> wrote: > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, Feb 20, 2020 at 11:00 AM paul mccarthy <[log in to unmask] (mailto:[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] (mailto:[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] (mailto:[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] (mailto:[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 > > > > > > > > > > > > > > > > > > > > > > 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