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Dear Ruiwang, I've downloaded the tar file and tried to find the problem here, but it all looks fine to me. Just to check: I am loading the struct_brain image followed by SagMask8359 into fslview and they are in the same space and look completely sensible. The image SagMask8359_out is also fine and is exactly the same as SagMask8359 as far as I can tell. I don't know what has gone wrong at your end. Maybe a problem with clashing filenames. I suggest making a new directory and copying only the files struct_brain.nii.gz and SagMask8359.nii.gz into it, then trying fslview from there. Hopefully it will be fine. Let me know if you still have problems. All the best, Mark On 11 Jul 2005, at 18:38, Ruiwang Huang (MR-Group, IME Juelich Germany) wrote: > Dear Mark > > Thanks a lot for your kind help. I would like to ask your help to > check the > mask transform. The tarred file 'FlirtMaskChecking.tar' can be > downloaded by > ftp. The username and passwd for entering the ftp-site is added at the > end of > the email. > > I am looking forward to hearing from you > > Very best wishes > > Ruiwang > > > * If you cannot open the tar file, I will re-tar and re-ftp it again. > > +++++++++++++++++++++++++++++++++++++++++++++++++++++ > %% > ftp exftp.kfa-juelich.de > name: anonymous > passwd: your email-address > > %% > > Rules for data exchange: > There are two public directories: /pub/inbound /pub/outbound > Access mode is: > Users at Research Centre Juelich READ READ/WRITE > Users from outside WRITE READ > Allowed filetypes: normal, no directories! > Number of files: 10 per user/directory > Number of data bytes: 1 GB per user/directory > Time data kept: 4 days > Session total time: 30 minutes > Session idle time: 3 minutes > ++++++++++++++++++++++++++++++++++++++++++++++++ > > On Monday 11 July 2005 18:40, you wrote: >> Hi, >> >> If I understand correctly, you are saying that FSLView and >> avwinfo tell you different voxel sizes for the same dataset. >> Based on the avwinfo output, everything looks like it is >> going OK. >> >> I assume that the voxel sizes are really quite different, >> not just a rounding issue (any difference of less than >> 0.0001mm can be safely attributed to this and >> ignored for any practical purpose). >> >> So, if there is a problem with fslview/avwinfo on this data >> then, in order to know what is happening, we will need a >> copy of the data. Could you please put it on a web/ftp-site >> for us? >> >> All the best, >> Mark >> >> R Huang wrote: >>> Hello >>> >>> I meet a problem to use FLIRT to transform a mask >>> (GroupAverage3D_AxiaMask.nii.gz) >>> from the group average space >>> (GroupAverage3D.nii.gz) >>> to the individual space >>> (struct_brain.nii.gz). >>> >>> Their spatial resolutions are listed here: >>> group_average_space (resolution=2x2x2, dims=91x109x91x1), >>> individual_space (resolution=1x1x1, dims=160x256x256x1), >>> mask (resolution=2x2x2, dims=91x109x91x1). >>> The details of avwinfo are added at the end of this email. >>> >>> Using FLIRT, the transform matrix from individual_space to >>> group_average_space was calculated. The inverse matrix was obtained >>> by >>> using 'convert_xfm'. >>> >>> By following Item_58 of FSL_faq at >>> <http://www.fmrib.ox.ac.uk/fslfaq/#flirt_notwork>, >>> I converted the mask from group_average_space to individual_space, >>> and >>> named the obtained mask as 'SagMask8359'. The reference was >>> 'individual_space'. >>> >>> Uisng FSLview to open the obtained mask, 'SagMask8359', I found that >>> the >>> voxel size of the obtained mask is not (1mm x 1mm x 1mm), the >>> resolution >>> of the reference space (individual_space), though the result of >>> avwinfo >>> showed the dimension of the obtained mask is same as that of the >>> individual space. >>> >>> I also tried using ApplyXFM to convert the obtained mask >>> 'SagMask8359' >>> through changing the option 'Based on: Voxlel Dimensions, >>> 160x256x256 and >>> 1x1x1'. Checking it with FSLview, the voxel size are still not >>> exactly >>> 1x1x1. >>> >>> Any comments and suggestions please, >>> >>> rhuang >>> >>> ++++++++++++++++++++++++++++++++ >>> >>>>>> avwinfo GroupAverage3D.nii.gz >>> >>> dim1 91 >>> dim2 109 >>> dim3 91 >>> dim4 1 >>> datatype 16 >>> pixdim1 2.0000000000 >>> pixdim2 2.0000000000 >>> pixdim3 2.0000000000 >>> pixdim4 1.0000000000 >>> cal_max 105.0000 >>> cal_min 0.0000 >>> file_type NIFTI-1+ >>> >>>>>> avwinfo struct_brain.nii.gz >>> >>> dim1 160 >>> dim2 256 >>> dim3 256 >>> dim4 1 >>> datatype 4 >>> pixdim1 1.0000000000 >>> pixdim2 1.0000000000 >>> pixdim3 1.0000000000 >>> pixdim4 1.0000000000 >>> cal_max 550.0000 >>> cal_min 16.0000 >>> file_type NIFTI-1+ >>> >>>>>> avwinfo GroupAverage3D_AxiaMask.nii.gz >>> >>> dim1 91 >>> dim2 109 >>> dim3 91 >>> dim4 1 >>> datatype 4 >>> pixdim1 2.0000000000 >>> pixdim2 2.0000000000 >>> pixdim3 2.0000000000 >>> pixdim4 1.0000000000 >>> cal_max 4.0000 >>> cal_min 0.0000 >>> file_type NIFTI-1+ >>> >>>>>> avwinfo SagMask8359.nii.gz (not binaried) >>> >>> dim1 160 >>> dim2 256 >>> dim3 256 >>> dim4 1 >>> datatype 64 >>> pixdim1 1.0000000000 >>> pixdim2 1.0000000000 >>> pixdim3 1.0000000000 >>> pixdim4 1.0000000000 >>> cal_max 4.0000 >>> cal_min 0.0000 >>> file_type NIFTI-1+ >>> >>> ++++++++++++++++++++++++++++++++ > > -- > +++++++++++++++++++++++++++ > Ruiwang Huang > MR-Group > Institute of Medicine > Research Center Juelich > Juelich 52425 > Germany > > Tel: +49 (0)2461 61 2085 > Fax: +49 (0)2461 61 2820 > ++++++++++++++++++++++++++++++++