Hi Ariel, here is the help message of fslmeants: Best, Tashrif
$ ./fsl-6.0.7/bin/fslmeants *************************************************** The following COMPULSORY options have not been set: -i <filename> input 4D image *************************************************** Part of FSL (ID: "") fslmeants Copyright(c) 2004-2009, University of Oxford (Mark Jenkinson, Christian F. Beckmann) Prints average timeseries (intensities) to the screen (or saves to a file). The average is taken over all voxels in the mask (or all voxels in the image if no mask is specified). Usage: fslmeants -i filtered_func_data -o meants.txt -m my_mask fslmeants -i filtered_func_data -m my_mask fslmeants -i filtered_func_data -c 24 19 10 Compulsory arguments (You MUST set one or more of): -i <filename> input 4D image Optional arguments (You may optionally specify one or more of): -o <filename> output text matrix -m <filename> input 3D mask -c <x y z> requested spatial coordinate (instead of mask) --usemm use mm instead of voxel coordinates (for -c option) --showall show all voxel time series (within mask) instead of averaging --eig calculate Eigenvariate(s) instead of mean (output will have 0 mean) --order select number of Eigenvariates (default 1) --no_bin do not binarise the mask for calculation of Eigenvariates --label input 3D label image (generate separate mean for each integer label value - cannot be used with showall) --transpose output results in transpose format (one row per voxel/mean) -v,--verbose switch on diagnostic messages -h,--help display this message -w output weighted mean, using mask values as weights, and exit. ________________________________ From: Ariel Rokem <[email protected]> Sent: Friday, January 26, 2024 12:53 AM To: Adnan Hirad <[email protected]> Cc: [email protected] <[email protected]> Subject: [DIPY] Re: Track Segmentation External Email - Use Caution Hi Adnan, Thanks for your email. I couldn't really find out what fslmeants does (can you provide a link to some documentation?). But it sounds like what you want is part of what BUAN does? See https://docs.dipy.org/stable/interfaces/buan_flow.html<https://secure-web.cisco.com/1aw_hRGLNHnXvoYNsJJUqPEa_fj50plDTM3FwEynfOJ9R4bbTb2_fNvu0uCA5_wY-Emj5B4Bau7OTaGH5NMAwSfJWWgvs9QrC-p843XNCWxEIgkou1CKFommXeHzPd_Sd1hoiowaCIpxuxPQpaXnkciyPjq4pnS87x24Yu5lAn0Gi7csgVEyryhAQZYAvlzdN4V-pJouIJ6QHahOASM4yoW1LrOMYLo9uPBDfI-VXpD4o0x-dDmcENbQZYd2TTj1Cc5K2qZ6umT8pGqDGgvoBFYQUqBHVB5if5gcPNYcEflZdj2K3AGGcxxBSSXlcdTeu/https%3A%2F%2Fdocs.dipy.org%2Fstable%2Finterfaces%2Fbuan_flow.html>, and the paper for more details: https://www.nature.com/articles/s41598-020-74054-4<https://secure-web.cisco.com/1Hy0JCbafH9c9A6XYFglUxBmeTDUfa3FdCHKF25PuSJM1eJ6OQUWzetBtcjS63JFpGYgb1Sai1M6ySXIeV08OpwcgCZgvPITxQ4tD5PE56-7pxhxCGzPX8I9fQsY_AAHLQlAkfhZT1NnKy07tJjH6WanamAL5m5YnQeWInAVj_XfAfKozPh3qOlfbuz4d2CYK149OCmmXnnzA0DjyAKekKc4RT_RW_neUoO3vP3hW7TTHhM3cRd_n87nWA6AEvpMXqBQ6VXi69RuNTPWymj_yCqYVSMdeol3ggHuiQGruM02VPNgYvnvQFQRde7YkHmc3AdK0xNbeX_R_00rs5zwC7A/https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41598-020-74054-4> Cheers, Ariel On Sat, Jan 20, 2024 at 7:43 PM Adnan Hirad <[email protected]<mailto:[email protected]>> wrote: Hi there - I was wondering if y'all know a way I can ouput along tract data using a mask, in controlable segments and ouput into a csv or another similar format. Basically what fslmeants does but better in that it doesn't use straight planes (for example, i want to output data from the forceps minor of the corpus callosum from the left cortical insertion point into segments that end in the right cortical insertion point). I hope this makes sense. Thank you in advance Adnan _______________________________________________ DIPY mailing list -- [email protected]<mailto:[email protected]> To unsubscribe send an email to [email protected]<mailto:[email protected]> https://mail.python.org/mailman3/lists/dipy.python.org/<https://secure-web.cisco.com/18TpwFLKtffmofFKKIUAhNxWQfD5bbzTMUDstCtQ69LyXgvCm_Jl3brhw9r5j3oSS0HpgDXHZWbyelOEHecK5igq_vyAJVDC01pio3k_7y2Dkhawp021wrW4lbldkBLVMdHIko_TipCYgcU46CfJwx3OURyJq_zqBsSr3FpDcWdR5HdMkFpSKr3W81dw8vl2ArpL_4vDf4qA5j5APYFHGVwn4W4DbC06-Ny-RpxCDHpWz4g7eL7M1F3rO-RZ_boVYSKakbz3yUy8l505ZPEKqCgKS7Tlvih0A2HmQTVeBMjfCoW4t97Z8pTHQgIpqeosr/https%3A%2F%2Fmail.python.org%2Fmailman3%2Flists%2Fdipy.python.org%2F> Member address: [email protected]<mailto:[email protected]> Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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