Hi Adnan, I don't think that buan would work on an atlas defined in a 3d image space, because it is indeed streamline-centric. And I don't think that DIPY implements anything that would operate the way you'd like on a mask in a 3d image. If this has to be in an atlas space (why not in subject space?), you might consider using an atlas that is defined as streamlines (e.g., https://brain.labsolver.org/hcp_trk_atlas.html), and run buan on that. I am not 100% sure how/if that would work, but seems worth a try.
Cheers, Ariel On Fri, Jan 26, 2024 at 8:25 AM Billah, Tashrif <[email protected]> wrote: > 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://urldefense.com/v3/__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__;JSUlJSUl!!K-Hz7m0Vt54!knRFjZh80hww0blfsfRw-OwjsDSXvpwna8hWzf3CxZKDU1ehzjYNcZez13dW4FBQR_5XScLrJRy0z5Ff6HIlow$>, > and the paper for more details: > https://www.nature.com/articles/s41598-020-74054-4 > <https://urldefense.com/v3/__https://secure-web.cisco.com/1Hy0JCbafH9c9A6XYFglUxBmeTDUfa3FdCHKF25PuSJM1eJ6OQUWzetBtcjS63JFpGYgb1Sai1M6ySXIeV08OpwcgCZgvPITxQ4tD5PE56-7pxhxCGzPX8I9fQsY_AAHLQlAkfhZT1NnKy07tJjH6WanamAL5m5YnQeWInAVj_XfAfKozPh3qOlfbuz4d2CYK149OCmmXnnzA0DjyAKekKc4RT_RW_neUoO3vP3hW7TTHhM3cRd_n87nWA6AEvpMXqBQ6VXi69RuNTPWymj_yCqYVSMdeol3ggHuiQGruM02VPNgYvnvQFQRde7YkHmc3AdK0xNbeX_R_00rs5zwC7A/https*3A*2F*2Fwww.nature.com*2Farticles*2Fs41598-020-74054-4__;JSUlJSU!!K-Hz7m0Vt54!knRFjZh80hww0blfsfRw-OwjsDSXvpwna8hWzf3CxZKDU1ehzjYNcZez13dW4FBQR_5XScLrJRy0z5H-X2xQJg$> > > > Cheers, > Ariel > > On Sat, Jan 20, 2024 at 7:43 PM Adnan Hirad <[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] > To unsubscribe send an email to [email protected] > https://mail.python.org/mailman3/lists/dipy.python.org/ > <https://urldefense.com/v3/__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__;JSUlJSUlJQ!!K-Hz7m0Vt54!knRFjZh80hww0blfsfRw-OwjsDSXvpwna8hWzf3CxZKDU1ehzjYNcZez13dW4FBQR_5XScLrJRy0z5HS-3wQrQ$> > Member address: [email protected] > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > https://www.massgeneralbrigham.org/complianceline > <https://urldefense.com/v3/__https://www.massgeneralbrigham.org/complianceline__;!!K-Hz7m0Vt54!knRFjZh80hww0blfsfRw-OwjsDSXvpwna8hWzf3CxZKDU1ehzjYNcZez13dW4FBQR_5XScLrJRy0z5Hl8FVsqA$> > . >
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