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, and the paper for more details: https://www.nature.com/articles/s41598-020-74054-4 Cheers, Ariel On Sat, Jan 20, 2024 at 7:43 PM Adnan Hirad <adnanhirad@gmail.com> 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 -- dipy@python.org To unsubscribe send an email to dipy-leave@python.org https://mail.python.org/mailman3/lists/dipy.python.org/ Member address: arokem@gmail.com

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 <tbillah@bwh.harvard.edu> 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 <arokem@uw.edu> *Sent:* Friday, January 26, 2024 12:53 AM *To:* Adnan Hirad <adnanhirad@gmail.com> *Cc:* dipy@python.org <dipy@python.org> *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_hRGLNHnXvoYNsJJ...>, and the paper for more details: https://www.nature.com/articles/s41598-020-74054-4 <https://urldefense.com/v3/__https://secure-web.cisco.com/1Hy0JCbafH9c9A6XYFg...>

Cheers, Ariel

On Sat, Jan 20, 2024 at 7:43 PM Adnan Hirad <adnanhirad@gmail.com> 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 -- dipy@python.org To unsubscribe send an email to dipy-leave@python.org https://mail.python.org/mailman3/lists/dipy.python.org/ <https://urldefense.com/v3/__https://secure-web.cisco.com/18TpwFLKtffmofFKKIU...> Member address: arokem@gmail.com

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/compliancelin...> .

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, and the paper for more details: https://www.nature.com/articles/s41598-020-74054-4 Cheers, Ariel On Sat, Jan 20, 2024 at 7:43 PM Adnan Hirad <adnanhirad@gmail.com> 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 -- dipy@python.org To unsubscribe send an email to dipy-leave@python.org https://mail.python.org/mailman3/lists/dipy.python.org/ Member address: arokem@gmail.com

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 <tbillah@bwh.harvard.edu> 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 <arokem@uw.edu> *Sent:* Friday, January 26, 2024 12:53 AM *To:* Adnan Hirad <adnanhirad@gmail.com> *Cc:* dipy@python.org <dipy@python.org> *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_hRGLNHnXvoYNsJJ...>, and the paper for more details: https://www.nature.com/articles/s41598-020-74054-4 <https://urldefense.com/v3/__https://secure-web.cisco.com/1Hy0JCbafH9c9A6XYFg...>

Cheers, Ariel

On Sat, Jan 20, 2024 at 7:43 PM Adnan Hirad <adnanhirad@gmail.com> 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 -- dipy@python.org To unsubscribe send an email to dipy-leave@python.org https://mail.python.org/mailman3/lists/dipy.python.org/ <https://urldefense.com/v3/__https://secure-web.cisco.com/18TpwFLKtffmofFKKIU...> Member address: arokem@gmail.com

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/compliancelin...> .