From stjeansam at gmail.com Sat Aug 1 08:27:18 2020 From: stjeansam at gmail.com (Samuel St-Jean) Date: Sat, 1 Aug 2020 08:27:18 -0400 Subject: [Neuroimaging] CZI grant - what would you like to see in Nibabel? In-Reply-To: References: <20200728210236.dqmjjl6s5uruvrbm@phare.normalesup.org> <20200729161235.uezevmmxhrd267xk@phare.normalesup.org> Message-ID: <4af0309c-e666-c6dc-562a-f0b1c4717bc7@gmail.com> Even before talking multimodality, it would be useful to have something multi MRI weighting. As of now you have the bval/bvec for diffusion you need to carry around, if you are a bit fancy you have the gradient timings an other things, and if you use non spin-echo stuff you also need to carry around another layer of information. Other stuff like fmri seems to also carry around relevant info, and you can add to the game relaxometry experiments (I'd guess inversion time, flip angle and other things for T1 mapping for example), and if you play with more advanced diffusion sequences you have new data structures you need to know. That's a lot of side files that can go around beyond your everyday nifti. And pretty much every tool uses his own internal format to keep track of all that because of this (on top of my mind there is .mif for mrtrix, exploredti stash everything in a matlab file after conversion, there is also an .xps format also for advanced diffusion with is using matlab, probably others).? I personally started stashing everything in a json file for convenience, but having a flexible, throw everything in it file would definitely be useful, and could potentially be used by other software, making mixing tools far easier if everything was read from a central file, just as now it is easy to go around with a nifti, bval and bvec files. So I'd vote for something similar, say based on json because it is somewhat readable and standard, which would record relevant experimental info (similar to what dcm2niix does I'd guess, but with only the necessary info). It would also make it easy to add new stuff in it over time. I have a rough and barebone xps to json converter I made somewhere if it can serve and an example of what I mean. Samuel Le 2020-07-30 ? 11 h 27, thomas VINCENT a ?crit?: > Hello, > > I think providing tools for multimodality would be great. The basic > experimental use case is that we have several simultaneous imaging > measures, eg fmri eeg and breathing. The first concern is to have a > common container for neuroimaging data from different modalities. The > second one is to conveniently handle temporal synchronization between > measures and then interpolation on the same temporal grid. > > My one cent. > > Thanks for all the great work on nibabel so far! > > Thomas. > > > Le jeu. 30 juill. 2020 11 h 01, Matthew Brett > a ?crit?: > > Hi, > > Although this is pushing things close the wire, I am currently trying > to work out whether to apply for a Chan Zuckerberg grant for Nibabel: > > https://chanzuckerberg.com/wp-content/uploads/2020/06/EOSS-3-RFA-Announcement-and-Instructions-CYCLE-3-COMBINED-1.pdf > > Before we do that, I wanted to ask - if y'all could get anything into > Nibabel - what > would it be? > > So far, in various conversations, Chris Markiewicz and I came up with: > > * More comprehensive DICOM to NIfTI etc support > * Labelled axes for images, maybe via xarray > * Integrated API for surface formats [1] > * HDF5 serialization for many image formats > * Ability to read images directly from URLs, read / write images to / > from AWS, GCS, Azure data storage addresses [2] > * Optimized visualization for web and desktop > > Is there anything else you'd like to see? > > See you, > > Matthew > > [1] https://github.com/nipy/nibabel/issues/936 > [2] c.f. > https://pandas.pydata.org/pandas-docs/version/1.1.0/whatsnew/v1.1.0.html#fsspec-now-used-for-filesystem-handling > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.brett at gmail.com Sat Aug 1 08:32:53 2020 From: matthew.brett at gmail.com (Matthew Brett) Date: Sat, 1 Aug 2020 13:32:53 +0100 Subject: [Neuroimaging] CZI grant - what would you like to see in Nibabel? In-Reply-To: <4af0309c-e666-c6dc-562a-f0b1c4717bc7@gmail.com> References: <20200728210236.dqmjjl6s5uruvrbm@phare.normalesup.org> <20200729161235.uezevmmxhrd267xk@phare.normalesup.org> <4af0309c-e666-c6dc-562a-f0b1c4717bc7@gmail.com> Message-ID: Hi, On Sat, Aug 1, 2020 at 1:27 PM Samuel St-Jean wrote: > > Even before talking multimodality, it would be useful to have something multi MRI weighting. As of now you have the bval/bvec for diffusion you need to carry around, if you are a bit fancy you have the gradient timings an other things, and if you use non spin-echo stuff you also need to carry around another layer of information. Other stuff like fmri seems to also carry around relevant info, and you can add to the game relaxometry experiments (I'd guess inversion time, flip angle and other things for T1 mapping for example), and if you play with more advanced diffusion sequences you have new data structures you need to know. > > That's a lot of side files that can go around beyond your everyday nifti. And pretty much every tool uses his own internal format to keep track of all that because of this (on top of my mind there is .mif for mrtrix, exploredti stash everything in a matlab file after conversion, there is also an .xps format also for advanced diffusion with is using matlab, probably others). I personally started stashing everything in a json file for convenience, but having a flexible, throw everything in it file would definitely be useful, and could potentially be used by other software, making mixing tools far easier if everything was read from a central file, just as now it is easy to go around with a nifti, bval and bvec files. > > So I'd vote for something similar, say based on json because it is somewhat readable and standard, which would record relevant experimental info (similar to what dcm2niix does I'd guess, but with only the necessary info). It would also make it easy to add new stuff in it over time. I have a rough and barebone xps to json converter I made somewhere if it can serve and an example of what I mean. Thanks for this. Would you mind opening an issue on the lines of "Attach metadata to images, and record on disk" with text a bit like this? We can then link to relevant stuff like the JSON header NEP, and Brendon's stuff about dcmstack, possible xarray integration. Cheers, Matthew From markiewicz at stanford.edu Mon Aug 3 12:52:29 2020 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Mon, 3 Aug 2020 16:52:29 +0000 Subject: [Neuroimaging] Neuroimaging package stats (was RE: CZI grant - what would you like to see in Nibabel?) In-Reply-To: References: <20200728210236.dqmjjl6s5uruvrbm@phare.normalesup.org> <20200729161235.uezevmmxhrd267xk@phare.normalesup.org> <4af0309c-e666-c6dc-562a-f0b1c4717bc7@gmail.com>, Message-ID: Hi all, Following up on the CZI discussion, for the grant we need to situate NiBabel in the neuroimaging world. I suspect some Nipy projects might have recently compiled some kind of usage metrics of their packages and the non-Nipy packages (SPM, FSL, AFNI, FreeSurfer, ANTs, ITK-SNAP?) that we're "competing" with. If anybody has this kind of data, or knows off-hand where to find it, I would appreciate any help you can give. Best, Chris ________________________________ From: Neuroimaging on behalf of Matthew Brett Sent: Saturday, August 1, 2020 8:32 AM To: Neuroimaging analysis in Python Subject: Re: [Neuroimaging] CZI grant - what would you like to see in Nibabel? Hi, On Sat, Aug 1, 2020 at 1:27 PM Samuel St-Jean wrote: > > Even before talking multimodality, it would be useful to have something multi MRI weighting. As of now you have the bval/bvec for diffusion you need to carry around, if you are a bit fancy you have the gradient timings an other things, and if you use non spin-echo stuff you also need to carry around another layer of information. Other stuff like fmri seems to also carry around relevant info, and you can add to the game relaxometry experiments (I'd guess inversion time, flip angle and other things for T1 mapping for example), and if you play with more advanced diffusion sequences you have new data structures you need to know. > > That's a lot of side files that can go around beyond your everyday nifti. And pretty much every tool uses his own internal format to keep track of all that because of this (on top of my mind there is .mif for mrtrix, exploredti stash everything in a matlab file after conversion, there is also an .xps format also for advanced diffusion with is using matlab, probably others). I personally started stashing everything in a json file for convenience, but having a flexible, throw everything in it file would definitely be useful, and could potentially be used by other software, making mixing tools far easier if everything was read from a central file, just as now it is easy to go around with a nifti, bval and bvec files. > > So I'd vote for something similar, say based on json because it is somewhat readable and standard, which would record relevant experimental info (similar to what dcm2niix does I'd guess, but with only the necessary info). It would also make it easy to add new stuff in it over time. I have a rough and barebone xps to json converter I made somewhere if it can serve and an example of what I mean. Thanks for this. Would you mind opening an issue on the lines of "Attach metadata to images, and record on disk" with text a bit like this? We can then link to relevant stuff like the JSON header NEP, and Brendon's stuff about dcmstack, possible xarray integration. Cheers, Matthew _______________________________________________ Neuroimaging mailing list Neuroimaging at python.org https://mail.python.org/mailman/listinfo/neuroimaging -------------- next part -------------- An HTML attachment was scrubbed... URL: From gael.varoquaux at normalesup.org Mon Aug 3 17:45:43 2020 From: gael.varoquaux at normalesup.org (Gael Varoquaux) Date: Mon, 3 Aug 2020 23:45:43 +0200 Subject: [Neuroimaging] Neuroimaging package stats (was RE: CZI grant - what would you like to see in Nibabel?) In-Reply-To: References: <20200728210236.dqmjjl6s5uruvrbm@phare.normalesup.org> <20200729161235.uezevmmxhrd267xk@phare.normalesup.org> <4af0309c-e666-c6dc-562a-f0b1c4717bc7@gmail.com> Message-ID: <20200803214543.p2fc7554dsxb3afc@phare.normalesup.org> Hi Chris, With regards to situating the usage on the Python stack in neuroimaging, you may be interested in the evaluation that I did for our Annual Reviews paper on Neuroimaging software tools, fig 2 in: https://www.annualreviews.org/doi/full/10.1146/annurev-biodatasci-072018-021237 The methodology involved manually recording the number of answers with a year limitation to a well specified query on Google scholar. HTH, G On Mon, Aug 03, 2020 at 04:52:29PM +0000, Christopher Markiewicz wrote: > Hi all, > Following up on the CZI discussion, for the grant we need to situate NiBabel in > the neuroimaging world. I suspect some Nipy projects might have recently > compiled some kind of usage metrics of their packages and the non-Nipy packages > (SPM, FSL, AFNI, FreeSurfer, ANTs, ITK-SNAP?) that we're "competing" with. > If anybody has this kind of data, or knows off-hand where to find it, I would > appreciate any help you can give. > Best, > Chris > ??????????????????????????????????????????????????????????????????????????????? > From: Neuroimaging on > behalf of Matthew Brett > Sent: Saturday, August 1, 2020 8:32 AM > To: Neuroimaging analysis in Python > Subject: Re: [Neuroimaging] CZI grant - what would you like to see in Nibabel? > Hi, > On Sat, Aug 1, 2020 at 1:27 PM Samuel St-Jean wrote: > > Even before talking multimodality, it would be useful to have something multi > MRI weighting. As of now you have the bval/bvec for diffusion you need to carry > around, if you are a bit fancy you have the gradient timings an other things, > and if you use non spin-echo stuff you also need to carry around another layer > of information. Other stuff like fmri seems to also carry around relevant info, > and you can add to the game relaxometry experiments (I'd guess inversion time, > flip angle and other things for T1 mapping for example), and if you play with > more advanced diffusion sequences you have new data structures you need to > know. > > That's a lot of side files that can go around beyond your everyday nifti. And > pretty much every tool uses his own internal format to keep track of all that > because of this (on top of my mind there is .mif for mrtrix, exploredti stash > everything in a matlab file after conversion, there is also an .xps format also > for advanced diffusion with is using matlab, probably others). I personally > started stashing everything in a json file for convenience, but having a > flexible, throw everything in it file would definitely be useful, and could > potentially be used by other software, making mixing tools far easier if > everything was read from a central file, just as now it is easy to go around > with a nifti, bval and bvec files. > > So I'd vote for something similar, say based on json because it is somewhat > readable and standard, which would record relevant experimental info (similar > to what dcm2niix does I'd guess, but with only the necessary info). It would > also make it easy to add new stuff in it over time. I have a rough and barebone > xps to json converter I made somewhere if it can serve and an example of what I > mean. > Thanks for this. Would you mind opening an issue on the lines of > "Attach metadata to images, and record on disk" with text a bit like > this? > We can then link to relevant stuff like the JSON header NEP, and > Brendon's stuff about dcmstack, possible xarray integration. > Cheers, > Matthew > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging -- Gael Varoquaux Research Director, INRIA Visiting professor, McGill http://gael-varoquaux.info http://twitter.com/GaelVaroquaux From gael.varoquaux at normalesup.org Mon Aug 3 17:58:59 2020 From: gael.varoquaux at normalesup.org (Gael Varoquaux) Date: Mon, 3 Aug 2020 23:58:59 +0200 Subject: [Neuroimaging] Neuroimaging package stats (was RE: CZI grant - what would you like to see in Nibabel?) In-Reply-To: <20200803214543.p2fc7554dsxb3afc@phare.normalesup.org> References: <20200728210236.dqmjjl6s5uruvrbm@phare.normalesup.org> <20200729161235.uezevmmxhrd267xk@phare.normalesup.org> <4af0309c-e666-c6dc-562a-f0b1c4717bc7@gmail.com> <20200803214543.p2fc7554dsxb3afc@phare.normalesup.org> Message-ID: <20200803215859.b7lszjbpohk4ljha@phare.normalesup.org> Python usage figures updated for this year: https://twitter.com/GaelVaroquaux/status/1263413593615273986 (same methodology as the paper). G On Mon, Aug 03, 2020 at 11:45:43PM +0200, Gael Varoquaux wrote: > Hi Chris, > With regards to situating the usage on the Python stack in neuroimaging, > you may be interested in the evaluation that I did for our Annual Reviews > paper on Neuroimaging software tools, fig 2 in: > https://www.annualreviews.org/doi/full/10.1146/annurev-biodatasci-072018-021237 > The methodology involved manually recording the number of answers with a > year limitation to a well specified query on Google scholar. > HTH, > G > On Mon, Aug 03, 2020 at 04:52:29PM +0000, Christopher Markiewicz wrote: > > Hi all, > > Following up on the CZI discussion, for the grant we need to situate NiBabel in > > the neuroimaging world. I suspect some Nipy projects might have recently > > compiled some kind of usage metrics of their packages and the non-Nipy packages > > (SPM, FSL, AFNI, FreeSurfer, ANTs, ITK-SNAP?) that we're "competing" with. > > If anybody has this kind of data, or knows off-hand where to find it, I would > > appreciate any help you can give. > > Best, > > Chris > > ??????????????????????????????????????????????????????????????????????????????? > > From: Neuroimaging on > > behalf of Matthew Brett > > Sent: Saturday, August 1, 2020 8:32 AM > > To: Neuroimaging analysis in Python > > Subject: Re: [Neuroimaging] CZI grant - what would you like to see in Nibabel? > > Hi, > > On Sat, Aug 1, 2020 at 1:27 PM Samuel St-Jean wrote: > > > Even before talking multimodality, it would be useful to have something multi > > MRI weighting. As of now you have the bval/bvec for diffusion you need to carry > > around, if you are a bit fancy you have the gradient timings an other things, > > and if you use non spin-echo stuff you also need to carry around another layer > > of information. Other stuff like fmri seems to also carry around relevant info, > > and you can add to the game relaxometry experiments (I'd guess inversion time, > > flip angle and other things for T1 mapping for example), and if you play with > > more advanced diffusion sequences you have new data structures you need to > > know. > > > That's a lot of side files that can go around beyond your everyday nifti. And > > pretty much every tool uses his own internal format to keep track of all that > > because of this (on top of my mind there is .mif for mrtrix, exploredti stash > > everything in a matlab file after conversion, there is also an .xps format also > > for advanced diffusion with is using matlab, probably others). I personally > > started stashing everything in a json file for convenience, but having a > > flexible, throw everything in it file would definitely be useful, and could > > potentially be used by other software, making mixing tools far easier if > > everything was read from a central file, just as now it is easy to go around > > with a nifti, bval and bvec files. > > > So I'd vote for something similar, say based on json because it is somewhat > > readable and standard, which would record relevant experimental info (similar > > to what dcm2niix does I'd guess, but with only the necessary info). It would > > also make it easy to add new stuff in it over time. I have a rough and barebone > > xps to json converter I made somewhere if it can serve and an example of what I > > mean. > > Thanks for this. Would you mind opening an issue on the lines of > > "Attach metadata to images, and record on disk" with text a bit like > > this? > > We can then link to relevant stuff like the JSON header NEP, and > > Brendon's stuff about dcmstack, possible xarray integration. > > Cheers, > > Matthew > > _______________________________________________ > > Neuroimaging mailing list > > Neuroimaging at python.org > > https://mail.python.org/mailman/listinfo/neuroimaging > > _______________________________________________ > > Neuroimaging mailing list > > Neuroimaging at python.org > > https://mail.python.org/mailman/listinfo/neuroimaging -- Gael Varoquaux Research Director, INRIA Visiting professor, McGill http://gael-varoquaux.info http://twitter.com/GaelVaroquaux From markiewicz at stanford.edu Mon Aug 3 21:41:38 2020 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Tue, 4 Aug 2020 01:41:38 +0000 Subject: [Neuroimaging] Neuroimaging package stats (was RE: CZI grant - what would you like to see in Nibabel?) In-Reply-To: <20200803215859.b7lszjbpohk4ljha@phare.normalesup.org> References: <20200728210236.dqmjjl6s5uruvrbm@phare.normalesup.org> <20200729161235.uezevmmxhrd267xk@phare.normalesup.org> <4af0309c-e666-c6dc-562a-f0b1c4717bc7@gmail.com> <20200803214543.p2fc7554dsxb3afc@phare.normalesup.org>, <20200803215859.b7lszjbpohk4ljha@phare.normalesup.org> Message-ID: Thanks, Gael! This is very helpful. ________________________________ From: Neuroimaging on behalf of Gael Varoquaux Sent: Monday, August 3, 2020 5:58 PM To: Neuroimaging analysis in Python Subject: Re: [Neuroimaging] Neuroimaging package stats (was RE: CZI grant - what would you like to see in Nibabel?) Python usage figures updated for this year: https://twitter.com/GaelVaroquaux/status/1263413593615273986 (same methodology as the paper). G On Mon, Aug 03, 2020 at 11:45:43PM +0200, Gael Varoquaux wrote: > Hi Chris, > With regards to situating the usage on the Python stack in neuroimaging, > you may be interested in the evaluation that I did for our Annual Reviews > paper on Neuroimaging software tools, fig 2 in: > https://www.annualreviews.org/doi/full/10.1146/annurev-biodatasci-072018-021237 > The methodology involved manually recording the number of answers with a > year limitation to a well specified query on Google scholar. > HTH, > G > On Mon, Aug 03, 2020 at 04:52:29PM +0000, Christopher Markiewicz wrote: > > Hi all, > > Following up on the CZI discussion, for the grant we need to situate NiBabel in > > the neuroimaging world. I suspect some Nipy projects might have recently > > compiled some kind of usage metrics of their packages and the non-Nipy packages > > (SPM, FSL, AFNI, FreeSurfer, ANTs, ITK-SNAP?) that we're "competing" with. > > If anybody has this kind of data, or knows off-hand where to find it, I would > > appreciate any help you can give. > > Best, > > Chris > > ??????????????????????????????????????????????????????????????????????????????? > > From: Neuroimaging on > > behalf of Matthew Brett > > Sent: Saturday, August 1, 2020 8:32 AM > > To: Neuroimaging analysis in Python > > Subject: Re: [Neuroimaging] CZI grant - what would you like to see in Nibabel? > > Hi, > > On Sat, Aug 1, 2020 at 1:27 PM Samuel St-Jean wrote: > > > Even before talking multimodality, it would be useful to have something multi > > MRI weighting. As of now you have the bval/bvec for diffusion you need to carry > > around, if you are a bit fancy you have the gradient timings an other things, > > and if you use non spin-echo stuff you also need to carry around another layer > > of information. Other stuff like fmri seems to also carry around relevant info, > > and you can add to the game relaxometry experiments (I'd guess inversion time, > > flip angle and other things for T1 mapping for example), and if you play with > > more advanced diffusion sequences you have new data structures you need to > > know. > > > That's a lot of side files that can go around beyond your everyday nifti. And > > pretty much every tool uses his own internal format to keep track of all that > > because of this (on top of my mind there is .mif for mrtrix, exploredti stash > > everything in a matlab file after conversion, there is also an .xps format also > > for advanced diffusion with is using matlab, probably others). I personally > > started stashing everything in a json file for convenience, but having a > > flexible, throw everything in it file would definitely be useful, and could > > potentially be used by other software, making mixing tools far easier if > > everything was read from a central file, just as now it is easy to go around > > with a nifti, bval and bvec files. > > > So I'd vote for something similar, say based on json because it is somewhat > > readable and standard, which would record relevant experimental info (similar > > to what dcm2niix does I'd guess, but with only the necessary info). It would > > also make it easy to add new stuff in it over time. I have a rough and barebone > > xps to json converter I made somewhere if it can serve and an example of what I > > mean. > > Thanks for this. Would you mind opening an issue on the lines of > > "Attach metadata to images, and record on disk" with text a bit like > > this? > > We can then link to relevant stuff like the JSON header NEP, and > > Brendon's stuff about dcmstack, possible xarray integration. > > Cheers, > > Matthew > > _______________________________________________ > > Neuroimaging mailing list > > Neuroimaging at python.org > > https://mail.python.org/mailman/listinfo/neuroimaging > > _______________________________________________ > > Neuroimaging mailing list > > Neuroimaging at python.org > > https://mail.python.org/mailman/listinfo/neuroimaging -- Gael Varoquaux Research Director, INRIA Visiting professor, McGill http://gael-varoquaux.info http://twitter.com/GaelVaroquaux _______________________________________________ Neuroimaging mailing list Neuroimaging at python.org https://mail.python.org/mailman/listinfo/neuroimaging -------------- next part -------------- An HTML attachment was scrubbed... URL: From yoh at onerussian.com Mon Aug 3 21:58:39 2020 From: yoh at onerussian.com (Yaroslav Halchenko) Date: Mon, 03 Aug 2020 21:58:39 -0400 Subject: [Neuroimaging] Neuroimaging package stats (was RE: CZI grant - what would you like to see in Nibabel?) In-Reply-To: References: <20200728210236.dqmjjl6s5uruvrbm@phare.normalesup.org> <20200729161235.uezevmmxhrd267xk@phare.normalesup.org> <4af0309c-e666-c6dc-562a-f0b1c4717bc7@gmail.com>, Message-ID: <1A47C050-15F3-4DBC-AEAE-21692E1DA4CA@onerussian.com> Fwiw, since not really a comparison asked for. According to https://libraries.io/pypi/nibabel/sourcerank rank is 20! Psychopy (supported by czi) is 9. Pip 23. Nibabel is THE core package for neuroimaging in Python, like numpy for numeric computation in general (rank 29). Python adoption in neuroimaging grows, and with that the use of nibabel since there simply no alternative. On August 3, 2020 12:52:29 PM EDT, Christopher Markiewicz wrote: >Hi all, > >Following up on the CZI discussion, for the grant we need to situate >NiBabel in the neuroimaging world. I suspect some Nipy projects might >have recently compiled some kind of usage metrics of their packages and >the non-Nipy packages (SPM, FSL, AFNI, FreeSurfer, ANTs, ITK-SNAP?) >that we're "competing" with. > >If anybody has this kind of data, or knows off-hand where to find it, I >would appreciate any help you can give. > >Best, >Chris > >________________________________ >From: Neuroimaging > on behalf of >Matthew Brett >Sent: Saturday, August 1, 2020 8:32 AM >To: Neuroimaging analysis in Python >Subject: Re: [Neuroimaging] CZI grant - what would you like to see in >Nibabel? > >Hi, > >On Sat, Aug 1, 2020 at 1:27 PM Samuel St-Jean >wrote: >> >> Even before talking multimodality, it would be useful to have >something multi MRI weighting. As of now you have the bval/bvec for >diffusion you need to carry around, if you are a bit fancy you have the >gradient timings an other things, and if you use non spin-echo stuff >you also need to carry around another layer of information. Other stuff >like fmri seems to also carry around relevant info, and you can add to >the game relaxometry experiments (I'd guess inversion time, flip angle >and other things for T1 mapping for example), and if you play with more >advanced diffusion sequences you have new data structures you need to >know. >> >> That's a lot of side files that can go around beyond your everyday >nifti. And pretty much every tool uses his own internal format to keep >track of all that because of this (on top of my mind there is .mif for >mrtrix, exploredti stash everything in a matlab file after conversion, >there is also an .xps format also for advanced diffusion with is using >matlab, probably others). I personally started stashing everything in >a json file for convenience, but having a flexible, throw everything in >it file would definitely be useful, and could potentially be used by >other software, making mixing tools far easier if everything was read >from a central file, just as now it is easy to go around with a nifti, >bval and bvec files. >> >> So I'd vote for something similar, say based on json because it is >somewhat readable and standard, which would record relevant >experimental info (similar to what dcm2niix does I'd guess, but with >only the necessary info). It would also make it easy to add new stuff >in it over time. I have a rough and barebone xps to json converter I >made somewhere if it can serve and an example of what I mean. > >Thanks for this. Would you mind opening an issue on the lines of >"Attach metadata to images, and record on disk" with text a bit like >this? > >We can then link to relevant stuff like the JSON header NEP, and >Brendon's stuff about dcmstack, possible xarray integration. > >Cheers, > >Matthew >_______________________________________________ >Neuroimaging mailing list >Neuroimaging at python.org >https://mail.python.org/mailman/listinfo/neuroimaging -- Yaroslav O. Halchenko (mobile version) Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, NH, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: