Re: [Freesurfer] thickness file data structure
It has to do with being able to store it in analyze/nifti (which cannot handle more than 32k in any dimension). It is possible to prevent the reshaping. doug On Tue, 29 Apr 2008, Bruce Fischl wrote: I think it's because of nifti. Doug is out of town, but he's the one who will be able to tell you definitively. cheers, Bruce On Tue, 29 Apr 2008, Nick Schmansky wrote: Yaroslav, You do indeed need to collapse the 23406 x 7 arrays into a single array. I don't remember why it is split into 7 vectors, something to do with being able to read into AFNI I think. Doug will know and will probably answer. But in any case you can collapse 23406 x 7 data into a single array. Nick On Tue, 2008-04-29 at 18:12 -0400, Yaroslav Halchenko wrote: > Dear Freesurfers, > > First thanks everyone who helped me out with reading-in .mgh data from > within Python (especial thanks to Krish). > > Now I wonder what actually I got ;-) and please pardon my ignorance > > When I read in thickness file in I get an array of > (23406, 7, 58) > dimensionality, where 58 makes sense to me since we have 58 subjects. > > P.S. I've got the same dimensions whenever I didn't use Krish's python > binding but converted to minc and loaded using NetCDF module (in python > though again, but python's numpy.ndarray dimensionality is not limited > by short) > > What I wonder about is that why 23406 and 7? ok - the product is equal > to the surface number of vertices:23406*7=163842, so it seems that > I can simply collapse those two dimensions (which one goes first?) > > but why is that done so? > > according to > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat > and mri.h in particular I don't see any limit on width/hight to be of > short (not int) type and int (4 bytes) should be good enough to store > full index. Is that due to some historical perspective? or am I just > completely missing smth? > > > Thanks in advance for the hints! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] thickness file data structure
well -- yeah... nifti is indeed has a 'short' limit on the size of a dimension but I leave it open question 'what .mgh format has to do with .nii' ;-) Thank you guys very much for your rapid replies! Cheers Yarik On Tue, 29 Apr 2008, Bruce Fischl wrote: > I think it's because of nifti. Doug is out of town, but he's the one who > will be able to tell you definitively. > > cheers, > Bruce -- Yaroslav Halchenko Research Assistant, Psychology Department, Rutgers-Newark Student Ph.D. @ CS Dept. NJIT Office: (973) 353-5440x263 | FWD: 82823 | Fax: (973) 353-1171 101 Warren Str, Smith Hall, Rm 4-105, Newark NJ 07102 WWW: http://www.linkedin.com/in/yarik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] thickness file data structure
I think it's because of nifti. Doug is out of town, but he's the one who will be able to tell you definitively. cheers, Bruce On Tue, 29 Apr 2008, Nick Schmansky wrote: Yaroslav, You do indeed need to collapse the 23406 x 7 arrays into a single array. I don't remember why it is split into 7 vectors, something to do with being able to read into AFNI I think. Doug will know and will probably answer. But in any case you can collapse 23406 x 7 data into a single array. Nick On Tue, 2008-04-29 at 18:12 -0400, Yaroslav Halchenko wrote: Dear Freesurfers, First thanks everyone who helped me out with reading-in .mgh data from within Python (especial thanks to Krish). Now I wonder what actually I got ;-) and please pardon my ignorance When I read in thickness file in I get an array of (23406, 7, 58) dimensionality, where 58 makes sense to me since we have 58 subjects. P.S. I've got the same dimensions whenever I didn't use Krish's python binding but converted to minc and loaded using NetCDF module (in python though again, but python's numpy.ndarray dimensionality is not limited by short) What I wonder about is that why 23406 and 7? ok - the product is equal to the surface number of vertices:23406*7=163842, so it seems that I can simply collapse those two dimensions (which one goes first?) but why is that done so? according to http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat and mri.h in particular I don't see any limit on width/hight to be of short (not int) type and int (4 bytes) should be good enough to store full index. Is that due to some historical perspective? or am I just completely missing smth? Thanks in advance for the hints! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] thickness file data structure
Yaroslav, You do indeed need to collapse the 23406 x 7 arrays into a single array. I don't remember why it is split into 7 vectors, something to do with being able to read into AFNI I think. Doug will know and will probably answer. But in any case you can collapse 23406 x 7 data into a single array. Nick On Tue, 2008-04-29 at 18:12 -0400, Yaroslav Halchenko wrote: > Dear Freesurfers, > > First thanks everyone who helped me out with reading-in .mgh data from > within Python (especial thanks to Krish). > > Now I wonder what actually I got ;-) and please pardon my ignorance > > When I read in thickness file in I get an array of > (23406, 7, 58) > dimensionality, where 58 makes sense to me since we have 58 subjects. > > P.S. I've got the same dimensions whenever I didn't use Krish's python > binding but converted to minc and loaded using NetCDF module (in python > though again, but python's numpy.ndarray dimensionality is not limited > by short) > > What I wonder about is that why 23406 and 7? ok - the product is equal > to the surface number of vertices:23406*7=163842, so it seems that > I can simply collapse those two dimensions (which one goes first?) > > but why is that done so? > > according to > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat > and mri.h in particular I don't see any limit on width/hight to be of > short (not int) type and int (4 bytes) should be good enough to store > full index. Is that due to some historical perspective? or am I just > completely missing smth? > > > Thanks in advance for the hints! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] thickness file data structure
Dear Freesurfers, First thanks everyone who helped me out with reading-in .mgh data from within Python (especial thanks to Krish). Now I wonder what actually I got ;-) and please pardon my ignorance When I read in thickness file in I get an array of (23406, 7, 58) dimensionality, where 58 makes sense to me since we have 58 subjects. P.S. I've got the same dimensions whenever I didn't use Krish's python binding but converted to minc and loaded using NetCDF module (in python though again, but python's numpy.ndarray dimensionality is not limited by short) What I wonder about is that why 23406 and 7? ok - the product is equal to the surface number of vertices:23406*7=163842, so it seems that I can simply collapse those two dimensions (which one goes first?) but why is that done so? according to http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat and mri.h in particular I don't see any limit on width/hight to be of short (not int) type and int (4 bytes) should be good enough to store full index. Is that due to some historical perspective? or am I just completely missing smth? Thanks in advance for the hints! -- Yaroslav Halchenko Research Assistant, Psychology Department, Rutgers-Newark Student Ph.D. @ CS Dept. NJIT Office: (973) 353-5440x263 | FWD: 82823 | Fax: (973) 353-1171 101 Warren Str, Smith Hall, Rm 4-105, Newark NJ 07102 WWW: http://www.linkedin.com/in/yarik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
