I appreciate it may seem forboding to go around messing with byte ordering in your own code based on specs you've downloaded, esp if you don't write code much.
miconv from my memory is a good tool for your issue. http://od1n.sourceforge.net/manual/html/miconv.html it reads ima and supports a siemens specific dialect if you want. it outputs all the types listed above. you would play with options till it worked. lots of options. check results in "mango" is my advice, but fslview or caret works too (but nifti byte ordering between fsl and caret often confuses me. mango is simple and clear) It's part of "odin" http://od1n.sourceforge.net/download.html there is a windows binary I see. however in debian related systems you can get miconv usually by installing the "mitools" package seperately. NB: there was a problem for a while on ubuntu in 2011 with the dicomm library versions which broke mitools. I put in a bug report; I think it has been fixed now. I'm sure debian/neurodebian works, it will be more conservative usually. ubuntu 10.04 works well. new ubuntu probably too, I'm off ubuntu now don't know. I'm not sure why something this useful is so obscure. good luck - I think this will work for your issue very quickly. On 13 March 2012 08:14, Colin Reveley <[email protected]> wrote: > all those programs are nice (there's also miconv which you can get > from the ubuntu or debian or neurodebian package manager, or by > compiling "odin" which is some sort of thing. not sure what, but it > comes with miconv. miconv is really good for DICOMM and other low > level stuff, and understands scanner dialects and things) > > the shell is nice. > > but also, you have a load of bytes ultimately. you know what they mean > because it's specified. you can find the specification. it's on the > web. > > you can read the bytes into a data structure (in matlab is easiest, > for example a 3 or 4d matrix). > > you can manipulate their order to conform to some other specification > like nifti (there's a matlab package that helps with the nifti header > and stuff) > > then you can write the new manipulated bytes onto the hard disk of > your computer. > > you can do what you want. > > A while ago, for example, I remember taking a stack of png or maybe > svg images which were labels for a brain from > scalablebrainatlas.incf.org and making them into a nifti with matlab. > > Since I did it, it cannot be hard, because I'm no good at hard things. > I probably have that code. > > On 12 March 2012 23:27, <[email protected]> wrote: > > Send caret-users mailing list submissions to > > [email protected] > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > or, via email, send a message with subject or body 'help' to > > [email protected] > > > > You can reach the person managing the list at > > [email protected] > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of caret-users digest..." > > > > Today's Topics: > > > > 1. Re: Question regarding plotting ROIs and connections between > > them on surface (Donna Dierker) > > 2. Re: ima images (Maestri, Matthew) > > 3. Re: ima images (Timothy Coalson) > > 4. Fwd: ima images (Timothy Coalson) > > > > > > ---------- Forwarded message ---------- > > From: Donna Dierker <[email protected]> > > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > > Cc: > > Date: Mon, 12 Mar 2012 11:11:34 -0500 > > Subject: Re: [caret-users] Question regarding plotting ROIs and > connections between them on surface > > Regarding the connections, this is something we're working on, and I > don't think we have anything ready for public release. If you have > something in volumetric form, you could display it, and you could view > surface and volume together, varying the opacity, but I suspect you have > something else in mind. > > > > You can plot the ROIs by mapping the paint volume onto one of the atlas > surfaces: > > > > > http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MapVolumeToSurface > > > > You can choose the PALS atlas and use one of the standard scenes in this > dataset: > > > > CARET_TUTORIAL_SEPT06.zip > > http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030 > > > > ... or you can map to one of our mean midthickness "fs_LR" surfaces in > FNIRT space (i.e., actually mni152, but fnirted that way, rather than > flirted or SPM'd that way). While these surfaces align better with the > Harvard-Oxford atlas, we haven't yet released standard scenes datasets for > the fs_LR surfaces. It's among the many items on our do-list. You might > find a figure in this paper that has surfaces like the ones you want to use: > > > > Van Essen, D.C., Glasser, M.F., Dierker, D., Harwell, J., and Coalson, > T. (2011) Parcellations and hemispheric asymmetries of human cerebral > cortex analyzed on surface-based atlases. Cerebral Cortex doi: > 10.1093/cercor/bhr291. > > > http://cercor.oxfordjournals.org/content/early/2011/11/02/cercor.bhr291.full.pdf+html > > > > Those datasets are here: > > > > HUMAN_ATLAS_CC11 > > http://sumsdb.wustl.edu/sums/directory.do?id=8286149 > > > > Keep in mind that the surface onto which you map your ROI volume need > not be the same surface on which you display it; however, both need to be > on the same mesh. > > > > > > On Mar 12, 2012, at 10:44 AM, SURIL GOHEL yahoo wrote: > > > >> > >> Hi Experts, > >> I am learning to start using caret for displaying results from one > analysis. > >> I have set of ROIs defined using Harvard-oxford atlas available through > FSL and i performed connectivity analysis between these ROI -pairs. > >> After statistics i have group difference where ROI-pairs show > difference in connectivity between two groups. > >> I am trying to plot this ROIs on a surface and show connections between > them using caret. > >> > >> I have been able to create surface based data from the volume but i am > not being able to show ROIs on the surface and display connections between > them. > >> can anyone please help me about how its done? > >> -- > >> -Suril > >> 973-972-7076 > >> > >> > >> _______________________________________________ > >> caret-users mailing list > >> [email protected] > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > > > ---------- Forwarded message ---------- > > From: "Maestri, Matthew" <[email protected]> > > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > > Cc: > > Date: Mon, 12 Mar 2012 19:01:59 +0000 > > Subject: Re: [caret-users] ima images > > Hi Tim, > > > > I was unable to use AFNI's to3d. Is there any way I can convert them in > Caret or compile them somehow? What is a FSL in Caret? > > > > Thank you, > > Matthew > > ________________________________________ > > From: [email protected] [ > [email protected]] on behalf of Donna Dierker [ > [email protected]] > > Sent: Friday, March 09, 2012 12:10 PM > > To: Caret, SureFit, and SuMS software users > > Subject: Re: [caret-users] ima images > > > > Try something like AFNI's to3d. > > > > > > On Mar 9, 2012, at 11:04 AM, Timothy Coalson wrote: > > > >> I believe .ima is an extension used for dicom data, try a dicom to > nifti converter such as dinifti or dcm2nii (part of mricron). > >> > >> Tim > >> > >> On Fri, Mar 9, 2012 at 9:09 AM, Maestri, Matthew < > [email protected]> wrote: > >> Hi Donna, > >> > >> Is it possible for me to open ima images in Caret? If not, is it > possible for me to convert the ima images into a Caret friendly image? If > so, how would I got about doing this? > >> > >> Thanks, > >> Matthew > >> > >> _______________________________________________ > >> caret-users mailing list > >> [email protected] > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> > >> _______________________________________________ > >> caret-users mailing list > >> [email protected] > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > ---------- Forwarded message ---------- > > From: Timothy Coalson <[email protected]> > > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > > Cc: > > Date: Mon, 12 Mar 2012 15:59:13 -0500 > > Subject: Re: [caret-users] ima images > > FSL is another software package for viewing and manipulating MRI images, > etc, which is entirely separate from Caret: > > > > http://www.fmrib.ox.ac.uk/fsl/ > > > > to3d's help suggests that it should understand .ima, but it doesn't seem > to give much detail on how to use it: > > "* Siemens .ima image files can now be read. The program will detect if > > byte-swapping is needed on these images, and can also set voxel grid > > sizes and orientations (correctly, I hope)." > > > > Did you try dinifti or dcm2nii? I know at least one of them understood > .ima, but I can't remember which. > > > > http://cbi.nyu.edu/software/dinifti.php > > > > http://www.cabiatl.com/mricro/mricron/dcm2nii.html > > > > If all that fails, you may be able to run it through dcm_to_4dfp and > nifti_4dfp from the 4dfp suite, but that will probably involve building it > from source unless you already have it installed. > > > > Tim > > > > On Mon, Mar 12, 2012 at 2:01 PM, Maestri, Matthew < > [email protected]> wrote: > >> > >> Hi Tim, > >> > >> I was unable to use AFNI's to3d. Is there any way I can convert them in > Caret or compile them somehow? What is a FSL in Caret? > >> > >> Thank you, > >> Matthew > >> ________________________________________ > >> From: [email protected] [ > [email protected]] on behalf of Donna Dierker [ > [email protected]] > >> Sent: Friday, March 09, 2012 12:10 PM > >> To: Caret, SureFit, and SuMS software users > >> Subject: Re: [caret-users] ima images > >> > >> Try something like AFNI's to3d. > >> > >> > >> On Mar 9, 2012, at 11:04 AM, Timothy Coalson wrote: > >> > >> > I believe .ima is an extension used for dicom data, try a dicom to > nifti converter such as dinifti or dcm2nii (part of mricron). > >> > > >> > Tim > >> > > >> > On Fri, Mar 9, 2012 at 9:09 AM, Maestri, Matthew < > [email protected]> wrote: > >> > Hi Donna, > >> > > >> > Is it possible for me to open ima images in Caret? If not, is it > possible for me to convert the ima images into a Caret friendly image? If > so, how would I got about doing this? > >> > > >> > Thanks, > >> > Matthew > >> > > >> > _______________________________________________ > >> > caret-users mailing list > >> > [email protected] > >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > > >> > > >> > _______________________________________________ > >> > caret-users mailing list > >> > [email protected] > >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> > >> _______________________________________________ > >> caret-users mailing list > >> [email protected] > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> _______________________________________________ > >> caret-users mailing list > >> [email protected] > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > ---------- Forwarded message ---------- > > From: Timothy Coalson <[email protected]> > > To: <[email protected]> > > Cc: > > Date: Mon, 12 Mar 2012 18:21:57 -0500 > > Subject: [caret-users] Fwd: ima images > > The list isn't liking donna's home email for some reason, forwarding her > message at her request. > > > > Tim > > > > Begin forwarded message: > > > > From: [email protected] > > Subject: Re: [caret-users] ima images > > Date: March 12, 2012 6:14:03 PM CDT > > To: [email protected] > > > > You are not allowed to post to this mailing list, and your message has > > been automatically rejected. If you think that your messages are > > being rejected in error, contact the mailing list owner at > > [email protected]. > > > > > > From: Donna Dierker <[email protected]> > > Subject: Re: [caret-users] ima images > > Date: March 12, 2012 6:08:37 PM CDT > > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > > > > > > And I think once perhaps I computed xdim*ydim*bytes-per-pixel and used > the Linux tail command to strip the header off the ima files. Then I used > cat to put them together to form a raw file. Or I dreamed it. > > > > What can be nightmarish about this is when the slice order differs from > the Linux shell file sort order. Then you must come to grips with the fact > that you need a software utility to import these for you. > > > > Freesurfer's mri_convert probably fits the bill, too. > > > > > > On Mar 12, 2012, at 3:59 PM, Timothy Coalson wrote: > > > > FSL is another software package for viewing and manipulating MRI images, > etc, which is entirely separate from Caret: > > > > http://www.fmrib.ox.ac.uk/fsl/ > > > > to3d's help suggests that it should understand .ima, but it doesn't seem > to give much detail on how to use it: > > "* Siemens .ima image files can now be read. The program will detect if > > byte-swapping is needed on these images, and can also set voxel grid > > sizes and orientations (correctly, I hope)." > > > > Did you try dinifti or dcm2nii? I know at least one of them understood > .ima, but I can't remember which. > > > > http://cbi.nyu.edu/software/dinifti.php > > > > http://www.cabiatl.com/mricro/mricron/dcm2nii.html > > > > If all that fails, you may be able to run it through dcm_to_4dfp and > nifti_4dfp from the 4dfp suite, but that will probably involve building it > from source unless you already have it installed. > > > > Tim > > > > On Mon, Mar 12, 2012 at 2:01 PM, Maestri, Matthew < > [email protected]> wrote: > >> > >> Hi Tim, > >> > >> I was unable to use AFNI's to3d. Is there any way I can convert them in > Caret or compile them somehow? What is a FSL in Caret? > >> > >> Thank you, > >> Matthew > >> ________________________________________ > >> From: [email protected] [ > [email protected]] on behalf of Donna Dierker [ > [email protected]] > >> Sent: Friday, March 09, 2012 12:10 PM > >> To: Caret, SureFit, and SuMS software users > >> Subject: Re: [caret-users] ima images > >> > >> Try something like AFNI's to3d. > >> > >> > >> On Mar 9, 2012, at 11:04 AM, Timothy Coalson wrote: > >> > >> > I believe .ima is an extension used for dicom data, try a dicom to > nifti converter such as dinifti or dcm2nii (part of mricron). > >> > > >> > Tim > >> > > >> > On Fri, Mar 9, 2012 at 9:09 AM, Maestri, Matthew < > [email protected]> wrote: > >> > Hi Donna, > >> > > >> > Is it possible for me to open ima images in Caret? If not, is it > possible for me to convert the ima images into a Caret friendly image? If > so, how would I got about doing this? > >> > > >> > Thanks, > >> > Matthew > >> > > >> > _______________________________________________ > >> > caret-users mailing list > >> > [email protected] > >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > > >> > > >> > _______________________________________________ > >> > caret-users mailing list > >> > [email protected] > >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> > >> _______________________________________________ > >> caret-users mailing list > >> [email protected] > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> _______________________________________________ > >> caret-users mailing list > >> [email protected] > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > > > > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > >
_______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
