Hi Krish, hi Doug,
I would recommend to drop the following script (00.05*) in the session base directory (for both functionals and anatomicals) to correct consistently for the monkeys sphinx position. While most of the heavy lifting is handed to mri_convert this scripts shows what to do if the animal was not scanned in HeadFirstSupine (HFS) position. After this have a look at the 10.05* script on how to call tkregister2 to safely get your volumes aligned by looking at the MRI header (--regheader). This will work okay if both func and anat have been de-sphinxed... And for good measure have a look at 20.05* for displaying the func on surfaces. All scripts are just examples and wil; not run in your system as they are, but they might give you ideas of how you can solve the problem... best Sebastian
00.05_correct_all_vols_4_sphinx_position.csh
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10.05_register_func_2_arbitrary_struct.csh
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20.05_overlay_analysis_on_vol_and_surf.csh
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On Dec 7, 2010, at 11:51 , Douglas N Greve wrote: > And how did you reorient to run FS on the anats? > > Krishna Srihasam wrote: >> Hi, >> >> Yes. We took the anatomicals with the monkey in sphinx position in a >> stereotax. >> >> Rgds, >> krsihna >> >> -----Original Message----- >> From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] >> Sent: Tuesday, December 07, 2010 2:32 PM >> To: Krishna Srihasam >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] aligning functionals to anatomicals >> >> How did you re-orient your anatomicals? Was the monkey in the sphinx >> position? >> >> doug >> >> Krishna Srihasam wrote: >> >>> Hi, >>> >>> >>> >>> I have a question regarding overlay of functional activations on a >>> freesurfer map. After much work, I flattened my monkey brain. But, I >>> just realized that the input volume , which I used to generate the >>> flat maps, had orientation set to LIA. I want to over lay my >>> functional activations, which are in RAS orientation on them. One >>> way would be to realign all functional data into LIA orientation and >>> then analyze the data and then simply use spmregister-see or >>> fslregister-sess to register. Is there any simpler way? >>> >>> >>> >>> My functionals are 65x85x56 for each slice. I tried using flirt to get >>> the alignment matrix. But, it is failing badly.. Any ideas would be >>> welcome.. >>> >>> >>> >>> Regards, >>> >>> krishna >>> >>> >>> >>> ---------------------------------------------------------------------- >>> -- >>> >>> _______________________________________________ >>> 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 >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> 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 Partners Compliance >> HelpLine at http://www.partners.org/complianceline . If the e-mail was sent >> to you in error but does not contain patient information, please contact the >> sender and properly dispose of the e-mail. >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sebastian Moeller telephone: 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 US CDMA: + 1 - 626 - 807 - 5242 moel...@caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
