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
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:greve@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
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