below worked for us

carl schwartz

---------- Forwarded message ---------- From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Fri, Sep 5, 2008 at 1:26 PM Subject: Re: more inflation To: Doug Greve greve@nmr.mgh.harvard.edu

two things:

1. use -n <i>, where the default <i> is 10 (try 20) 2. -dist <l>, where the default l is 0.1 (try something smaller, or 0)

you could also dl

-f <rms> where default <rms> is 0.015 (try smaller for smoother surfaces)

for example:

mris_inflate -n 20 -f 0.001 -dist 0 lh.white lh.inflated_more

should make a smoother surface

On Fri, 5 Sep 2008, Doug Greve wrote:

Bruce, off the top of your head, do you know how an inflated surface can be inflated more? I've tried mris_inflate, but it does not seem to help. It's just for display, but a little annoying.

thanks

doug

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As far as the first, This happens sometimes when you make your own average subject. You just need to inflate it more. I will try to dig up an old email I have on the commands.

As for the second, just click the redraW BUTTON

CARL SCHWARTZ

On 2/17/09 12:44 PM, "Devdutta W" devdutta.w@gmail.com wrote:

Oops, forgot the attachment.

On Tue, Feb 17, 2009 at 11:42 AM, Devdutta W devdutta.w@gmail.com wrote: Hello again, My questions refer to the attached image. The image is of the average subject I created from our subjects using the "make_average_subject" command. As you can see, in an inflated view there are many gyri and sulci looking structures that shouldn't be there. Clearly something is not right.

My first question is what aspect of our subjects' brains could be causing this? I have inspected the brains in tksurfer and have not found any defects that could account for this.

My second question refers to the oddness at the bottom left of the image. That is something I notice happening all the time. Everytime I drag any window across the tksurfer or tkmedit window that happens. It goes away once I rotate the brain or zoom in or out or anything like that. Is this something that people have encountered before or is this an anomaly unique to our system?

Once again, I really appreciate any help these matters.

Thank you, Devdutta

Carl E. Schwartz, M.D. Harvard Medical School Director, Developmental Neuroimaging & Psychopathology Laboratory Psychiatric Neuroscience Program Massachusetts General Hospital tel 617-726-8965 fax 617-726-4078