[Freesurfer] optseq and psychometric function
Dear List: I have a question concerning optimizing the presentation of a psycho- metric SCASE procedure with optseq. Subjects will view two interleaved SCASE in the scanner. SCASE1 and SCASE2 test the whole length of stimuli strengths for two different conditions. To obtain the best sequences in optseq do I register SCASE1 and SCASE2 as two conditions, or should the individual test steps (ie at 10, 20, 30 % ...) be listed individually as conditions ? Does registering only SCASE1 or SCASE2 without breaking down into individual test units provide accurate efficiency and cost functions in optseq ? Finally, is an efficiency of 25 good for such a design ? Thank you very much for your help! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] registration problems
I agree with Nick. Are you sure it's not still running? Looks to me like it is. Did it actually segfault? mri_ca_register can take a *long* time to run: 10-20 hours depending on the computer and the brain. Bruce On Mon, 3 Jul 2006 [EMAIL PROTECTED] wrote: Dear freesurfers, I got some problems running the mri_ca_register bit of recon-all. The script suddenly brakes down while labeling for the right thalamus is running. Occured twice on the same spot... my specifications: freesurfer-Darwin-tiger-stable-pub-v3.0.3 recon.log file is attached any help is greatly appreciated many thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cluster analysis with mri_glmfit
Hi, I have a couple of specific questions regarding cluster analysis with mri_glmfit that weren't answered at the course the other week and on which the documentation is slightly vauge. My data includes continuous variables (age and IQ, matching the documentaion!) so I should use MC simulation instead of permutation. I have 70 subjects in each group (case/control). The course notes say I can use the mc-z if I have O(80) subjects. How can I tell if I have enough subjects; is there a statistical test that would show if the outputs are reasonable? I would think 70 is close enough to 80, but would like to be able to test it as I assume it is going to depend to a certain extent on the data. The notes say I need to supply the fwhm of the residual. This value is easy to find in the y file, but it is not clear how to specify it to mri_glmfit. Do we use the --fwhm flag as in the example on page 104/202 in the coursebook? Note that the example uses mc-full, not mc-z, and that the --fwhm flag an arguement to mri_glmfit, not a part of the --sim flag. Finally, with regard to the clustering. The commmand as given in the course notes (pg 104/202) works, but the example does not match mri_surfcluster --help. Specifically, the --help text does not mention (that I could see) the --src flag or the --ocp flag. We are using the example from the course as our template. What is the output of the --ocp flag? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] printing out from tksurfer and tkmedit
If there is interest, I could post my shell script for generating a tcl script and running tksurfer (with an option to write to rgb). I have another one that will render all w files in a particular directory (as rgb's) and another that will render all frames from an mgh (painted surface) file (as tif's). With the older version of tksurfer, you can render offscreen, which is convenient for batches of files (because otherwise your monitor is unusable for a long time). From: Bruce Fischl <[EMAIL PROTECTED]> To: Kevin Teich <[EMAIL PROTECTED]> CC: Chacko Cherian <[EMAIL PROTECTED]>, freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] printing out from tksurfer and tkmedit Date: Fri, 30 Jun 2006 11:39:03 -0400 (EDT) but you could write a tcl script to do it automatically On Fri, 30 Jun 2006, Kevin Teich wrote: How can I can I print out the display images from tksurfer and tkmedit other than manually saving them into tiff and then printing them.IS there any way to print them directly? No, sorry, saving TIFFs is the only output that tkmedit and tksurfer do of that kind. ___ 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
