eXTReMe Tracker
Mar 092010

Ubuntu came out with the Alpha 3 version of Lucid Lynx (Ubuntu 10.04) in the last week of February. The window control buttons (minimize, maximize and close) were still on the right hand side. Then on March 8th, there was a change in metacity. Regardless of which theme you choose, the window controls are seen on the top left hand corner of each window. Its taking me a bit of getting used to. Since I have been using OS-X theme for my windowing, this has come freakishly close to looking like a Mac, and its not good.

Location of controls is switched to left in Lucid Lynx Alpha 3

Location of controls is switched to left in Lucid Lynx Alpha 3

The release is still in its alpha stage. If a lot of people express dissatisfaction at the new placement of these buttons, it might be reverted back to its old location.

ETA: There is a workaround to get the window controls to the desired location.

  • start gconf-editor, go to /apps/metacity/general/button_layout
  • Colon separates what goes in the left corner versus the right. eg:
  • menu:minimize,maximize,close means menu on the left, min max close on the right.

This workaround was found at: http://www.ivankamajic.com/?p=281#comment-30647

Mar 082010

In order to convert files in .img and .hdr format to a single .nii file, we first need to install the nifti tools toolbox for matlab.

nifti tools

Once the path for nifti tools has been set in matlab, the files in .hdr and .img format can be combined to create a .nii file by running the following two commands:

save_nii(nii, ‘desired_filename_for_niftifile.nii’);

If you have freesurfer installed, you can convert between the files types with mri_convert by specifying the input (-it) and the output (-ot) type.

mri_convert -i name_of_input_file -it nifti1 -ot nii -o name_of_output_file

If you have functional dataset with several volumes over the course of your experiment, you can use the fslmerge function available in FSL to combine all the nifti files into a single 4D file.

fslmerge -t output_name.nii *.nii

Where *.nii would cover the entire set of nifti files if they are arranged sequentially.

Its not required to type in the extension .hdr or .img for the input image or output image if you have specified the input and the output types. By specifying the input type of nifti1, you tell the program that it will be a .hdr/.img pair, and specifying output type as nii goes for having your output with .nii extension.

To gzip the nifti file for use in freesurfer:

gzip filename.nii filename1.nii.gz

This will create a gzipped nifti file.

To automatically segment the structural volume:

recon_all -i filename1.nii.gz -subjid SUBJID -all

This will segment the structures containing in the structural file filename.nii.gz. Complete information on using recon-all for freesurfer can be found at FreeSurfer Wiki.

For some reason, Freesurfer seems to work well in tcsh. I’ve often encountered problems of weird nature when running it under bash. In order to run your autosegmentation with freesurfer type in tcsh at the terminal, since by default it is set to bash in most linux distros.