This wiki page contains the students questions and answers from the April 29 2013 Freesurfer course.

Question List

It is easier for me to get a NIFTI file of the T1 structural image than the original DICOM files. I have been converting the NIFTI to a freesurfer format using mri_convert. I can get the original DICOM files if that's better. Is it worth going back to the DICOM if NIFTI are more readily available?

and

Could you please repeat the pros and cons of different fyletypes for input to recon-all? I believe I heard Doug say he strongly recommended DICOM. Why is this? thank you very much!

The danger of using a different input than DICOM is that sometimes important header information gets lost. This can result in flipped images (you may not even notice a left-right flip) etc. Usually NIFTI should be fine (assuming the header did not get corrupted). MartinReuter

Can you use skull stripped images as input files?

It is not recommended to use skull stripped images, as several procedures assume that the skull is there. The skull also contains important information used during the atlas (talairach) registration. MartinReuter

Freesurfer makes use of different scan characteristics to recon surfaces and estimate thickness etc. What if the groups you compare differ on either of these characteristics? For example, like with the Huntington scans you mentioned, what if one of your groups has more movement artifacts? Or with the nudging of the grey-white matter surface, what if this border is (in reality) more nudged in one of your groups than in the other?

If the scans differ with respect to these characteristics, your study will be biased. You will never know if the effect you measure is due to the disease or due to, e.g., motion artifacts. That is why it is extremely important to control these parameters (use the same pillow, place supporting cushion at the side of the head, scan a few times, select the best scan without motion, etc.). There can be other problems, e.g. differences in hydration level. MartinReuter

I want to use FreeSurfer to create subject specific ROI's for subcortical structures. Is there an easy way to convert an ROI from FreeSurfer to work with FSL? I have used the conversion tool to make it a NIFTI, but then I always get an error that the dimensions are not right.

How did you convert the ROI label image? The conversion usually does not change the resolution of the image. You can try to mri_convert -rl <target_with_correct_dimensions> -it nearest roi.mgz roi-in-new-space.nii.gz, which will reslice the image into the new resolution using nearest neighbor interpolation. This may however affect the ROI labels as the result may look very noisy. If you manually label the image, better do it directly in the target space. Without more information it is difficult to help. Post your question with more details on the FreeSurfer list. MartinReuter