Hi Tamara,

three out of how many? I would probably remove those three as whatever you measure in them could be driven by the acquisition differences, but it depends on what acquisition differences you have. If it is only small differences, like tiny deviations in the voxel size etc, it should be OK.

I have no idea where the other intensity differences could come from. If you see them in the original inputs, maybe an MR physicist could take a look and advise. If you have a concrete case where the inputs are OK, but you think that in FS processed images show different contrast or intensities, I would need to have those images to see if I can replicate that.

Best, Martin

On 20 Dec 2016, at 20:57, Tamara Tavares ttavare@uwo.ca wrote:

Thank you for your reply Dr. Reuter.

I have about 3 scans in which the acquisition parameters are slightly different between time 1 and time 2 which probably contributes to these differences. Do you recommend that I do not use these scans?

For my other scans, sometimes the differences in intensity are very subtle. For example, I have one scan where the contrast between the GM and WM are more apparent at one time point vs. the other time point. In another example, the thalamus looks a bit darker at time 1 vs. time 2. Again these differences are very subtle and only noticeable if you are looking for them. I am just wondering at what point do these differences become problematic? I should also note that sometimes these differences are not readily apparent in the original T1 scan.

Thank you again for your help.

Best, Tamara _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer