Hi Janosch
there should be some corrected subjects in the tutorial. The white matter surface shouldn follow the perceived boundary, although it may look wrong when it is when it is curving sharply out of plane. I don't have much experience with MDEFT, so I can't comment on the parameters
cheers Bruce
On Fri, 31 Jan 2014, Janosch Linkersdörfer wrote:
Hi Bruce,
thanks for your answer!
Am 30.01.2014 um 14:40 schrieb Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Janosch
it's impossible to tell from a single slice whether those points should be added or not. The white matter in your image is *very* dark in these regions, do you know why?
No, I don't know why, is that something to worry about? The screen shot is from a child participant, but it seems my images (includung the ones from adults) are darker than the ones provided in the tutorial overall. We used an optimized MDEFT sequence with the following settings
Slices 176 Voxel size 1x1x1mm Orientation sagittal FoV 256x224 Matrix 224x256 TR 7.92 FA 16 TE 2.48 TI 910 PAT mode Grappa 2 Fat suppr fat sat Coil 8ch. Head Bandwidth 195 Phase enc.dir A->P
see Deichmann, R., Schwarzbauer, C., & Turner, R. (2004). Optimisation of the 3D MDEFT sequence for anatomical brain imaging: technical implications at 1.5 and 3 T. NeuroImage, 21(2), 757–767.
To decide whether to add them or not you should check a couple of slices in each direction (or look in multiple orientations) to make sure that the white matter is actually dark and it's not partial volume effects. The approach I would take is iterative - add a couple then rerun up to the first inflation and see if things have been improved significantly. This is fast, maybe 5-10 minutes, not sure.
Thanks, I will try this approach.
You shouldn't need to add a ton. Even one control point in the middle of a dark region can have a large effect.
I still wonder which is the desired outcome state. Is it important that the white matter border follows *exactly* the one I perceive on every slice or is it OK when on some sclices it does not.
Regarding the tutorial data: Can cp_after considered to be a completely corrected example subject or is only the one area corrected that the tutorial points to and the rest of the images would also have to be modified?! I see some areas in cp_before AND cp_after where I am not sure whether adding control points would be needed.
It would help me if you could point me to one or two completely corrected and perfectly processed images so I could determine what level of accuracy is desirable.
Sorry for all these questions, but I think modifying the images is a crucial point in the process that influences all further steps, and I just don't yet have a feeling for it...
Thanks,
Janosch
cheers Bruce
On Thu, 30 Jan 2014, Janosch Linkersdörfer wrote:
Dear Freesurfers,
I am just getting started using Freesurfer. I ran recon-all on my subjects for the first time and now would like to troubleshoot the output.
I watched the tutorial lectures and worked through the troubleshooting tutorial. Nevertheless, I am still uncertain which things I will have to correct (especially as editing too much and/or not to the same degree between subjects might do more harm than good).
Some errors are relatively obvious like the exclusion of white matter voxels from the white matter surface (see *1* on the screen shot of my own data)
I am far more uncertain about adding control points. For example, I do not know whether I should add those at the location denoted with *2* in my own data.
If so, there would be a lot of other, similar locations where I would add control points in my data. But this would also be true for the image used in the "Adding control points" tutorial. In the second screen shot, which displays this image, I have marked some locations where the white matter surface does not follow the one I would draw if I had to do it manually.
Is one supposed to correct all those imprecisions by adding control points?! What are the criteria for adding vs. not adding control points?
Thank you very much,
Janosch
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