Hi Sebastian,
it is clear to us how to fix this, this is not the issue here.
The issue is that my colleague and I ran the same image, he used the original dicom as source and I a nifti version prepared for other processing, and we get very different results! And this even thought the actual images vary quite a bit. So thanks for the input, but this does not explain our processing difference. Especially not, since the wm.mgz files are basically identical.
Cheers,
Melanie
On 26-08-2014 15:12, Sebastian Moeller wrote:
it is clear to us how to fix this, this is not the issue here.
The issue is that my colleague and I ran the same image, he used the original dicom as source and I a nifti version prepared for other processing, and we get very different results! And this even thought the actual images vary quite a bit. So thanks for the input, but this does not explain our processing difference. Especially not, since the wm.mgz files are basically identical.
Cheers,
Melanie
On 26-08-2014 15:12, Sebastian Moeller wrote:
Hi Melanie,
this looks like your brain mask contains bright dura mater that gets mis-classified as white matter, this I assumed happened n the skull stripping step, If you edit the brain mask to exclude the offending dura you should be fine (or alternatively it might help to edit the wm.mgz so the voxels contain a value of 1 where the offending dura sits, but I am not sure that this will work) and then re-run the following steps of the recon. So have a look at brainmask.mgz. I assume with image you mean volume? I believe this really is showing that you might need to play with the skull-stripping process a bit to get rid of the sure better (or with your sequence so you get less signal from those structures in the first place ;) )
Best RegardsSebastian
On Aug 26, 2014, at 13:50 , Melanie Ganz <Melanie.Ganz@nru.dk> wrote:
Dear Freesurfer community,
We've encountered a strange situation where the pial and wm surface delineation is successful for one image but contains wm (and subsequent pial) errors for another, almost identical structural image (see attached image, red and yellow are for the successful surface and blue and green are for the failed one). We've tried to identify the source for this discrepancy but I'm at a loss. All voxels of the original input images are identical to the 4th decimal and when converted to orig.mgz only a few voxels appear to be different due to rounding, none of which overlap with the wm surface errors. Both images were processed on the same setup (hardware and software, Freesurfer stable 5.3). Unfortunately, this error is quite systematic in my dataset; about 10% of the images show this type of error. Any suggestions on how to investigate this? I've uploaded example of good and bad at recon ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming/failed_wm_recon.tar.gz in case you'd like to have a closer look.
Thanks for your help.
Vincent and Melanie
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Melanie Ganz, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: Melanie.Ganz@nru.dk web: http://melanie.clausundmelanie.de/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.