Hi Antonella Are the sequence parameters the same? The way you convert should have no effect Bruce
On Jul 27, 2011, at 11:51 AM, Antonella Kis <ator...@yahoo.com> wrote: > Hi Bruce, > > I highly appreciate your great help/advice. > > Unfortunately, today I have another question: I finished running the > recon-all for the new subjects for which I converted the dicom files in the > NIFTI format as you advised me, using mri_convert. I was telling you that the > .nii.gz file for this new subjects are very big , around 38 MB. Today I was > analysing the volumes and I see there is a poor image in comparison with my > other brains that were converted in a NIFTI format (having just 4 MB size) by > someone else before me. > > My question is: is this poor image due to a different conversion way (I > understood the other person used Mricron to convert the files) OR I need to > do manually corrections adding control points for the intensity > normalization. > > What is your suggestion/advise? > > Many thanks. > Antonella > > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > To: Antonella Kis <ator...@yahoo.com> > Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Sent: Tuesday, July 26, 2011 5:53 PM > Subject: Re: [Freesurfer] Loading atlases > > Hi Antonella > > the atlas is not guaranteed to be correct. If it were we would just take the > labels from it :) The only way to tell if it is correct is to look at the > segmentations on top of the MR and see if they follow the visible boundary > > To get the surfaces you should do > > tkmedit SUBJECT1 brainmask.mgz lh.white \ > -aux T1.mgz -surfs \ > -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt > > cheers > Bruce > > > > On Tue, 26 Jul 2011, Antonella Kis wrote: > > > Hi, > > > > I would like to check if my subcortical segmentation is correct so I was > > running: > > > > tkmedit SUBJECT1 brainmask.mgz \ > > -aux T1.mgz -surfs \ > > -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt > > > > 1). Pial (red line), and white (yellow line) surfaces are shown and I > > wonder how I can add a green lie for my orig surface? > > 2). After I load the aparc+aseg.mgz is theer a way to load and overlay the > > original/correct atlas so I can see if my segmentation is correct? > > > > Thank you very much. > > Antonella > > > > > > > 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. > > > <P27.tiff>
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