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 atorok9@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 fischl@nmr.mgh.harvard.edu To: Antonella Kis atorok9@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>
Dear FS experts,
I'm correcting the pial surface when it includes more than it is supposed, but now I got to a subject where the pial is not incluing what is supposed. How do I correct this? You can see the problem in the attachd image.
Thank you! Andreia
There is some white matter there being excluded as well. If you include that, the pial surface will likely grow out and include that gm.
On Aug 1, 2011, at 7:37 AM, _andreia_@sapo.pt wrote:
Dear FS experts,
I'm correcting the pial surface when it includes more than it is supposed, but now I got to a subject where the pial is not incluing what is supposed. How do I correct this? You can see the problem in the attachd image.
Thank you! Andreia <** brainmask.mgz ** (T1.mgz).png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Andreia
it's tough to tell from one slice. There appear to be some bright stuff in the superficial gray matter, which may be messing stuff up, not sure what it is, or it could be something happening through-plane that we can't see. If you want to upload the dataset I'll take a look
cheers Bruce On Mon, 1 Aug 2011, _andreia_@sapo.pt wrote:
Dear FS experts,
I'm correcting the pial surface when it includes more than it is supposed, but now I got to a subject where the pial is not incluing what is supposed. How do I correct this? You can see the problem in the attachd image.
Thank you! Andreia
Hi,
I'm not being able to solve the segmentation problem on in this subject. What files do I need to upload and were, please?
Thank you, Andreia
Citando Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Andreia
it's tough to tell from one slice. There appear to be some bright stuff in the superficial gray matter, which may be messing stuff up, not sure what it is, or it could be something happening through-plane that we can't see. If you want to upload the dataset I'll take a look
cheers Bruce On Mon, 1 Aug 2011, _andreia_@sapo.pt wrote:
Dear FS experts,
I'm correcting the pial surface when it includes more than it is supposed, but now I got to a subject where the pial is not incluing what is supposed. How do I correct this? You can see the problem in the attachd image.
Thank you! Andreia
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.
If you can compress the whole subject dir and load them here, that'd be great.
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-Khoa
On Tue, 2 Aug 2011, _andreia_@sapo.pt wrote:
Hi,
I'm not being able to solve the segmentation problem on in this subject. What files do I need to upload and were, please?
Thank you, Andreia
Citando Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Andreia
it's tough to tell from one slice. There appear to be some bright stuff in the superficial gray matter, which may be messing stuff up, not sure what it is, or it could be something happening through-plane that we can't see. If you want to upload the dataset I'll take a look
cheers Bruce On Mon, 1 Aug 2011, _andreia_@sapo.pt wrote:
Dear FS experts,
I'm correcting the pial surface when it includes more than it is supposed, but now I got to a subject where the pial is not incluing what is supposed. How do I correct this? You can see the problem in the attachd image.
Thank you! Andreia
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.
freesurfer@nmr.mgh.harvard.edu
-
_andreia_＠sapo.pt -
Allison Stevens -
Bruce Fischl -
Khoa Nguyen