Hi and thanks for the fast reply.

Pardon my ignorance, but I am not sure that the PD images are?

thanks, mads

On 5 October 2015 at 21:59, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Mads

my guess is that this is a problem with the MP2RAGE. We don't see this in the mprage or memprage. Can you look at the PD images in that region? Is the PD close to 0? Maybe you can threshold it out? That region is usually very dark on an mprage

cheers Bruce

On Mon, 5 Oct 2015, Mads Jensen wrote:

...

Hi,

I got a problem with recon-all of T1's. The problem is that the surfaces extent into what is essential noise, see linked images. The problem is reoccurring in all the subjects I have ran so far, so I was wondering if there could be a generic fix or if it will be necessary to fix each recon individually.

The sequence is a MP2RAGE recorded from a Siemens Skyra.

thanks, mads

https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.jp... https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.jp... https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.jp... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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.

I think the standard MP2RAGE only generates the T1 image on the scanner. With the Bloch simulation you can also figure out PD but the online image analysis doesn't do it.

On 10/05/2015 04:21 PM, Bruce Fischl wrote:

I thought mp2rage lets you derive a proton-density (PD) weighted image, but I could be wrong. I'll cc Andre van der Kouwe who will know

On Mon, 5 Oct 2015, Mads Jensen wrote:

...

Hi and thanks for the fast reply.

Pardon my ignorance, but I am not sure that the PD images are?

thanks, mads

On 5 October 2015 at 21:59, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Mads

my guess is that this is a problem with the MP2RAGE. We don't see this in the mprage or memprage. Can you look at the PD images in that region? Is the PD close to 0? Maybe you can threshold it out? That region is usually very dark on an mprage

cheers Bruce

On Mon, 5 Oct 2015, Mads Jensen wrote:

...

Hi,

I got a problem with recon-all of T1's. The problem is that the surfaces extent into what is essential noise, see linked images. The problem is reoccurring in all the subjects I have ran so far, so I was wondering if there could be a generic fix or if it will be necessary to fix each recon individually.

The sequence is a MP2RAGE recorded from a Siemens Skyra.

thanks, mads

https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg

https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.jp...

https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg

https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.jp...

https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg

https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.jp...

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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.

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Hi Mads

yes, you should be able to use mri_convert to change it to .mgz format and name it brainmask.mgz, after which I think it will look as if you've manually edited it and it will be applied

cheers Bruce On Mon, 12 Oct 2015, Mads Jensen wrote:

I got a skullstrippen mask from another pipeline to remove the noise in the MP2RAGE. Is it possible to give that to the recon-all? it is either a mnc or nii

thanks, mads

On 5 October 2015 at 23:11, Andre van der Kouwe andre@nmr.mgh.harvard.edu wrote:

...

I think the standard MP2RAGE only generates the T1 image on the scanner. With the Bloch simulation you can also figure out PD but the online image analysis doesn't do it.

On 10/05/2015 04:21 PM, Bruce Fischl wrote:

...

I thought mp2rage lets you derive a proton-density (PD) weighted image, but I could be wrong. I'll cc Andre van der Kouwe who will know

On Mon, 5 Oct 2015, Mads Jensen wrote:

...

Hi and thanks for the fast reply.

Pardon my ignorance, but I am not sure that the PD images are?

thanks, mads

On 5 October 2015 at 21:59, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Mads

my guess is that this is a problem with the MP2RAGE. We don't see this in the mprage or memprage. Can you look at the PD images in that region? Is the PD close to 0? Maybe you can threshold it out? That region is usually very dark on an mprage

cheers Bruce

On Mon, 5 Oct 2015, Mads Jensen wrote:

...

Hi,

I got a problem with recon-all of T1's. The problem is that the surfaces extent into what is essential noise, see linked images. The problem is reoccurring in all the subjects I have ran so far, so I was wondering if there could be a generic fix or if it will be necessary to fix each recon individually.

The sequence is a MP2RAGE recorded from a Siemens Skyra.

thanks, mads

https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg

https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.jp...

https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg

https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.jp...

https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg

https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.jp...

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

---

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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.

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

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

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