Hi,

Thanks, yes, we have this problem on our scans from the Allegra and 7 T scanners, where there's a local transmit coil (no body transmit coil) and therefore blood with non-inverted spins enters the head after the inversion pulse and appears bright in the images. With our Allegra scans this has indeed caused problems with FreeSurfer, where the vessels are included as part of some labelled structures. I did try to segment and label the vessels with only partial success (since the images are already collected). In your case, a sat band might help... is your inversion pulse non-selective? If you have an axial slab and axial slab-selective inversion, maybe just making the inversion pulse non-selective will help. If the coil has no coverage of the neck, I guess your sat band won't work and you'll have to address the issue in post-processing. Sorry, I don't have a specific solution, but we've also seen the problem. First thing perhaps is to verify whether you're using a local transmit coil.

Cheers,

Andre.

On 08/01/2014 12:50 PM, Bruce Fischl wrote:

Hi Kate

I'll cc Andre and Dylan, but I would have thought some sat bands in the neck would do it. I think vessels are usually bright in the mprage, but don't usually case problems. Comments welcome....

cheers

Bruce

On Fri, 1 Aug 2014, McLaughlin, Katie wrote:

...

Hi Doug, Bruce, et al. We've used the MGH meMPRAGE protocol successfully with children and adolescents previously on a Siemens 3T. I've recently moved to a new institution and am using the protocol on a Philips 3T Achieva scanner and we've been having a lot of issues with high-intensity blood vessels (appearing bright white and interfering with segmentation in FreeSurfer). Screenshot of an example attached.

We have added some rest slabs/sat bands to the protocol to address this, but it hasn't fully solved the problem.

I'm wondering if you have any recommendations about adjusting things in FreeSurfer to help us get better segmentation?

Thanks for your thoughts on this, Kate

you could get a T2 or FLAIR and use it to fix the pial surface On Fri, 1 Aug 2014, McLaughlin, Katie wrote:

Hi Andre and Bruce,

Thanks for your input here. The sat band has helped, although it hasn't entirely corrected the problem (the image attached was from a subject with the sat bands included). We are using a local transmit coil.

I'm going to check with our physicist about the inversion pulse - thanks for the suggestion.

Any other thoughts about strategies for improving this are welcome! Andre, would you mind sharing how you segmented the blood vessels and labeled in FreeSurfer? We could try that approach...

Thanks, Kate

---

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Andre van der Kouwe [andre@nmr.mgh.harvard.edu] Sent: Friday, August 01, 2014 1:00 PM To: Bruce Fischl; Freesurfer support list Cc: Dylan Tisdall Subject: Re: [Freesurfer] High intensity blood vessels in children with meMPRAGE

Hi,

Thanks, yes, we have this problem on our scans from the Allegra and 7 T scanners, where there's a local transmit coil (no body transmit coil) and therefore blood with non-inverted spins enters the head after the inversion pulse and appears bright in the images. With our Allegra scans this has indeed caused problems with FreeSurfer, where the vessels are included as part of some labelled structures. I did try to segment and label the vessels with only partial success (since the images are already collected). In your case, a sat band might help... is your inversion pulse non-selective? If you have an axial slab and axial slab-selective inversion, maybe just making the inversion pulse non-selective will help. If the coil has no coverage of the neck, I guess your sat band won't work and you'll have to address the issue in post-processing. Sorry, I don't have a specific solution, but we've also seen the problem. First thing perhaps is to verify whether you're using a local transmit coil.

Cheers,

Andre.

On 08/01/2014 12:50 PM, Bruce Fischl wrote:

...

Hi Kate

I'll cc Andre and Dylan, but I would have thought some sat bands in the neck would do it. I think vessels are usually bright in the mprage, but don't usually case problems. Comments welcome....

cheers

Bruce

On Fri, 1 Aug 2014, McLaughlin, Katie wrote:

...

Hi Doug, Bruce, et al. We've used the MGH meMPRAGE protocol successfully with children and adolescents previously on a Siemens 3T. I've recently moved to a new institution and am using the protocol on a Philips 3T Achieva scanner and we've been having a lot of issues with high-intensity blood vessels (appearing bright white and interfering with segmentation in FreeSurfer). Screenshot of an example attached.

We have added some rest slabs/sat bands to the protocol to address this, but it hasn't fully solved the problem.

I'm wondering if you have any recommendations about adjusting things in FreeSurfer to help us get better segmentation?

Thanks for your thoughts on this, Kate

---

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