I have two subjects where the white surface does not follow the gray-white gradient (see attached pic for example). Is there any way to fix this? I'm assuming it has to do with the limitations of my scan too (it's FLASH data). I'm running 3.0.4, thanks.
-Derin
Hi Derin,
What does the orig surface look like? and the wm? Are those correct?
Jenni
On Fri, 13 Apr 2007, Derin Cobia wrote:
I have two subjects where the white surface does not follow the gray-white gradient (see attached pic for example). Is there any way to fix this? I'm assuming it has to do with the limitations of my scan too (it's FLASH data). I'm running 3.0.4, thanks.
-Derin
Did you mean wm.mgz? It looks fine. The orig surface is not good either. Here's a pic.
-Derin
Hi Derin,
What does the orig surface look like? and the wm? Are those correct?
Jenni
On Fri, 13 Apr 2007, Derin Cobia wrote:
I have two subjects where the white surface does not follow the gray-white gradient (see attached pic for example). Is there any way to fix this? I'm assuming it has to do with the limitations of my scan too (it's FLASH data). I'm running 3.0.4, thanks.
-Derin
this is probably a topology fixing problem. Look at the ?h.orig.nofix and see how it is On Fri, 13 Apr 2007, Derin Cobia wrote:
Did you mean wm.mgz? It looks fine. The orig surface is not good either. Here's a pic.
-Derin
Hi Derin,
What does the orig surface look like? and the wm? Are those correct?
Jenni
On Fri, 13 Apr 2007, Derin Cobia wrote:
I have two subjects where the white surface does not follow the gray-white gradient (see attached pic for example). Is there any way to fix this? I'm assuming it has to do with the limitations of my scan too (it's FLASH data). I'm running 3.0.4, thanks.
-Derin
The ?h.orig.nofix looks ok, meaning it follows the white-gray boundary appropriately. What should I try next?
-Derin
this is probably a topology fixing problem. Look at the ?h.orig.nofix and see how it is On Fri, 13 Apr 2007, Derin Cobia wrote:
Did you mean wm.mgz? It looks fine. The orig surface is not good either. Here's a pic.
-Derin
Hi Derin,
What does the orig surface look like? and the wm? Are those correct?
Jenni
On Fri, 13 Apr 2007, Derin Cobia wrote:
I have two subjects where the white surface does not follow the gray-white gradient (see attached pic for example). Is there any way to fix this? I'm assuming it has to do with the limitations of my scan too (it's FLASH data). I'm running 3.0.4, thanks.
-Derin
look at the ?h.inflated.nofix to see what is causing the defect, and correct the wm.mgz manually to remove it. Jenni: can you point Derin at the appropriate wiki page?
thanks, Bruce
On Fri, 13 Apr 2007, Derin Cobia wrote:
The ?h.orig.nofix looks ok, meaning it follows the white-gray boundary appropriately. What should I try next?
-Derin
this is probably a topology fixing problem. Look at the ?h.orig.nofix and see how it is On Fri, 13 Apr 2007, Derin Cobia wrote:
Did you mean wm.mgz? It looks fine. The orig surface is not good either. Here's a pic.
-Derin
Hi Derin,
What does the orig surface look like? and the wm? Are those correct?
Jenni
On Fri, 13 Apr 2007, Derin Cobia wrote:
I have two subjects where the white surface does not follow the gray-white gradient (see attached pic for example). Is there any way to fix this? I'm assuming it has to do with the limitations of my scan too (it's FLASH data). I'm running 3.0.4, thanks.
-Derin
Here is a pic of the inflated.nofix, how do I know what to edit? I've checked the wm.mgz and it looks fine (at least I can't see any errors). Maybe I'm missing something, I've attached a shot of it as well. Thanks.
-Derin
look at the ?h.inflated.nofix to see what is causing the defect, and correct the wm.mgz manually to remove it. Jenni: can you point Derin at the appropriate wiki page?
thanks, Bruce
On Fri, 13 Apr 2007, Derin Cobia wrote:
The ?h.orig.nofix looks ok, meaning it follows the white-gray boundary appropriately. What should I try next?
-Derin
this is probably a topology fixing problem. Look at the ?h.orig.nofix and see how it is On Fri, 13 Apr 2007, Derin Cobia wrote:
Did you mean wm.mgz? It looks fine. The orig surface is not good either. Here's a pic.
-Derin
Hi Derin,
What does the orig surface look like? and the wm? Are those correct?
Jenni
On Fri, 13 Apr 2007, Derin Cobia wrote:
I have two subjects where the white surface does not follow the gray-white gradient (see attached pic for example). Is there any way to fix this? I'm assuming it has to do with the limitations of my scan too (it's FLASH data). I'm running 3.0.4, thanks.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
it looks like there is an (incorrect) connection in the wm.mgz from the temporal lobe across the insula. The data also looks really noisy - what is the acquisition? You'll need to erase some stuff form the wm.mgz I think.
On Fri, 13 Apr 2007, Derin Cobia wrote:
Here is a pic of the inflated.nofix, how do I know what to edit? I've checked the wm.mgz and it looks fine (at least I can't see any errors). Maybe I'm missing something, I've attached a shot of it as well. Thanks.
-Derin
look at the ?h.inflated.nofix to see what is causing the defect, and correct the wm.mgz manually to remove it. Jenni: can you point Derin at the appropriate wiki page?
thanks, Bruce
On Fri, 13 Apr 2007, Derin Cobia wrote:
The ?h.orig.nofix looks ok, meaning it follows the white-gray boundary appropriately. What should I try next?
-Derin
this is probably a topology fixing problem. Look at the ?h.orig.nofix and see how it is On Fri, 13 Apr 2007, Derin Cobia wrote:
Did you mean wm.mgz? It looks fine. The orig surface is not good either. Here's a pic.
-Derin
Hi Derin,
What does the orig surface look like? and the wm? Are those correct?
Jenni
On Fri, 13 Apr 2007, Derin Cobia wrote:
> I have two subjects where the white surface does not follow the > gray-white > gradient (see attached pic for example). Is there any way to fix > this? > I'm assuming it has to do with the limitations of my scan too (it's > FLASH > data). I'm running 3.0.4, thanks. > > -Derin > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
What should I erase? Sorry, I did mean to say I saw the surface errors overlaid on the volume, but couldn't discern any in the wm.mgz alone. It's 3D FLASH on a Vision 1.5T, TR/TE= 20/5.4 ms, flip=30 deg, 1 acquisition, 1x1x1 mm^3 voxels. Nothing fancy, maybe that's the problem...
-Derin
it looks like there is an (incorrect) connection in the wm.mgz from the temporal lobe across the insula. The data also looks really noisy - what is the acquisition? You'll need to erase some stuff form the wm.mgz I think.
On Fri, 13 Apr 2007, Derin Cobia wrote:
Here is a pic of the inflated.nofix, how do I know what to edit? I've checked the wm.mgz and it looks fine (at least I can't see any errors). Maybe I'm missing something, I've attached a shot of it as well. Thanks.
-Derin
look at the ?h.inflated.nofix to see what is causing the defect, and correct the wm.mgz manually to remove it. Jenni: can you point Derin at the appropriate wiki page?
thanks, Bruce
On Fri, 13 Apr 2007, Derin Cobia wrote:
The ?h.orig.nofix looks ok, meaning it follows the white-gray boundary appropriately. What should I try next?
-Derin
this is probably a topology fixing problem. Look at the ?h.orig.nofix and see how it is On Fri, 13 Apr 2007, Derin Cobia wrote:
Did you mean wm.mgz? It looks fine. The orig surface is not good either. Here's a pic.
-Derin
> Hi Derin, > > What does the orig surface look like? and the wm? Are those > correct? > > Jenni > > On Fri, 13 Apr 2007, Derin Cobia wrote: > >> I have two subjects where the white surface does not follow the >> gray-white >> gradient (see attached pic for example). Is there any way to fix >> this? >> I'm assuming it has to do with the limitations of my scan too >> (it's >> FLASH >> data). I'm running 3.0.4, thanks. >> >> -Derin >> >> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I see. 1x1x1 with standard coils is pretty noisy at 1.5T. That's why we used to use 1.3x1.3x1 instead, although now we do 1mm is at 3T with a 12 or 32 channel. Sorry, it's hard to describe what to fix since it depends on exactly what happened. You have to find what string of wm voxels in the wm.mgz are causing the connection and erase them. If you can't find it, you can upload and we'll take a look.
cheers, Bruce
p.s. your CNR will increase if you miniize the TE. I would think you can get it less than 5.4ms, but I don't remember what the Vision gradients are like
On Fri, 13 Apr 2007, Derin Cobia wrote:
What should I erase? Sorry, I did mean to say I saw the surface errors overlaid on the volume, but couldn't discern any in the wm.mgz alone. It's 3D FLASH on a Vision 1.5T, TR/TE= 20/5.4 ms, flip=30 deg, 1 acquisition, 1x1x1 mm^3 voxels. Nothing fancy, maybe that's the problem...
-Derin
it looks like there is an (incorrect) connection in the wm.mgz from the temporal lobe across the insula. The data also looks really noisy - what is the acquisition? You'll need to erase some stuff form the wm.mgz I think.
On Fri, 13 Apr 2007, Derin Cobia wrote:
Here is a pic of the inflated.nofix, how do I know what to edit? I've checked the wm.mgz and it looks fine (at least I can't see any errors). Maybe I'm missing something, I've attached a shot of it as well. Thanks.
-Derin
look at the ?h.inflated.nofix to see what is causing the defect, and correct the wm.mgz manually to remove it. Jenni: can you point Derin at the appropriate wiki page?
thanks, Bruce
On Fri, 13 Apr 2007, Derin Cobia wrote:
The ?h.orig.nofix looks ok, meaning it follows the white-gray boundary appropriately. What should I try next?
-Derin
this is probably a topology fixing problem. Look at the ?h.orig.nofix and see how it is On Fri, 13 Apr 2007, Derin Cobia wrote:
> Did you mean wm.mgz? It looks fine. The orig surface is not good > either. > Here's a pic. > > -Derin > > > >> Hi Derin, >> >> What does the orig surface look like? and the wm? Are those >> correct? >> >> Jenni >> >> On Fri, 13 Apr 2007, Derin Cobia wrote: >> >>> I have two subjects where the white surface does not follow the >>> gray-white >>> gradient (see attached pic for example). Is there any way to fix >>> this? >>> I'm assuming it has to do with the limitations of my scan too >>> (it's >>> FLASH >>> data). I'm running 3.0.4, thanks. >>> >>> -Derin >>> >>> >> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Derin,
As Bruce said it's tough to say where you should edit unless I can look at the whole thing. Can you tar this one subject and put it on the filedrop. I'll take a look and see if I can set you in the right direction to fix this one up!
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, April 13, 2007 4:56 PM To: Derin Cobia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bad white surface
I see. 1x1x1 with standard coils is pretty noisy at 1.5T. That's why we used to use 1.3x1.3x1 instead, although now we do 1mm is at 3T with a 12 or 32 channel. Sorry, it's hard to describe what to fix since it depends on exactly what happened. You have to find what string of wm voxels in the wm.mgz are causing the connection and erase them. If you can't find it, you can upload and we'll take a look.
cheers, Bruce
p.s. your CNR will increase if you miniize the TE. I would think you can get it less than 5.4ms, but I don't remember what the Vision gradients are like
On Fri, 13 Apr 2007, Derin Cobia wrote:
What should I erase? Sorry, I did mean to say I saw the surface errors overlaid on the volume, but couldn't discern any in the wm.mgz alone. It's 3D FLASH on a Vision 1.5T, TR/TE= 20/5.4 ms, flip=30 deg, 1 acquisition, 1x1x1 mm^3 voxels. Nothing fancy, maybe that's the problem...
-Derin
it looks like there is an (incorrect) connection in the wm.mgz from the temporal lobe across the insula. The data also looks really noisy - what is the acquisition? You'll need to erase some stuff form the wm.mgz I think.
On Fri, 13 Apr 2007, Derin Cobia wrote:
Here is a pic of the inflated.nofix, how do I know what to edit? I've checked the wm.mgz and it looks fine (at least I can't see any errors). Maybe I'm missing something, I've attached a shot of it as well. Thanks.
-Derin
look at the ?h.inflated.nofix to see what is causing the defect, and correct the wm.mgz manually to remove it. Jenni: can you point Derin at the appropriate wiki page?
thanks, Bruce
On Fri, 13 Apr 2007, Derin Cobia wrote:
The ?h.orig.nofix looks ok, meaning it follows the white-gray boundary appropriately. What should I try next?
-Derin
this is probably a topology fixing problem. Look at the ?h.orig.nofix and see how it is On Fri, 13 Apr 2007, Derin Cobia wrote:
> Did you mean wm.mgz? It looks fine. The orig surface is not good > either. > Here's a pic. > > -Derin > > > >> Hi Derin, >> >> What does the orig surface look like? and the wm? Are those >> correct? >> >> Jenni >> >> On Fri, 13 Apr 2007, Derin Cobia wrote: >> >>> I have two subjects where the white surface does not follow the >>> gray-white >>> gradient (see attached pic for example). Is there any way to fix >>> this? >>> I'm assuming it has to do with the limitations of my scan too >>> (it's >>> FLASH >>> data). I'm running 3.0.4, thanks. >>> >>> -Derin >>> >>> >> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Derin,
The tutorial pages showing which defects to look for and how to fix them start here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
this includes white matter edits:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
Nick
On Fri, 2007-04-13 at 15:31 -0500, Derin Cobia wrote:
Here is a pic of the inflated.nofix, how do I know what to edit? I've checked the wm.mgz and it looks fine (at least I can't see any errors). Maybe I'm missing something, I've attached a shot of it as well. Thanks.
-Derin
look at the ?h.inflated.nofix to see what is causing the defect, and correct the wm.mgz manually to remove it. Jenni: can you point Derin at the appropriate wiki page?
thanks, Bruce
On Fri, 13 Apr 2007, Derin Cobia wrote:
The ?h.orig.nofix looks ok, meaning it follows the white-gray boundary appropriately. What should I try next?
-Derin
this is probably a topology fixing problem. Look at the ?h.orig.nofix and see how it is On Fri, 13 Apr 2007, Derin Cobia wrote:
Did you mean wm.mgz? It looks fine. The orig surface is not good either. Here's a pic.
-Derin
Hi Derin,
What does the orig surface look like? and the wm? Are those correct?
Jenni
On Fri, 13 Apr 2007, Derin Cobia wrote:
> I have two subjects where the white surface does not follow the > gray-white > gradient (see attached pic for example). Is there any way to fix > this? > I'm assuming it has to do with the limitations of my scan too (it's > FLASH > data). I'm running 3.0.4, thanks. > > -Derin > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Nick. I am familiar with those pages, but none of those defects are apparent in this subject (e.g., no misclassifications, lesions, or failure to have the ventricles filled). The surface just appears to jump from one section to another over blank space (or over gm in the brainmask.mgz volume). Maybe I'll have to scrap this one. Thanks again.
-Derin
Derin,
The tutorial pages showing which defects to look for and how to fix them start here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
this includes white matter edits:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
Nick
On Fri, 2007-04-13 at 15:31 -0500, Derin Cobia wrote:
Here is a pic of the inflated.nofix, how do I know what to edit? I've checked the wm.mgz and it looks fine (at least I can't see any errors). Maybe I'm missing something, I've attached a shot of it as well. Thanks.
-Derin
look at the ?h.inflated.nofix to see what is causing the defect, and correct the wm.mgz manually to remove it. Jenni: can you point Derin
at
the appropriate wiki page?
thanks, Bruce
On Fri, 13 Apr 2007, Derin Cobia wrote:
The ?h.orig.nofix looks ok, meaning it follows the white-gray
boundary
appropriately. What should I try next?
-Derin
this is probably a topology fixing problem. Look at the
?h.orig.nofix
and see how it is On Fri, 13 Apr 2007, Derin Cobia wrote:
Did you mean wm.mgz? It looks fine. The orig surface is not good either. Here's a pic.
-Derin
> Hi Derin, > > What does the orig surface look like? and the wm? Are those > correct? > > Jenni > > On Fri, 13 Apr 2007, Derin Cobia wrote: > >> I have two subjects where the white surface does not follow the >> gray-white >> gradient (see attached pic for example). Is there any way to fix >> this? >> I'm assuming it has to do with the limitations of my scan too
(it's
>> FLASH >> data). I'm running 3.0.4, thanks. >> >> -Derin >> >> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Derin Cobia -
Jenni Pacheco -
Nick Schmansky