Hi all,
Now I got some results by freesurfer, finally I selected two vertexs which the
coordinate values were(Talx=-40.5, Taly= -14.5,Talz=-12.7 and Tal x=55.1, Tal
y=-23.9, Tal z=-1.8 ), the corresponding regions reported by freesurfer were
left superiortemporal and right superiortemporal. In
Hi Doug,
Thank you for the answers.
2013/4/26 Douglas N Greve gr...@nmr.mgh.harvard.edu
Hi Fang,
On 04/26/2013 12:35 PM, Fang CAO wrote:
Hi, I have some question on mri_segstats
1) --seg-erode Nerodes
Is it the size of the window for erosion?
I'm not sure what you mean. Nerodes is
Hi Claudia
it really depends on the individual case and what's causing the
exclusion. Does the wm.mgz look accurate? If so, you may have a
topological defect that is being fixed incorrectly. Usually we focus on
fixing the white boundary and that will also correct the pial. You can
set the
Hi Fred
we don't have much experience with this. Which synthesis are you using? You
might need to use a different one for the talairaching to more closely
match the atlas (maybe a TR=20,TE=2.5,flip=20-30 one)
On Mon, 29 Apr 2013, Fred Dick wrote:
Dear all
I'm having difficulties getting
Dear all
I'm having difficulties getting correct Talairach.lta's from synthetic flash
volumes (Bruce, you are probably sorry you ever told me about this!).
Basically the brain is over-scaled (bigger than it should be), which I think is
happening because the contrast is so good (gm much darker
Hi Bruce,
I think wm.mgz it's accurate enough, but what you mean?
I'm trying to upload data, but I've problems with your server.
Cheers,
Claudia
2013/4/29 Claudia Dacquino claudia.dacqu...@gmail.com
Hi Bruce,
I think wm.mgz it's accurate enough, but what you mean?
I'm trying to upload data,
Hi Bruce
I'm using TR=20, flip=30, TE=5 - but possibly irrelevant as also have the -w
flag on.
I originally thought this was from a bad brainmask, but then generated a good
one and same thing happening.
On 29 Apr 2013, at 14:27, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Fred
is the intensity at those voxels 110 after you have processed with
autorecon2-cp?
On Mon, 29 Apr 2013, Claudia Dacquino wrote:
The problem is that after editng manually WM by adding control points, I
still have some WM and GM areas not included in either the pial or WM
boundaries, but I can
yes, the -w will create an optimal weighting to maximize gray/white
contrast. The image it generates won't in general be physically
realizable in an real MR acquisition. Not surprising that the tal stuff
fails
On Mon, 29 Apr 2013, Fred Dick wrote:
Hi Bruce
I'm using TR=20, flip=30, TE=5 -
Aha, I shall quickly try with the non -w weighting and see what happens.
Thanks!
On 29 Apr 2013, at 15:05, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
yes, the -w will create an optimal weighting to maximize gray/white contrast.
The image it generates won't in general be physically
Hi Claudia,
Make sure you use the filedrop to upload your data
https://gate.nmr.mgh.harvard.edu/filedrop2/
Cheers, Shantanu
On Mon, April 29, 2013 9:53 am, Claudia Dacquino wrote:
Hi Bruce,
I think wm.mgz it's accurate enough, but what you mean?
I'm trying to upload data, but I've problems
Bruce,
no the intensity is lesser then 110 at those voxels, it's like 60-70.
Claudia
2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu
is the intensity at those voxels 110 after you have processed with
autorecon2-cp?
On Mon, 29 Apr 2013, Claudia Dacquino wrote:
The problem is that after
Dear all,
I've had some trouble feeding a flip angle map into mri_ms_fitparms. If I don't
provide it, the estimates look fine; with the FA map however, all brain voxels
in the resultant T1.mgz are set to 5. I've checked that all images are
registered, and the nominal values in the FA map
then it's not rerunning the -cp. And is it really wm if it's that dark?
On
Mon, 29 Apr 2013, Claudia Dacquino wrote:
Bruce,no the intensity is lesser then 110 at those voxels, it's like 60-70.
Claudia
2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu
is the intensity at those voxels
Dear FreeSurfers,
I want to convert cortical labels to volumetric masks, the mask created are
used to register with the normalized functional data and to define the roi, so
could I run the following command?
tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg
./register.dat/
Yes it's my doubt too, but how can I check this?
2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu
then it's not rerunning the -cp. And is it really wm if it's that dark?
On Mon, 29 Apr 2013, Claudia Dacquino wrote:
Bruce,no the intensity is lesser then 110 at those voxels, it's like
visually is the only way. Do you think it is white matter?
On Mon, 29 Apr
2013, Claudia Dacquino wrote:
Yes it's my doubt too, but how can I check this?
2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu
then it's not rerunning the -cp. And is it really wm if it's
that dark?
Actually it could not be WM, but I'm quite sure that there is grey matter
excluded by pial bounaries as well, how can I add that?
2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu
visually is the only way. Do you think it is white matter?
On Mon, 29 Apr 2013, Claudia Dacquino wrote:
Yes
But in brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white
-segmentation aseg.mgz it's labeled as white matter, could it be possible?
2013/4/29 Claudia Dacquino claudia.dacqu...@gmail.com
Actually it could not be WM, but I'm quite sure that there is grey matter
excluded by pial bounaries
Hi Claudia
now I'm confused. Did you put control points in those voxels? You
definitely, definitely must avoid putting them in voxels that contain
anything other than WM. The pial surface will usually be incorrect if the
white surface is incorrect, so the first thing to do is make sure it is
I'm sorry Bruce I'm confusing you.
The fact is that those areas are labelled as WM, so I thought those were
white matter, but looking with more attention at wm.mgz I did realize that
they could me no WM, as you seggested me, because they are too dark.
I'm new and I'm learning by trial and error.
Hi Claudia
if you upload your whole subject and send us some example voxel coords of
where you are looking we will take a look
Bruce
On Mon, 29 Apr 2013, Claudia Dacquino wrote:
I'm sorry Bruce I'm confusing you.The fact is that those areas are labelled
as WM, so I thought those were white
I'm uploading my subjdir on FTP server.
Thanks a lot.
Claudia
2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu
Hi Claudia
if you upload your whole subject and send us some example voxel coords of
where you are looking we will take a look
Bruce
On Mon, 29 Apr 2013, Claudia Dacquino
my subjdir is on FTP server.
thanks
claudia
2013/4/29 Claudia Dacquino claudia.dacqu...@gmail.com
I'm uploading my subjdir on FTP server.
Thanks a lot.
Claudia
2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu
Hi Claudia
if you upload your whole subject and send us some example voxel
Dear Freesurfers,
I am doing an ROI analysis (group comparison) of cortical thickness, and I
have some questions that I could use some help with. Many thanks in advance!
Tudor
1) I used aparcstats2table to extract CT values for structures from the
Destrieux atlas, but I cannot identify some
On 04/29/2013 04:13 PM, Tudor Popescu wrote:
Dear Freesurfers,
I am doing an ROI analysis (group comparison) of cortical thickness,
and I have some questions that I could use some help with. Many thanks
in advance!
Tudor
1) I used aparcstats2table to extract CT values for structures
Dear Doug,
I have uploaded the files to the filedrop (file name: Rotem_try.tar.gz)
and activated the link (I hope I did it OK).
I will appreciate your help as I'm stuck - can't see the problem...:)
Thanks for all your help !!
Rotem
--
Message: 9
Date: Thu, 11
Hi Rotem, I don't think I ever got an email notifying me. Did you use
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html ? Can you
upload it again, and make sure to put my email in the contact list.
doug
On 4/29/13 9:08 PM,
28 matches
Mail list logo
