Hi Julia,
I usually remove the voxels from brainmaks.mgz for the pial edits but also
from wm.mgz. If you deselect the button of the pial surface in tkmedit, you
will see that the white matter surface is coincident with the pial, so you
also need to correct that volume. With wm.mgz as auxi
Dear FreeSurfers,
To get a better view on the pial surface of the Heschl' Gyri I used the
command mri_vol2surf after having created the suitable volume with
label2vol. My goal is to get the pial surface of this single label.
My Command is: *mri_vol2surf --src pf_lh_vol.mgz --hemi lh --surf pial
Hi Holger
the file you are outputing isn't a surface, it's a surface overlay. Try
loading the inflated surface then load the .w file with tksurfer
load overlay
cheers
Bruce
On Thu, 16 Feb 2012, Klein, Holger wrote:
>
> Dear FreeSurfers,
>
> To get a better view on the pial surface of the H
if they are coincident then it is accurately detected as non-cortical and
won't affect any thickness/volume corrections, so fixing it is really
just aesthetic.
cheer
Bruce
On Thu, 16 Feb 2012, _andre...@sapo.pt wrote:
Hi Julia,
I usually remove the voxels from brainmaks.mgz for the pial ed
Ah ok! :)
So it won't affect any stats?
Anyway, not correcting this will make the inflated surface to have a
prominence, right? In that case it will only look better for results'
displaying.
Andreia
Citando Bruce Fischl :
> if they are coincident then it is accurately detected as
> non-
try using label2patch and loading the resulting patch in tksurfer from the
interface after loading another surface on the command line
On Thu, 16 Feb 2012, Klein, Holger wrote:
Dear Bruce,
Thanks for your help. I did what you advised me to do in freeview. It works,
but the problem is that an
yes, exactly. it will have a tiny effect on total surface area, but that
includes noncortical regions anyway
On Thu, 16 Feb 2012, _andre...@sapo.pt
wrote:
Ah ok! :)
So it won't affect any stats?
Anyway, not correcting this will make the inflated surface to have a
prominence, right? In that
Since it is such a straightforward correction, I've been making it
because I thought that it would have some effect (though tiny).
Thanks!
Andreia
Citando Bruce Fischl :
> yes, exactly. it will have a tiny effect on total surface area, but
> that includes noncortical regions anyway
> On Thu,
Dear Bruce,
The patch (only 16 kb ???) was successfully created via label2patch. But
loading it in tksurfer after having loaded a surface the following error
occured:
% surface not flattened - disabling 2d code...
What am I doing wrong? Isn't there a way via the command mri_vol2surf? What
output
hi all
excuse me for this "simple question" but i am quiet new to freesurfer (i
use it just for the parcellations). i've some functionnal maps (i've used spm
for that) that i want to use as an overlay on the pial surface of the subject.
is there an easy way to do it
thanks
_
what is your command line? That isn't an error - it just detects that the
patch isn't flattened and so will show it in the original space. Does it
show up?
On Thu, 16 Feb 2012, Klein, Holger
wrote:
Dear Bruce,
The patch (only 16 kb ???) was successfully created via label2patch. But
loading
yes, use bbregister to register your functional maps, then mri_vol2surf
to sample them onto the surface and load them in tksurfer.
cheers
Bruce
On Thu, 16 Feb
2012, LAOUCHEDI MAKHLOUF wrote:
hi all
excuse me for this "simple question" but i am quiet new to freesurfer
(i use it just fo
Dear Bruce,
Command for the patch: label2patch wh lh lh.G_temp_sup-G_T_trans.label PAC
Then I loaded tksurfer with: tksurfer wh lh inflated (pial)
Then I loaded the patch in tksufer with the GUI, but it doesn't show up,
respectively everything vanished to black.
Thanks, Holger
2012/2/16 Bru
Hi Hemant, sorry for the delay in getting back to you. I'm not sure what
could be causing the problem. FreeSurfer definitely reads the direction
cosines from the dicom. If you upload the dicom volume to our file drop,
I'll take a look. filedrop url is at the end of this email.
doug
Hemant Bokil
is it really entirely gone or is there a little piece of the surface
there where Heschl's is?
On Thu, 16 Feb 2012, Klein, Holger wrote:
Dear Bruce,
Command for the patch: label2patch wh lh lh.G_temp_sup-G_T_trans.label PAC
Then I loaded tksurfer with: tksurfer wh lh inflated (pial)
Then I lo
Sorry, this is a bug. The work-around requires that you:
1. Re-run mkbrainmask-sess without the "-nero 1"
2. cd into the mask directory in each run and run mri_binarize, like this
cd /autofs/space/moe_002/users/mayucel/PROJECT/Subject20/bold/001/masks
mri_binarize --i brain.nii.gz --o brain.e3.nii.
Is this individual data or group? If individual, are you planning to do
a surface-based group analysis? If so, make sure that the fMRI data are
in the native functional space.
doug
Bruce Fischl wrote:
> yes, use bbregister to register your functional maps, then
> mri_vol2surf to sample them ont
This is because the mac executables in freesurfer where compiled on the
leopard verion of OSX. There's an update here compiled on snow leopard
that should solve this error:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
On Thu, 16 Feb 2012, Tetiana Dadakova wrote:
> Thanks for the note. I
Dear Bruce,
I tried it again, and it worked out well. Mea culpa - I'm deeply sorry.
Is there a chance to load the patch in freeview?
Thanks a lot, Holger
2012/2/16 Klein, Holger
> Dear Bruce,
>
> Command for the patch: label2patch wh lh lh.G_temp_sup-G_T_trans.label PAC
>
> Then I loaded tk
no worries. Not sure about freeview. Ruopeng?
On Thu, 16 Feb 2012, Klein, Holger wrote:
Dear Bruce,
I tried it again, and it worked out well. Mea culpa - I'm deeply sorry.
Is there a chance to load the patch in freeview?
Thanks a lot, Holger
2012/2/16 Klein, Holger
Dear Bruce,
Co
Dear all,
I completed my DTI group analysis at subcortical level on the CVS space and
found clusters that survived by multiple comparisons. The results shows that FA
is decreasing in patients vs. controls.
I used then the same subject to do a structural group analysis to compare the
cortica
Dear Doug,
Is possible to get more clusters if I correct by multiple comparisons so I run:
mri_glmfit-sim \
--glmdir lh.GroupAnalysis_Thickness_15.glmdir \
--cache 2 pos \
--cwpvalthresh .999 \
--overwrite
than the number of clusters in the sig.mgh so the uncorrected results?
cwpvalthresh .999
Hi everyone,
Previous versions of FreeSurfer had a whole brain measure in the aseg.stats
file called BrainSegVolNotVent. The newest version no longer has this. I am
wondering where I can now find a measure of whole brain volume?
Thanks,
Dana
--
Dana W. Moore, Ph.D.
Instructor of Neuropsyc
It might be SupraTentorial depending on what you are looking for. They are
all explained on this wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
On Thu, 16 Feb 2012, Dana W. Moore wrote:
Hi everyone,
Previous versions of FreeSurfer had a whole brain measure in the aseg.stats
Thanks, Allison. This actually leads me to another question though. It says
in the wiki that SupraTentorial
includes Cortex + CorticalWhiteMatter + SubCortGray. I notice that subcortical
white matter is not mentioned. Does this mean the corpus callosum and internal
capusle is left out? Als
You're correct that it doesn't include cerebellum. I think it includes
corpus callosum and internal capsule but I defer to Doug who would know
for sure.
Allison
On Thu, 16 Feb 2012, Dana W. Moore wrote:
Thanks, Allison. This actually leads me to another question though. It
says in the wiki
I think I just found the answer to my question on the wiki:
More specifically, the CorticalWhiteMatter measurement is calculated by
determining which voxels are within the WM surface.
So the term "cortical" does not mean that deep structures are left out, it is
referring to how the measur
I think I just found the answer to my question on the wiki:
More specifically, the CorticalWhiteMatter measurement is calculated by
determining which voxels are within the WM surface.
So the term "cortical" does not mean that deep structures are left out, it is
referring to how the measur
I think I just found the answer to my question on the wiki:
More specifically, the CorticalWhiteMatter measurement is calculated by
determining which voxels are within the WM surface.
So the term "cortical" does not mean that deep structures are left out, it is
referring to how the measur
Hi there,
I was wondering if it would be possible to obtain a copy of the
freesurferstats2table script that is posted on the Wiki. When I try to
access it it requests a user name and password (I tried my mailing
list username and psswd, but didn't work).
Greatly appreciate it,
Fidel
___
That's all the clusters regardless of the cluster-wise p-value.
doug
Antonella Kis wrote:
> Dear Doug,
>
> Is possible to get more clusters if I correct by multiple comparisons
> so I run:
>
> mri_glmfit-sim \
> --glmdir lh.GroupAnalysis_Thickness_15.glmdir \
> --cache 2 pos \
> --cwpvalthresh .9
Hi Katie, the color wheel became difficult to support (and I think it is
inferior for viewing for various reasons). There is an alternative
called rtview. It is not in the distribution, but you can get it from
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview
Look at the --he
Without the color wheel, how are you supposed to see the different
meridians so that you can draw the boundaries for visual areas? I know
that field sign can do that in occipital if you have polar and eccen, but
it doesn't work well with parietal retinotopy or if you don't have eccen
data (which s
rtview will give you the colorwheel, see if that works for you
doug
Katie Bettencourt wrote:
> Without the color wheel, how are you supposed to see the different
> meridians so that you can draw the boundaries for visual areas? I
> know that field sign can do that in occipital if you have polar
Hello Freesurfer Mailing list,
I would like to know how to do the item mentioned in the subject>
Ideally not just write out the brain and aseg regions into isotropic voxels
in standard space, but also accomplish converting back to the
*original*resolution, would I have to specify an inverse transf
It does not look too bad to me. That is a significance map and it is
covering most of the occipital region. If you want to see the angle,
add -angle to your tksurfer-sess command.
doug
Daniel Cole wrote:
> I was mistaken, I only have *Polar* (Rotating wedge) not Eccentricity
> stimuli.
> Aft
Following up on this topic, is it possible to display functional maps on
a surface using Freeview? I have tried loading functional results as an
overlay without much success.
Kind regards,
Ivan Alvarez
On 16/02/2012 5:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
> Is this individual data o
Hi Antonella, I have created a registration file that will allow you to
get coordinates (this one assume that you performed your group analysis
in CVS space).
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg.cvs-to-fsaverage.dat
You can pass this to mris_volcluster. This will all
Hi Mario
from the mri dir:
mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.rawavg.mgz
should do the trick
cheers
Bruce
On Thu, 16
Feb 2012, Mario Ortega wrote:
> Hello Freesurfer Mailing list,
>
> I would like to know how to do the item mentioned in the subject>
> Ideally not just write
Dear freesurfer experts,
I am new to the freeview interface. How do I go about drawing a ROI on the
surfaces to create my own label? Both the voxel edit and ROI edit buttons are
not useful in this case.
Thank you in advance,
Tina Jeon
PhD Candidate
Advanced Imaging Research Center
UT Southweste
Hi Tina
this is easiest to do in tksurfer using the path drawing and custom fill
stuff
cheers
Bruce
On Thu, 16 Feb 2012, Tina Jeon wrote:
Dear freesurfer experts,
I am new to the freeview interface. How do I go about drawing a ROI on the
surfaces to create my own label? Both the voxel e
Sorry Doug this is a very basic question,
Should I put the rtview file in the freesurfer/fstast/bin directory or
somewhere else?
Thanks,
Maryam
On Thu, Feb 16, 2012 at 3:57 PM, Douglas N Greve
wrote:
> rtview will give you the colorwheel, see if that works for you
> doug
>
> Katie Bettencourt wr
freesurfer/fstast/bin is fine
Maryam Vaziri Pashkam wrote:
> Sorry Doug this is a very basic question,
> Should I put the rtview file in the freesurfer/fstast/bin directory or
> somewhere else?
>
> Thanks,
> Maryam
>
> On Thu, Feb 16, 2012 at 3:57 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harv
I have a follow-up question to my inquiry about whole brain volume. I have
some subjects completed with the older version, where I have BrainSegNotVent,
and some subjects completed with the new version. If I combine Supratentorial
with cerebellum to calculate whole brain, is this comparable to
Thanks, Bruce, Doug,
I will check how to do that.
Hemant
On Thu, Feb 16, 2012 at 11:21 AM, Douglas N Greve wrote:
> Hi Hemant, sorry for the delay in getting back to you. I'm not sure what
> could be causing the problem. FreeSurfer definitely reads the direction
> cosines from the dicom. If you
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