Thanks Doug,
When I overlay the results on L & R , I see different patterns on each
hemisphere. Is it something that I don't understand correctly?
BR
On Wed, Jul 10, 2013 at 5:45 PM, Douglas N Greve
wrote:
>
> On 07/10/2013 01:26 AM, amirhossein manzouri wrote:
> > Dear Doug and FS experts,
> >
Dear Bruce,
Finally the function work well.
Thank you for your help.
With best regards,
Fatma
2013/7/10 fatma zribi
> SURFACE INFO
> type: MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
> num vertices: 143704
> num faces : 287404
> num strips : 0
Dear Bruce,
Now i would like to use the function read_curv but I have a problem of
dimension .. curv is a vector of [143704,1] and vertices must be a matrix
of [3, 143704]
Would you mind help me and send an exemple of the use of the function wiht
the visualisation of the brain
[curv, fnum] = read
"mri_convert" just starts the man page for mri_convert.
I have been looking at other things and 3D view in FSL also crashes with a
2657 segmentation fault and a core dump. I think the problem is in the
virtualized 3D driver or something like that.
It seems that CentOS 6.4 does have some problems wi
Well the situation is as follows:
I had a polar angle session, of which I only have the labels and the
anatomical (not inflated) left due to a computer crash. In a different
session, I scanned both my main experiment and the eccentricity runs. Since
the eccentricity was in the same session as the
Ok thank you, I'll analyse them separately.
On Wed, Jul 10, 2013 at 6:33 PM, Douglas N Greve
wrote:
> Hi Bianca, it is not currently possible to this since it expects to have
> one cycle duration. You can analyze them separately, then create a field
> sign map outside of the regular stream.
>
>
Hi Anna and all Freesurfers,
I have sort of the same problem.
I know there is a flag called --noconform - but it doesnt seem to work on
my data with mri_nu_correct.mni . (does not recognize the flag )
I also tried the flag --cm which is supposed to only minimally conform -
but here I also got a
Dear FreeSurfer experts,
We have a question regarding the aparc output from the stats files, and
hopefulle you can help us.
We have 4 independent groups, of about 30 subjects per group, all scanned using
the same protocal on the same MRI scanner. We ran the cross sectional
FreeSurfer (5.2.0, Li
glad to hear it
Bruce
On Thu, 11 Jul 2013, fatma zribi wrote:
Dear Bruce,
Finally the function work well.
Thank you for your help.
With best regards,
Fatma
2013/7/10 fatma zribi
SURFACE INFO
type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO
Dear Bruce,
thank you very much
with best regards,
Fatma
2013/7/11 Bruce Fischl
> glad to hear it
> Bruce
>
> On Thu, 11 Jul 2013, fatma zribi wrote:
>
> Dear Bruce,
>>
>> Finally the function work well.
>> Thank you for your help.
>>
>> With best regards,
>>
>> Fatma
>>
>>
>> 2013/7/10 fatma
Hi Fatma
I don't understand your question. read_curv returns a scalar field over
the surface, not the surface itself, which is why it is nvertices x 1.
Use read_surf to read the surface topology in
cheers
Bruce
On Thu, 11 Jul 2013, fatma
zribi wrote:
Dear Bruce,
Now i would like to use th
Hi Cristian and Anna
just do it outside of FS. Convert the volume to minc with mri_convert and
run the MNI nu_correct on it directly
cheers
Bruce
On Thu, 11 Jul 2013, Cristian Paz wrote:
Hi Anna and all Freesurfers,
I have sort of the same problem.
I know there is a flag called --noconf
Hi Bruce,
I would like to use information about curv and sulc of a population and
plot the variance with plot_mesh (variance presented in one brain)
With best regards,
Fatma
2013/7/11 Bruce Fischl
> Hi Fatma
>
> I don't understand your question. read_curv returns a scalar field over
> the su
Hi Laura,
there were issues with 5.2 surface accuracy on some types of
acquisitions. You should rerun with 5.3 and see how the #s look.
cheers
Bruce
On Thu, 11
Jul 2013, L. Koenders wrote:
> Dear FreeSurfer experts,
>
> We have a question regarding the aparc output from the stats files, and
>
sorry, I still don't understand what the issue is. read_surf will give
you the surface geometry/topology, and read_curv will give you the scalar
fields to display over them. You can use mri_surf2surf to map them into a
common space (the fsaverage surface for example)
cheers
Bruce
On Thu, 11 Ju
-- Forwarded message --
From: fatma zribi
Date: 2013/7/11
Subject: Re: How to use read_curv?
To: Bruce Fischl
i have used read_surf to read ?h.white data. Now i would like to use curv
and sulc file of FreeSurfer and extract the variance compared two one
template of the average o
I don't know what you mean by overlaying the results on L & R. What is
your command line?
On 7/11/13 3:34 AM, amirhossein manzouri wrote:
Thanks Doug,
When I overlay the results on L & R , I see different patterns on each
hemisphere. Is it something that I don't understand correctly?
BR
Hi,
There seem to be a couple small bugs in recon-all (FS 5.3) regarding the interface of trying to do a "clean" run on top of processing that used an expert-options file:
1) The "-xopts-clean" flag doesn't work. It sets XOptsClean = 1, but doesn't set XOptsUse = 0. Consequently, because
As I mentioned before in my second question :
tksurfer fsaverage_sym rh inflated -aparc -overlay
lh.lh-rh.thickness.sm00.mgh
tksurfer fsaverage_sym lh inflated -aparc -overlay
lh.lh-rh.thickness.sm00.mgh
For Right and Left side!
BR
On Thu, Jul 11, 2013 at 4:38 PM, Douglas Greve wrote:
>
> I don'
Hi again,
Not sure if this is intentional or not, but I noticed that 'mris_curvature_stats' (FS 5.3) appends to Xh.curv.stats on successive invocation, rather than overwriting the existing file.
I noticed this in the context of comparing the stats results from a "-clean" run vs. a fresh run fr
Dear Freesurfers,
Do you think I should delete the extra dura-like structure in the attached
case?
Thank you very much!
Sincerely,
Ye
<>___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesur
yes
On 07/11/2013 11:22 AM, ye tian wrote:
> Dear Freesurfers,
>
> Do you think I should delete the extra dura-like structure in the
> attached case?
>
> Thank you very much!
>
> Sincerely,
> Ye
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.ha
the fix is to acquire a FLAIR or T2 image. What you are seing is the
tentorium of the cerebellum which is very difficult to distinguish from
cortical gray matter on a T1-weighted image. If you don't have either of
those datasets you probably will need to do manual editing Bruce
On Thu, 11 Jul
I'd like to make a circle of a pre-defined size on the freesurfer surface,
with RAS coordinates as the center of the circle. What would be the best
way to do this?
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.
Dear Bruce and Doug,
Thank you very much!
PS: I searched through my data folder and didn't find T2 images. There goes
all my afternoon!
Ye
On Thu, Jul 11, 2013 at 1:29 PM, Bruce Fischl wrote:
> the fix is to acquire a FLAIR or T2 image. What you are seing is the
> tentorium of the cerebellum
Dear Freesurfers,
I am trying to perform probabilistic tractography (FSL Probtrackx) between seed
and target VOIs made with Freesurfer's recon-all (T1) and dt_recon (DW)
pipelines.
I have the original T1 DICOMs, however, I only have the DW NIFTI image volumes.
I do not know how the DW DICOM
Dear freesurfers,
I have a subject for which I need to delete some dura in brainmask.mgz and
to add some control points. I wonder whether I can do it the following way
(to save time):
1. Manually delete extra dura in brainmask.mgz
2. recon-all autoreon1
3. Add control points
4. recon-all -autoreo
Dear all,
Is there a way in freesurfer to compute surface wise pearsons r (for
simple correlations) or adjusted r square / the vertex-wise explained
variance for a GLM?
Best, Martijn
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://ma
Hi Ye,
A couple control points should do the trick.
-Louis
On Thu, 11 Jul 2013, ye tian wrote:
> Dear Freesurfers,
> Is it true that a small piece of the brain is missing in the attached (all
> three
> views)? How do I correct this problem?
>
> Thank you very much!
>
> Sincerely,
> Ye
>
>
___
Hi Ye,
Is the dura in question affecting the surfaces? If so you can delete the
dura, add control points and then run command 4 below. You don't need to
rerun autorecon1.
-Louis
On Thu, 11 Jul 2013, ye tian wrote:
> Dear freesurfers,
> I have a subject for which I need to delete some dura in
Dear Louis,
Thank you very much!
Sincerely,
Ye
On Thu, Jul 11, 2013 at 4:12 PM, Louis Nicholas Vinke <
vi...@nmr.mgh.harvard.edu> wrote:
> Hi Ye,
> Is the dura in question affecting the surfaces? If so you can delete the
> dura, add control points and then run command 4 below. You don't need
Dear Louis,
Thank you very much!
Sincerely,
Ye
On Thu, Jul 11, 2013 at 4:09 PM, Louis Nicholas Vinke <
vi...@nmr.mgh.harvard.edu> wrote:
> Hi Ye,
> A couple control points should do the trick.
> -Louis
>
>
> On Thu, 11 Jul 2013, ye tian wrote:
>
> Dear Freesurfers,
>> Is it true that a small
I've attached a matlab script which should do it.
doug
On 07/11/2013 04:28 PM, Martijn Steenwijk wrote:
Dear all,
Is there a way in freesurfer to compute surface wise pearsons r (for
simple correlations) or adjusted r square / the vertex-wise explained
variance for a GLM?
Best, Martijn
_
you can run bbregister using the b=0 image as input. The final cost
function value should beless than .9, if it is more than that then it
probably means you have an LR flip.
doug
On 07/11/2013 03:52 PM, Barron, Daniel S wrote:
> Dear Freesurfers,
>
> I am trying to perform probabilistic tracto
p.s. if you upload the subject I'll take a look
On Thu, 11 Jul 2013, Giusy
Chinnici wrote:
Dear developers, I'm working with patients affected by cortical focal
dysplasia; images of these patients often show thickening in some areas of
the cortex.
In many cases the reconstruction of the pial
Hi Giusy
that's a tough one. Is there white matter in those gyri? It's hard to
tell from the 3 single-slice views. We have processed a bunch of
FCD-patient data without this type of issue
Bruce
On Thu, 11 Jul 2013, Giusy
Chinnici wrote:
Dear developers, I'm working with patients affected b
Hi Doug, thanks for the tip. I'm making a script to go in and grab the final
cost from each subject's registration and display it in a table. Just to make
sure, have I highlighted the correct Cost function below? This is from the log
file produced by bbregister --surf-cost
Thanks again, Daniel
Hi Doug, sorry to email again.
I just tested the bbregister --surf-cost method by registering a subject's
001.mgz (T1) with it's lowb.nii and lowbflipped.nii (intentionally L-R
flipped). They both gave me the same final cost function, the 0.2305
highlighted below.
I verified that the lowbflip
That is the right mincost (you can also find it in the .mincost file),
and that cost is very good. Maybe too good. Make sure to look at the
registration.
I don't know why things are not changing when you left right reverse.
Try doing the flip with mri_convert
mri_convert lowb.nii lowb.lrrev.
Is lh.lh-rh.thickness.sm00.mgh the left hemisphere overlay or the stack of
voxel-wise cortical thickness difference between left and right hemisphere
of each subject? I need to see the difference map of left and right (lh-rh)
overlaid on both hemispheres!
On Thu, Jul 11, 2013 at 6:01 PM, Douglas
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