ay to project CBF maps on fsaverage, then to smooth the data on
surfaces ? Is my process could be improved ?
Best regards,
--
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, F
oject first on the anatomical subject then on
fsaverage than what I've done ?
2) Smoothing with mris_fwhm is a good way with --mask option ?
Thank you for your precious advices !
Best regards,
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neur
--mask brain.fsaverage.lh.mgh*
Many thanks in advance !!
Best regards,
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
2015-03-02 21:13 GMT+01:00 Douglas N Greve :
>
> On 03/02/2015
sphere.reg*
*# Smooth*
*mris_fwhm --s fsaverage --hemi lh --smooth-only --i lh.fsaverage.cbf.mgh
--fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh --mask brain.fsaverage.lh.mgh*
Many thanks in advance !!
Best regards,
-
Matthieu Vanhoutte, MSc
Research Engineer
Thank you Douglas but I don't understand the solution you propose. Could
you please show me the command lines ?
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
2015-03-05 16:45 GMT+
Douglas N Greve :
>
> Just add --trgsubject fsaverage to the mri_vol2surf command line. Run
> mri_vol2surf with --help to get more info
>
> On 03/05/2015 10:52 AM, Matthieu Vanhoutte wrote:
> > Thank you Douglas but I don't understand the solution you propose.
>
--cortex
Best regards,
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
2015-03-05 17:24 GMT+01:00 Douglas N Greve :
> w format is the paint format output from your vol2surf command. We tend
&g
previously cached
(qcached) and use the "mri_preproc --cache-in" command ?
Best regards,
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
2015-03-05 18:02 GMT+01:00 Douglas N Greve :
intercept and the other
for slope, but concretely what significative results in both contrasts mean
?
Thank you in advance for helping !
Best regards,
-----
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, F
regards,
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu
these two steps ?
Best regards,
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard
Thank you Douglas.
Matthieu Vanhoutte, MSc
Research Engineer - Neuroradiology Department
Regional University Hospital, Lille, France
Le 16 mars 2015 18:17, "Douglas N Greve" a
écrit :
> you'll need to use .33
>
> On 03/16/2015 11:09 AM, Matthieu Vanhoutte
Thank you Douglas I will try this.
Matthieu Vanhoutte, MSc
Research Engineer - Neuroradiology Department
Regional University Hospital, Lille, France
Le 16 mars 2015 19:13, "Douglas N Greve" a
écrit :
>
> For visualizing the overlap, I would probably create a segmentation in
>
Dear experts,
I have some asl data on fsaverage surface and would like to compute them on
MNI305 volume. So I executed the commands below, but when merging left and
right hemispheres it seems that the *--fillribbon *option on
*MNI305.asl.nii.gz* output data didn't work for right hemisphere :
*m
d a bug. Try this version
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol
>
> On 03/26/2015 12:16 PM, Matthieu Vanhoutte wrote:
> > Dear experts,
> >
> > I have some asl data on fsaverage surface and would like to compute
> > them on MNI3
Hello Douglas,
I have downloaded a new license and it successfully runs !
Best regards,
Matthieu
2015-03-31 12:39 GMT+02:00 Matthieu Vanhoutte :
> Hello Douglas,
>
> I have download the new version of mri_surf2vol you supplied me, and have
> copied it in the FS5.3 /bin instal
Dear experts,
I had to make volumic statistical analysis for the need to use BPM toolbox.
So, I got in the output of this statistical analysis some volumic Tmaps.
As I did before some group analysis according to FStutorial, I would like
to apply the same method of Clusterwise Correction on my vol
rwise correction in the volume. How could I do ?
Best regards,
Matthieu
2015-04-13 16:27 GMT+02:00 Douglas Greve :
> If you did the analysis in the volume, then you have to do the
> clusterwise correction in the volume.
>
>
> On 4/13/15 6:05 AM, Matthieu Vanhoutte wrote:
>
> Dear e
the BPM toolbox (what's that?) not give you cluster correction? You
> can try using mri_volcluster with the --grf option, but you'll need to know
> the FWHM. Afterwards you can map the result to the surface
>
>
> On 4/13/15 10:46 AM, Matthieu Vanhoutte wrote:
>
> Hello Do
template
> space, then run the SPM T1 template through recon-all to get the surfaces
>
>
>
>
>
>
> On 04/13/2015 11:09 AM, Matthieu Vanhoutte wrote:
> > By the mean of SPM, the Biological Parmatring toolbox can do the FWE
> > correction and give me results on a glass
Dear FreeSurfer's experts,
For personnal need I use the BPM toolbox (Biological Parametric Mapping) to
compute GLM analysis. The outputs of this Toolbox gave me beta maps and
Tmaps.
However, precedently I used the whole FreeSurfer group analysis tutorial on
other datas, including the Clusterwise
ion? You could use mri_volcluster,
> but you'll need to know the FWHM of your BPM analysis
> doug
>
> On 4/14/15 12:17 PM, Matthieu Vanhoutte wrote:
>
> Dear FreeSurfer's experts,
>
> For personnal need I use the BPM toolbox (Biological Parametric Mapping)
> to compute
I guess I don't understand what you are asking for. If BPM outputs a
> cluster-corrected volume, then why can't you just map that to the surface
> and be done with it?
>
>
> On 4/14/15 6:48 PM, Matthieu Vanhoutte wrote:
>
> Hello Douglas,
>
> Indeed BPM does
e out of
> BPM, then that is a problem that I cannot help you with (talk to whoever
> programmed BPM).
>
> doug
>
>
> On 4/15/15 3:30 AM, Matthieu Vanhoutte wrote:
>
> Hello Douglas,
>
> Sorry if I haven't been clear. I'm trying to explain my need
Dear experts,
I have run GLM group analyses on another software than FreeSurfer for
personal needs. I have now beta coefficients and residual datas on
fsaverage space.
I'd like to use then the clusterwise correction for multiple comparisons
provided by FreeSurfer. But I need for that to know the
analysis. If it does not come out of
> BPM, then that is a problem that I cannot help you with (talk to whoever
> programmed BPM).
>
> doug
>
>
> On 4/15/15 3:30 AM, Matthieu Vanhoutte wrote:
>
> Hello Douglas,
>
> Sorry if I haven't been clear. I'm
t; in the t-value you want, not a -log10(p). Also, don't do the adjustment for
> 1-tailed test because then it will interpret the input as -log10(p).
>
> On 5/29/15 10:46 AM, Matthieu Vanhoutte wrote:
>
> Dear experts,
>
> I would like to use the clusterwise correction sp
(/Variables Age Gender) ?
/Many thanks in advance for helping !
Best regards,
Matthieu/
/
On 3/12/15 1:30 PM, Matthieu Vanhoutte wrote:
Hello,
I have run GLM group analyses with Freesurfer tools according DODS
model, with six classes ((Male,Female) ; (Control,Left,Right)) and
one age variable
Dear FreeSurfer's experts,
I would like to visualize on freeview two overlays on fsaverage cortical
surface.
I have used the code below found on the mailing list :
*mri_binarize --i sig1.mgh --min 0.1 --binval 1 --o sig1_th.mghmri_binarize
--i sig2.mgh --min 0.1 --binval 2 --o sig2_th.mgh*
I tried it but gave me a black surface.
Le 6 juin 2015 00:06, "Douglas N Greve" a
écrit :
> Try it with 0 0 0 instead of 128 128 128
>
> On 06/05/2015 07:44 AM, Matthieu Vanhoutte wrote:
> > Dear FreeSurfer's experts,
> >
> > I would like to visua
/FS_5.3/fsaverage/surf/lh.whiteWriting
annot to ./lh.CBF_CT.annot*
Best regards,
Matthieu
2015-06-06 0:15 GMT+02:00 Douglas N Greve :
> what is the terminal output for mris_seg2annot?
>
> On 06/05/2015 06:12 PM, Matthieu Vanhoutte wrote:
> >
> > I tried it but gave me a black
Dear Freesurfer's Experts,
Please find below an error occuring when I use mri_glmfit :
Design matrix --
1.000 0.000 0.000 0.000 0.000 0.000 9.804 0.000 0.000
0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000;
0.000 0.000 0.000 1.000 0
Hello experts,
Could anyone provide me an advice or answer to this problem ?
Thanks in advance !
Best regards,
Matthieu
Le 28 juil. 2015 14:12, "Matthieu Vanhoutte"
a écrit :
> Dear Freesurfer's Experts,
>
> Please find below an error occuring when I use mri_gl
Douglas,
Please fond attached the fsgd file.
Cheers,
Matthieu
Le 4 août 2015 21:45, "Douglas N Greve" a
écrit :
> can you send the fsgd file?
>
> On 08/04/2015 03:42 PM, Matthieu Vanhoutte wrote:
> >
> > Hello experts,
> >
> > Could anyone pro
u
> can't use that as a covariate if it does not have any variation
>
> On 08/04/2015 04:10 PM, Matthieu Vanhoutte wrote:
> >
> > Douglas,
> >
> > Please fond attached the fsgd file.
> >
> > Cheers,
> >
> > Matthieu
> >
> >
Hello Freesurfer's experts,
I used the group analysis clusterwise correction with glmfit-sim and I
found that "Annot" field in Cluster Summary Table don't always fit well
with the corresponding region on "?h.aparc.a2009s.annot" file.
How is determined precisely each localization of each cluster
Dear FS experts,
I have shown in mailing list and xhemi commands as explained here, a
beginning of a solution to my problem :
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
However, I didn't understand all the steps needed in may case. I have
patients with unilateralized problem on left or right
gt;
> On 8/19/15 1:25 PM, Matthieu Vanhoutte wrote:
> > Hello Freesurfer's experts,
> >
> > I used the group analysis clusterwise correction with glmfit-sim and I
> > found that "Annot" field in Cluster Summary Table don't always fit well
> >
Best regards,
Matthieu
Le 21 août 2015 19:49, "Douglas Greve" a écrit :
>
> Sorry, what is the problem? Is sounds like xhemi should be apprpriate for
> your application. fsaverage is not symmetric and will lead to biased
> results.
>
> On 8/20/15 9:27 AM, Matt
I upload you this day an exemple with number vertex with same title name.
Thanks in advance for helping !
Best regards,
Matthieu
Le 21 août 2015 23:57, "Douglas Greve" a écrit :
> Can you upload an example (with vertex numbers)?
>
> On 8/21/15 3:37 PM, Matthieu Vanhou
Dear Freesurfer experts,
It seems impossible to load ?h.aparc.annot annotation file on ?h.pial
surface of the fsaverage_sym subject. When I try under freeview, it crashes
and gives me this error :
*Did not find any volume geometry information in the surfacepBDid not fin
.
Do you have a comman line way to manage to load annotation file under
freeview ?
Matthieu
2015-08-28 16:42 GMT+02:00 Douglas Greve :
> what is your command line? Can you run it without the annotation?
>
>
> On 8/28/15 5:58 AM, Matthieu Vanhoutte wrote:
>
> Dear Freesurfer exp
ck out freeview -help. It lists this type of option
> cheers
> Bruce
>
> On Fri, 28 Aug 2015, Matthieu
> Vanhoutte wrote:
>
> > I launched freeview, then added manually lh.pial and rh.pial of
> > fsaverage_sym. A this point all is OK.
> >
> > Then it crashed
I can do it. Where could I send you these files ?
Best regards,
Matthieu
2015-08-28 17:12 GMT+02:00 Ruopeng Wang :
> Would it be possible to send us lh.pial and lh.aparc.annot that caused the
> crash?
>
> Best,
> Ruopeng
>
> On Aug 28, 2015, at 10:59 AM, Matthieu Vanhout
Dear experts,
I would like to know if it is possible to make a longitudinal study with
LME toolbox from volume FA maps registered in a common space ?
I don't have T1 images so the recon-all process couldn't be processed. But
if I put my 3D FA volume of dim = [nx,ny,nz] in a 1D nx*ny*nz voxels
for
thieu
2015-09-29 15:04 GMT+02:00 Martin Reuter :
> Hi Matthieu,
>
> if all your images are perfectly registered, you can do LME on a
> voxel-by-voxel basis, just as if you had hippocampal volume or any other
> ROI measure.
>
> Best, Martin
>
>
> On 09/29/2015 06:46 AM,
it or lme_mass_fit_vw functions in my mass
univariate case ? If yes, how do I have to format my 3D FA volume as input
of the LME toolbox ?
Best regards,
Matthieu
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, F
the y is a simple vector. I would mask the image
> before doing this and only pass the brain voxels (to increase speed and
> reduce comparisons).
>
> Best, Martin
>
>
> On 09/29/2015 10:43 AM, Matthieu Vanhoutte wrote:
>
> Hi Martin,
>
> I understand for the mul
Dear FS experts,
I tried to run the QA Tools on a subject with the following command:
*${QA_TOOLS}/recon_checker -s 207043_M0_2010-10-07 -outputFOF
${SUBJECTS_DIR}/FOF -gen-outputFOF -gen-asegLUT
${SUBJECTS_DIR}/AsegOutliers*
But I got all errors concerning the detection of Aseg outliers:
*Making
Dear FS experts,
Could you explained me how to interpret results from the QA tools. Please
find attached the recon_checker summary log.
1) How to know there is a problem according to results below:
*checking subcortical label: Left-Cerebral-Exterior, 0 +/-*
*checking subcortical label: Left-Cere
Dear experts,
I am in trouble with two ways of computing mean intensity with mri_segstats.
First I have used on .annot files with three different labels inside (SegId
1 to 3) :
*mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot --i
lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum*
which
Hello FS's experts,
Would anyone have an advice for my problem ?
Best regards,
Matthieu
2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte :
> Dear experts,
>
> I am in trouble with two ways of computing mean intensity with
> mri_segstats.
>
> First I have used on .annot fil
Dear Freesurfer’s experts,
I would like to use the longitudinal mixed-effects model for surface PET
analysis. Although I could find all the process to follow the longitudinal
analysis of cortical thickness, I couldn’t resolve the steps/commands to apply
successively to coregistered PET data on
> on everything should be identical to the thickness analysis.
>
> So this is really more a question how to get your PET data sampled onto the
> surface. If no one else replies, write that into the subject line and repost.
>
> Best, Martin
>
>
>> On Sep 17, 2016,
same steps than cortical
thickness from cross-sectional to -long subject directories ? If this is
the case, which commands should I use to mimic cortical thickness
longitudinal data ?
Many thanks in advance for helping !
Best regards,
Matthieu
2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte :
&
Dear Freesurfer's experts,
I would like to register PET image onto T1 anatomical. I used bbregister
with the following command and it failed :
*bbregister --s SUBJID --init-fsl --t2 --mov PET.nii.gz --reg
Pet2T1.register.dof6.dat --lta Pet2T1.register.dof6.lta --init-reg-out
Pet2T1.init.register.
ocess for PET. The idea is that you process the
> MRI in a longitudinal way, then sample the PET data onto the surface of
> the closest MRI time point. Then proceed in a way similar to the
> thickness analysis
>
>
> On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote:
> > Dea
Pet2T1.BS7.register.dof6.mri_coreg.lta --s 207118_M0_2014-01-29 --surfs *
*mri_coreg done*
Best regards,
Matthieu
2016-09-30 21:07 GMT+02:00 Douglas N Greve :
> Can you send the mri_coreg terminal output?
>
>
> On 09/29/2016 11:19 AM, Matthieu Vanhoutte wrote:
> > Dear Fr
Hi Douglas,
I have just sent it to you on Filedrop.
Best regards,
Matthieu
2016-10-03 17:45 GMT+02:00 Douglas Greve :
> Can you tar up the FS anat analysis and BS7_PET.lps.nii.gz and send it to
> me on our filedrop?
>
> On 10/3/16 6:55 AM, Matthieu Vanhoutte wrote:
>
> Hi D
Hi Douglas,
Dis you have time to take a look at ?
Best regards,
Matthieu
Le 3 oct. 2016 6:25 PM, "Matthieu Vanhoutte"
a écrit :
> Hi Douglas,
>
> I have just sent it to you on Filedrop.
>
> Best regards,
> Matthieu
>
> 2016-10-03 17:45 GMT+02:00 Douglas Greve
xel size error).
> But it is *much* better to get the voxel sizes right and use 6 dof
>
>
> On 10/06/2016 02:50 PM, Matthieu Vanhoutte wrote:
> >
> > Hi Douglas,
> >
> > Dis you have time to take a look at ?
> >
> > Best regards,
> > Mat
Dear Freesurfer's experts,
Could anyone please explain me the difference I got with command line in
below mail ?
Best regards,
Matthieu
2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte :
> Dear experts,
>
> I am in trouble with two ways of computing mean intensity with
> mri_segs
Thank you Douglas !
Le 10 nov. 2016 7:21 PM, "Douglas N Greve" a
écrit :
> You need to weight by the number of vertices
>
> n = [27805 2321 552];
> m = [8.8194 10.3661 10.3365];
> sum(n.*m)/sum(n)
>
> ans =
>
> 8.9637
>
>
> On 11/10/201
7.6819 1.4396 4.4862
10.9042 6.4180
As my inputs are all surface data could I consider that NVoxels is equal to
NVertices and Volume_mm3 is equal to SurfaceArea_mm2 ?
Best regards,
Matthieu
> Le 10 nov. 2016 à 23:18, Matthieu Vanhoutte a
> écrit :
>
> Thank
mri_segstats ?
Best regards,
Matthieu
Le 11 nov. 2016 9:21 PM, "Douglas N Greve" a
écrit :
> NVox is the number of vertices. The Volume_mm3 is not meaningful. Do you
> want area?
>
>
> On 11/11/2016 04:53 AM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> &g
gstats --i $SUBJECTS/fsaverage/surf/lh.white.avg.area.mgh --seg
lh.sign_clust.bin.mgh
--excludeid 0 --sum lh.bin.area.sum --accumulate
On 11/11/2016 04:48 PM, Matthieu Vanhoutte wrote:
>
> Dear Douglas,
>
> Yes I would like to in order to compute mean of some means. Maybe not
> if it i
Is it better to compute mean to weight by number of vertices or surface
area ?
Best,
Matthieu
Le 11 nov. 2016 11:33 PM, "Douglas N Greve" a
écrit :
> Vertices do not have equal areas and are not equally spaced
>
>
> On 11/11/2016 05:11 PM, Matthieu Vanhoutte wrote:
>
2016-09-30 23:05 GMT+02:00 Douglas N Greve :
> Yes
>
>
> On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote:
> >
> > Hi Douglas,
> >
> > Does the surface of the closest MRI time point mean the surface of the
> > -long subject time point directory rather t
to the PET first
> > registered onto native space ? In this case, how and where is this
> > transformation has been saved ?
> >
> > Best regards,
> > Matthieu
> >
> > 2016-09-30 23:05 GMT+02:00 Douglas N Greve > <mailto:gr...@nmr.mgh.harvard.edu>>:
> >
Thank you !
Best regards,
Matthieu
2016-11-14 17:48 GMT+01:00 Douglas N Greve :
> Rigid.
>
>
> On 11/14/2016 11:43 AM, Matthieu Vanhoutte wrote:
> > Still using rigid-body registration on --long subject directory ?
> >
> > Or is affine registration in this case
in the long
> mri/transforms directory and probably also in the base/mri/transforms dir.
>
> Best, Martin
>
> On Nov 14, 2016, at 5:49 PM, Matthieu Vanhoutte <
> matthieuvanhou...@gmail.com> wrote:
>
> Thank you !
>
> Best regards,
> Matthieu
>
>
Dear Freesurfer’s experts,
I would have some questions regarding the LME model to be used in longitudinal
stream:
1) Which are the ratio limits or % of missing timepoints accepted ? (according
time, I have less and less subjects time points)
2) Is it possible to include patients that would mis
the model
(three time points / subject ; if existing 6 time points for any subject ?)
Best regards,
Matthieu
>
> Best, Martin
>
>> On Nov 21, 2016, at 7:07 PM, Matthieu Vanhoutte > <mailto:matthieuvanhou...@gmail.com>> wrote:
>>
>> Dear Freesurfer’s expe
Hi Martin,
Please see inline below:
> Le 22 nov. 2016 à 17:04, Martin Reuter a écrit :
>
> Hi Matthieu,
> (also inline)
>
>> On Nov 21, 2016, at 10:28 PM, Matthieu Vanhoutte
>> mailto:matthieuvanhou...@gmail.com>> wrote:
>>
>> Hi Martin,
>&g
Dear FS's experts,
Could you answer me about questions from below inline precedent mail ?
Best regards,
Matthieu
2016-11-22 21:31 GMT+01:00 Matthieu Vanhoutte :
> Hi Martin,
>
> Please see inline below:
>
> Le 22 nov. 2016 à 17:04, Martin Reuter a
> écrit :
>
>
Hello experts,
I am running the first pre-processing
step in Tracula on FS 5.1 and come across the error:
*set: Variable name must begin with a
letter*
I have attached my dmrirc file. Did I make a mistake in this file?
Best regards,
Matthieu
dmrirc.tutorial
Description: Binary data
rformance and
> speed.
>
> a.y
>
>
> On Wed, 11 Dec 2013, Matthieu Vanhoutte wrote:
>
> Hello experts,
>>
>> I am running the first pre-processing
>> step in Tracula on FS 5.1 and come across the error:
>>
>> set: Variable name must begin with
#x27;s causing the
> error.
>
>
> a.y
>
> On Wed, 11 Dec 2013, Matthieu Vanhoutte wrote:
>
> Hi Anastasia,
>> I have taken this original file in "FSDIR5.1/bin/dmrirc.example" and
>> modify
>> into "dmrirc.tutorial", so this is meant for
ead volume
/home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri/data_slice_*
*An exception has been thrown*
*Failed to read volume
/home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri/data_slice_Trace:
read_volume4DROI.*
Thanks for helping !
Matthieu
2013/12/12 Matthieu Vanhoutte
> Hello exp
Hello Martin,
Could you please find any time to answer me ?
Many thanks !
Best regards,
Matthieu
Le 30 sept. 2015 13:57, "Matthieu Vanhoutte"
a écrit :
> Hi Martin,
>
> Thank you for helping !
>
> 1) What should I use for the parameter estimation: "mass univaria
Dear experts,
Could anyone please help me ? My group has small size (7 subjects) with non
equally spaced different timepoints (from 2 up to 4).
Best regards,
Matthieu
Le 30 sept. 2015 13:57, "Matthieu Vanhoutte"
a écrit :
> Hi Martin,
>
> Thank you for helping !
>
>
affect your
> results a lot (they severely violate the assumption of gaussian noise) and
> can produce spurious effects.
>
> Best, Martin
>
>
>
> On 10/11/2015 04:31 PM, Matthieu Vanhoutte wrote:
>
> Dear experts,
>
> Could anyone please help me ? My group
Dear FreeSurfer experts,
My question is in the title. I'm working on Alzheimer case where most of
the cases have large ventricles. Is it better in general use to apply
-bigventricles option on all subjects (for homogeneous calculus or
something like that...) or to distinct subtle cases of patients
sults. We have found that most early AD cases work fine
> without needing special flags. It's more for late stage AD or hydrocephalus
> and such.
>
> cheers
> Bruce
>
>
>
> On Thu, 3 Dec 2015, Matthieu
> Vanhoutte wrote:
>
> > Dear FreeSurfer experts,
>
Dear experts,
I am confronted with some problem in the "recon-all" of a few subjects
concerning Talairach space, but don't know how to manage these.
Please find below the recon-all log with errors :
#
#@# Talairach Failure Detection Fri Dec 4 15:29:38
Dear FS experts,
I got no answer to my question. Could anyone explain me what is the problem
and how to solve it ?
Best regards,
Matthieu
2015-12-04 16:11 GMT+01:00 Matthieu Vanhoutte :
> Dear experts,
>
> I am confronted with some problem in the "recon-all" of a few su
Hi Bruce,
I got no answer to my questions below with files provided thanks to
FileDrop.
Could you tell me if you received these questions and associated files ?
Thanks in advance !
Best regards,
Matthieu
2015-12-04 15:17 GMT+01:00 Matthieu Vanhoutte :
> Hi Bruce,
>
> Exactly I w
t; that your input volume has the correct direction cosines (that is, that
> what freeview thinks is anterior is actually anterior, etc...)
> cheers
> Bruce
>
>
>
> On Tue, 8 Dec 2015, Matthieu Vanhoutte wrote:
>
> Dear FS experts,
>>
>> I got no answer to
rated an empty
> norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang.
>
> cheers
> Bruce
>
> On Wed, 9 Dec 2015,
> Matthieu Vanhoutte wrote:
>
> > Dear FS epxerts,
> >
> > I have launched a recon-all process on a subject. Unfortunately, I tried
> tw
norm warped? Actaully, it shouldn't be warped, although it might be
> truncated if the skull stripping failed.
>
>
> cheers
> Bruce
> On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote:
>
> Hi Bruce,
>>
>> Indeed norm.mgz isn't empty but doesn't look well
Dear FS experts,
1) First Is it possible to use the partial volume correction provided in
the v6 beta version of FreeSurfer despite the fact that recon-all have been
done for all subjects with the v5.3 ?
2) Does this method supply an intensity normalisation for PET images ?
Best regards,
Matthie
Hi Bruce,
Do you have an idea of how to solve this problem of skull stripping (below)
?
Best regards,
Matthieu
2015-12-09 16:25 GMT+01:00 Matthieu Vanhoutte :
> Hi Bruce,
>
> In fact T1.mgz is ok, but the skull stripping failed and seemed to have
> taken only the jawbone and the ne
Hi Bruce,
Do you have an idea of what to do concerning this problem (below) ? I have
re-run with -notal-check and it worked not for all cases
Best regards,
Matthieu
2015-12-09 15:15 GMT+01:00 Matthieu Vanhoutte :
> Hi Bruce,
>
> I tried to follow the tutorial :
> http://freesurfe
>
> On Fri, 11 Dec 2015, Matthieu Vanhoutte wrote:
>
> Hi Bruce,
>>
>> Do you have an idea of what to do concerning this problem (below) ? I have
>> re-run with -notal-check and it worked not for all cases
>>
>> Best regards,
>> Matthieu
>>
>> 2015
Dear experts,
Could anyone answer to my questions below ?
Thanks !
Best regards,
Matthieu
2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte :
> Dear FS experts,
>
> 1) First Is it possible to use the partial volume correction provided in
> the v6 beta version of FreeSurfer despite t
Dear FS's experts,
I have tried the recon-all process on one subject with both FS v5.3 and
v6_beta.
Although subcortical structures seems to be better segmented in v6_beta, I
find that v6_beta over-segmented some other structures as cerebellum,
hippocampus, ...
I will attached in the FileDrop my
Dear Douglas,
Please see below :
2015-12-15 18:37 GMT+01:00 Douglas N Greve :
>
>
> On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
> > Dear experts,
> >
> > Could anyone answer to my questions below ?
> >
> > Thanks !
> >
> > Best regar
can
> at least replicate the software version you are using
>
>
> cheers
> Bruce
>
> On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:
>
> Hi Bruce,
>>
>> Is it better to overestimate than underestimate ? Please find joined this
>> two saggital images (FS v5
se that which I think will
> > outperform whatever beta you have and 5.3. If you can't wait you are
> > probably better off using 5.3 (although I think the v6 you have is
> > more accurate) so that people can at least replicate the software
> > version you are using
>
the new segmentation that include pons and a few other things
>
> On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > Please see below :
> >
> > 2015-12-15 18:37 GMT+01:00 Douglas N Greve > <mailto:gr...@nmr.mgh.harvard.edu>>:
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