Dear freesurfers:
I have 60 subjects manual segmentated on FreeSrufer 4.0.5, i want to know if i
run the recon2 or recon3 in the new FS 4.2.0, will have any problem?
the diferences between versions can cause any trouble with the analisis because
imcompability or something?
Regards Gabriel
Dear freesurfers: I have two questions:
1. I have FS v4.0.5 and i've downloaded the new mri_segstats to calculate the
eTIV,
this new calculation may cause any trouble in my group of manual segmented
subjects?
2. I have 60 subjects manual segmentated on FreeSrufer 4.0.5, i want to know
if i
dear Freesurfers
i'm exiting subcortical segmentations with: tkmedit sk024 aparc+aseg.mgz
-aparc+aseg
and load as aux volume the T1.mgz
then i recive the error message:
$ tkmedit sk024 aparc+aseg.mgz -aparc+aseg
Reading 1034 control points...
LoadSegmentationVolume main aparc+aseg.mgz
Hello
i'm trying to make a local Gyrification Index (lGI), i have image Processing
Toolbox instaled...
and i always recibe the next error message:
[r...@localhost ~]$ recon-all -s s001 -localGI
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0
Current Stamp: freesurfer-Li
hello everybody
i'n trying to convert a FS average to *.img, when i use mriconvert with one
subject i put the rawavg.mgz, but in the average subject this file does not
exist, so how can i make it? to convert the Fs average to an *.img
Regards
Gabriel
___
hello everybody
i'm trying to convert a FS average to *.img, when i use mriconvert with one
subject i put the rawavg.mgz, but in the average subject this file does not
exist, so how can i make it? to convert the Fs average to an *.img
Regards
Gabriel
Diferentes formas de estar
s
>
> Hi Gabriel,
>
> a couple of things:
>
> 1. You need to click in the interior of the region you want to fill.
> 2. You need to say "last clicked" not "all clicked".
> 3. You need to check the "up to paths" button.
>
>
I have created a ROI in an average subject, how can i transpose that ROI to
each subject?
i mean, use it like a mask to make some statistics on each subject
Regards
Gabriel
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hello
I want to use GM volume stats, i don't know whether it is or not, where?
I had understood that FS does not calculate the total GM volume, how can I make
it?
and can I calculate it for an individual ROI on a specific area?
Regards
Gabriel
___
hello
I want to use GM volume stats, i don't know whether it is or not, where?
I had understood that FS does not calculate the total GM volume, how can I make
it?
and can I calculate it for an individual ROI on a specific area?
Regards
Gabriel
hi
how can i compute the LGI and withe matter volume of my own ROIs?
regards
Gabriel
_
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Oficial de Messenger
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Dear freesurfers
im trying to obtain the wm volume for some ROIs created by myself, ando that
not fit with the parcellation of FS, i'm using mri_segstats but i can't make it
work, can any of you help me?
i always recibe a message that says:
"in Get MAC Adress (internal) : There was a c
Dear freesurfers
im trying to obtain the wm volume for some ROIs created by myself, ando that
not fit with the parcellation of FS, i'm using mri_segstats but i can't make it
work, can any of you help me?
i always recibe a message that says:
"in Get MAC Adress (internal) : There was a conf
hello
i'm running the LGI for all my subjects, and i have no problem with almost all,
but, i recibe an error message with one subject, and just with the right
hemisphere no problem when making Left hemisphere, does anybody knows what can
i do for correcting that error and to calculate the LGI?
Dear colleages,
I am trying to convert my dicom files to .mgz from Freesurfer (release 4.2) by
using the mri_convert command, but it provides me the following error:
[r...@localhost ~]$ cd /root/trabajo/freesurfer/subjects/mci_001/mri
[r...@localhost mri]$ mri_convert -it dicom -ot mgz orig
hello freesurfers
i have a doubt:
i have convert a subject brainmask from freesurfer to nii and then
i've convert a label that i create on freesurfer to *.nii using for
registration the brainmask.mgz, i've made that for working in SPM, but when i
open the ROI just not match with my subjec
hello Freesurfers
i have a doubt, i have read on the mail archive that you were working on get a
segmentation of the vermis, i have the V 4.2 of freesurfer wich hav not this
region,and i like to have that region, is there any way to get it? is it in
another version of FS? or does any one h
Hello
i have a question
i want to convert an MRI subject (brainmask.mgz in talairach apace) and a mask
of subcortical structure of the same subject, from freesurfer to MNI colins
space to work with SPM5, how can i make it?
and in fact i need to make this transformation to a set of subjec
Dear Fs experts
I'm trying to run a recon-all on one subject but FS gives me the following
error message:
#...@# Skull Stripping Mon Dec 21 17:25:55 CET 2009
Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006
x86_64 x86_64 x86_64 GNU/Linux
recon-all exite
Dear FreeSurfers
I run the autorecon1 using the flag -no-wsgcaatlas
for skullstripping, I'm using
freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0, you may find attached the
recon-all_status log
for any information you may need
Then I was trying to run the autorecon2: recon-all -subjid -auto
Dear FreeSurfers
I run an autorecon1 using the flag -no-wsgcaatlas
for skullstripping, I'm using
freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0, you may find attached the
recon-all_status log
for any information you may need
Then I was trying to run the autorecon2: recon-all -subjid -autor
Re: [Freesurfer] autorecon2 error
> Date: Mon, 31 May 2010 03:25:59 -0400
>
> Yes, looks like the one I fixed. Nick can point you to a download for the
> fixed files.
>
> Best, Martin
>
>
> - Original Message -----
> From: "Bruce Fischl"
> T
Thanks a lot Nick
Actually a I have already downloaded the file yesterday, but it gives another
error in the same step
when i re-run the recon-all autorecon2, says the version of the centos and FS,
later say "bus error" but continue the recon till it gets to the Subcortical
segmentation, where
Thank you
I redownloaded the mri_ca_label file and worked, it seems that gets corrupted
when donwloading, but now it appears a new error, from
the autorecon2, any idea???
#...@# Intensity Normalization2 Wed Jun 2 14:58:57 CEST 2010
/root/trabajo/freesurfer/subjects/T1_GE1/mri
mri_normal
g volume or anywhere else in
> the stream? The aseg should be 256^3 1imm iso, but for some reason it's
> not.
>
> Bruce
> On Wed, 2 Jun 2010, Gabriel Go.Es. wrote:
>
> >
> > Thank you
> > I redownloaded the mri_ca_label file and worked, it seems
Hello freesurfers
Does anyone knows wich is the method in which the FS makes an average of 2
images, in the autorecon1 step when doing the motion correction?. I mean how
can I explain it?
Thanx
Gabriel
__
Thank you Bruce for you answer, but i still have the doubt, is motion
correction from the FSL the method to average the images? or is another
method... I wrote motion correction cuz in the -help of recon-all says that
theyr made in the same step, but not to be the same process. but whatever is
OK, so the alignment is to perform a simple average? that way, the real goal of
the method is the registration before averaging, am I right?
in versions like 4.05 what was the alignmen method, was the flirt? Do you know
if Martin's robust registration is now implemented or will come in the next
a philips scanner, most of the time I think our tools work
> on philips data. Does this happen with all of your philips data or just
> this one series?
>
> doug
>
> Gabriel Go.Es. wrote:
> >
> >
> > Hello FreeSurfers
> >
> > I'm trying t
Mmm, now I just have a problem...
that dicom is from an structural MRI and still does not work... do you think
that can i solve it anyother way???
Gabriel
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harva
I'm going to run some analyses and have some doubts with respect to
the general approach that I should follow. We want to evaluate
differences in cortical thickness in three different groups. Shoud I
perform an ANOVA (to know if there is a group effect) followed by
pairwise comparisons (to
.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] groups stats doubts
>
> Yes, restrict the pair-wise comparisons to areas where the ANOVA is
> significant.
>
> doug
>
> Gabriel Go.Es. wrote:
> >
> >
> >
> > I'm going to run so
Thank you for you help Doug, of course I can explain it better
Let's suppose that resulting from the ANOVA I get three significative areas
(i.e. enthorhinal, parietal and frontal), do i have to make the pair-wise
comparisons on the three areas at once?, or can I perform a pair-wise for
enthorh
Hello
I'm wondering about how to create a label from a cluster wich is significant
from a group comparison, I mean, I have made group somparisons and i get some
significant clusters, and I want to susbtract that significative cluster and
transform it to a label file.
Best Regards
Gabr
Hello everybody
I'm wondering about how to perform an FDR correction using the glmfit on FS?,
I mean using command line if there is one;
And Could it be applied the same sentence to correct at cortex level and
clusters label, or need some special arguments on the command line for any of
them
Dear Freesurfers
I would like to perform regression analysis between volume
of subcortical structures (obtained from aseg) and psychometric scores removing
effects of age and gender. Is there any way to do it with FS?
Gabriel
__
Hello Freesurfers
I'm starting to work with DTI data and I have a couple of questions;
I have 2 identical DTI sequences for some subjects and I would like to work
with them, does anyone knows if it's better to concatenate them or to make an
average of them?
And I'm wondering when I make a
Hello Freesurfers
I'm starting to work with DTI data and I have a couple of questions;
I have 2 identical DTI sequences for some subjects and I would like to work
with them, does anyone knows if it's better to concatenate them or to make an
average of them?
And I'm wondering when I mak
, we're using a 3rd party dicom reader that is quite
> brittle, and I don't know a way around it. Can you convert to nifti
> using MRIcro and then use mri_convert to convert to mgz?
>
> doug
>
> Gabriel Go.Es. wrote:
> >
> > Dear FS users
Hello FreeSurfers
I'm running some permutation tests and this induce me to a question,
I'm using mri_glmfit-sim as recommended with the mc-z method, running 1000
permutations and seeding randomly, I have ran this with the same data two
different times, and the results are bit different, co
Hello Freesurfers,
I'm trying to mask the rawavg.mgz from some subjects with the brain.mgz after
doing some manual segmentation corrections by using mri_mask command, I have
donne it before and it always works but with this subject, the command line is
excacly the same so I have no idea what
Dear FreeSurfer experts,
I'm doing some group analyses and I'm a
little stocked with this:
I have Six Groups (2 Factors, one with
three levels and the other one with two levels), and one covariate. I don't
know the rule for setting the contrasts for an ANOVA and for the interaction
between t
Hello,
I'm making some manual segmentation changes in the brainmask.mgz and using
mri_vol2vol and mri_mask commands to apply these changes to the rawavg.mgz, the
output from the mri_vol2vol looks perfectly normal,and retains all changed made
by me, but when I use the mri_mask command over th
Hello everybody,Sorry for the insistance, but I need to solve this...
I'm making some manual segmentation changes in the brainmask.mgz and using
mri_vol2vol and mri_mask commands to apply these changes to the rawavg.mgz, the
output from the mri_vol2vol looks perfectly normal,and retains all c
n 3/9/11 7:33 PM, Gabriel Go.Es. wrote:
Thanks a lot,
just one another question Doug,
how to set an ANOVA for group differences??'
Gabriel
> Date: Wed, 9 Mar 2011 17:52:03 -0500
ay (i'm with the freesurfer group three days a week).
>
> i wonder if you can use the brain.mgz as your mask instead of
> brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but their
> actually not there (zeroed).
>
> n.
>
> On Thu, 2011-03-10 at 08:4
are
> 1).
>
> cheers
> Bruce
>
> On Mon, 14 Mar 2011,
> Gabriel Go.Es. wrote:
>
> >
> > Hello Nick
> >
> > I'm wondering if you're able to verify my data today,
> > I did try using brainmask.mgz to mask the rawavg.mgz, and didn't work
to be turned off are
> 1).
>
> cheers
> Bruce
>
> On Mon, 14 Mar 2011,
> Gabriel Go.Es. wrote:
>
> >
> > Hello Nick
> >
> > I'm wondering if you're able to verify my data today,
> > I did try using brainmask.mgz to mask the rawavg.
d brainmask2raw.mgz? It looks like you've checked
> brain2raw.mgz, but you're not using it for some reason. Make sure the
> background has values less than 2.
> doug
>
> Gabriel Go.Es. wrote:
> >
> > Hello Bruce and Nick, I've tryed these options
k problem
>
> For mri_vol2vol try using --interp nearest
> doug
>
> Gabriel Go.Es. wrote:
> >
> > Yes, I did check the brainmask2raw.mgz, Im using brain2raw.mgz and/or
> > brainmask2raw.gz to mask the rawavg.gz on the mri_mask. "mri_mask -T 2
> > -
Dear Freesurfer experts,
I'm wondering how to set a 2x2x2 anova
(diagnosis)x(gender)x(apoe)
g1MaleE4
g1MalenoE4
g1FemaleE4
g1FemalenoE4
g2MaleE4
g2MalenoE4
g2FemaleE4
g2FemalenoE4
option 1
[1 1 -1 -1 00 0 0]
[1 10 0
Re: [Freesurfer] 2x2x2 design
>
> Gabriel, what are options 1 and 2 supposed to represent?
> doug
>
> Gabriel Go.Es. wrote:
> >
> > Dear Freesurfer experts,
> > I'm wondering how to set a 2x2x2 anova
> >
> > (diagnosis)x(gender)x(apoe)
> >
&
Dear Doug,
I would like to be sure that I've understood the rules for the following
contrast in a 2x2x2 design with diagnosis (D1, D2), gender (Male, Female) and
handedness (Left, Right) as discrete factors.
D1MaleLeft
D1MaleRight
D1FemaleLeft
D1FemaleRight
D2MaleLeft
D2MaleRight
D2FemaleLeft
Dear Doug,
In the case of a 3x2 design the post hoc contrast for evaluating the
interaction effect would be as follows:
D1Male
D1Female
D2Male
D2Female
D3Male
D3Female
ANOVA to test the effect of diagnosis (D1, D2, D3) only for males
[ 1 0 -1 0 0 0]/2
[ 1 0 0 0 -1 0]/2
ANOVA to t
Dear Doug and FS experts,
I would like to be sure that I've understood the rules for the following
contrast in a 2x2x2 design with diagnosis (D1, D2), gender (Male, Female) and
handedness (Left, Right) as discrete factors.
D1MaleLeft
D1MaleRight
D1FemaleLeft
D1FemaleRight
D2MaleLeft
D2Male
Dear FS experts,
I would
like to be sure that I've understood the rules for the following contrast in a
2x2x2 design with diagnosis (D1, D2), gender (Male, Female) and handedness
(Left, Right) as discrete factors.
D1MaleLeft
D1MaleRight
D1FemaleLeft
D1FemaleRight
D2MaleLeft
D2MaleRig
Dear FreeSurfers
I'm wondering about the flattenning options of FS I've saw that the
"mris-flatten" command does the trick but, it asks for a patch, my questions
are: can I flat any cortical region? and, how do I create a patch to
mris_flatten?
Thanks in advanced,
Gabriel
the -complete
> option these days which minimizes the complete distance distortion matrix.
>
> cheers
> Bruce
>
>
> On Fri, 20 May 2011, Gabriel Go.Es. wrote:
>
> >
> > Dear FreeSurfers
> >
> > I'm wondering about the flattenning options of
Dear freesurfers
I want to convert an .mgh image to NIfTY format, but even when the conversion
using "mri_convert" seems to be ok, when I try to open the nii, an error
message appears "image doesn't appear to be a valid 2D or 3D image", there is
any other way to convert an mgh image to nii?
I
offers a "--reshape" option.
>
> doug
>
> Gabriel Go.Es. wrote:
> > Dear freesurfers
> >
> > I want to convert an .mgh image to NIfTY format, but even when the
> > conversion using "mri_convert" seems to be ok, when I try to open the
> >
what it reshapes it to. You can also try adding
> --reshape-factor 6.
> doug
>
> Gabriel Go.Es. wrote:
> > Dear Doug Im using :
> >
> > mri_surf2surf --sval $PATH/image.mgh --tval $PATH/image.nii --reshape
> > --s my_avg_subject --hemi lh
> >
> &
Dear FS experts,
I'm making some flattenings of one subject on FS and I'm wondering if it is
possible to see the ?h.curv or the ?h.sulc on grayscale and not in red-green
nor in the binary gray representations of tksurfer.
Regards,
Gabriel.
__
reesurfer] curvature of flattening
>
> I don't think so. You can display it in a heat scale by loading it as an
> overlay. If you save it as an rgb then strip out the color it might give
> you a decent gray scale.
> doug
>
> Gabriel Go.Es. wrote:
> > Dear FS
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