Dear freesurfer experts,
we want to do longitudinal analyses for two different time points in
only one group (We do not have a control group or different groups
within the intervention). So we did the longitudinal processing as
described in the tutorial
(http://ftp.nmr.mgh.harvard.edu/fswi
Hi Freesurfer Experts,
i have earlier worked in freesurfer previous versions. i was able to get
preliminary results.
i have trouble with freesurfer version V 5.3,
i have error in this step of the analysis
" minc_modify_header: posixio.c:210: px_pgin:Assertion `*posp ==
((off_t)(-1)) || *posp == lse
Hi Martin,
Unfortunately it is not a single subject, it happens to many.
If I run FS 5.3, I also have to rerun the cross-sectional exploration study,
otherwise differences between samples may be explained by different versions of
the software.
FYI, no editting was done, except for adjusting wate
Hi,
Thank you all for the wonderful project!
>From time to time while reading some of the wiki pages it has the feeling
of reading ancient Chinese.
https://surfer.nmr.mgh.harvard.edu/fswiki/gcareg
I'd be happy if anyone help me understand what GCA ? and ismri/no. are ?
Thanks in advance,
Dov
__
i meant mri/nu.mgz .
On Fri, Jun 28, 2013 at 2:21 PM, Dov Sadan wrote:
> Hi,
> Thank you all for the wonderful project!
>
> From time to time while reading some of the wiki pages it has the feeling
> of reading ancient Chinese.
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/gcareg
>
> I'd be hap
sorry, I didn't notice that. What were your min and max set to?
On Fri, 28
Jun 2013, Xiangzhen Kong wrote:
Thanks very much.
Another problem, do you know why the color bar is inversed in my first
email?
Might it be related to the right-left weird problem?
__
can you send us an example with a 500% increase?
On Fri, 28 Jun 2013,
Koolschijn, Cédric wrote:
Hi Martin,
Unfortunately it is not a single subject, it happens to many.
If I run FS 5.3, I also have to rerun the cross-sectional exploration study,
otherwise differences between samples may be ex
GCA = gaussian classifier array (a spatially varying set of Gaussians).
I don't see ismri/no. on the page, but maybe you mean the mri directory?
On
Fri, 28 Jun 2013, Dov Sadan wrote:
Hi,
Thank you all for the wonderful project!
From time to time while reading some of the wiki pages it has th
oh, it saves takes the volume nu.mgz in the directory
$SUBJECTS_DIR/$subject/mri as input
On Fri, 28 Jun 2013, Dov Sadan wrote:
i meant mri/nu.mgz .
On Fri, Jun 28, 2013 at 2:21 PM, Dov Sadan wrote:
Hi,
Thank you all for the wonderful project!
From time to time while reading some of t
Additional info on GCA:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GcaFormat
On Fri, 28 Jun 2013, Bruce Fischl wrote:
GCA = gaussian classifier array (a spatially varying set of Gaussians).
I don't see ismri/no. on the page, but maybe you mean the mri directory?
On Fri, 28 Jun 2013,
Do you mean the threshold?
min=2.0
max=5.0
Thanks!
【小孔成像】http://www.conxz.net
From: Bruce Fischl
Date: 2013-06-28 20:57
To: Xiangzhen Kong
CC: freesurfer
Subject: Re: Re: [Freesurfer] tksurfer display problem
sorry, I didn't notice that. What were your min and max set to?
On Fri, 28
Jun 201
can you resend the image? You don't have the "invert" button clicked, do
you?
On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
Do you mean the threshold?
min=2.0
max=5.0
Thanks!
【小孔成像】http://www.conxz.net
From: Br
Hi
i run mri_label2annot to get individual annot files for all labels, then i
run mri_label2vol to get nifti volumes of my labels using the following command
:
mri_label2vol --annot lh.G_and_S_cingul-Ant.annot --temp
SUBJ_DIR/ctr2/mri/brain.mgz --subject ctr2 --hemi lh --identity --
The image is attached.
The following cmd is all I did.
tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh
And I did not click any button.
I think the image is likely just a mirror image, but I failed to find a
"invert" button.
Where is the "invert" button?
Best!
Xiangzhen
Hi Xiangzhen, that is something I have never seen before. I don't think
it is a problem with freesurfer, and there is no button that will fix
it. I think it must be something in your environment. What are the
details of your platform?
doug
On 06/28/2013 10:18 AM, Xiangzhen Kong wrote:
> The
it's on the configure overlay window, but it wouldn't cause what you are
showing. I didn't notice this before but your entire color scale bar
(including the text!) is mirror imaged. This is very strange, and probably
explains why it looks like an rh. Can you give us the details of your
environ
Hi Sandra, you cannot do the longitudinal statistical analysis in QDEC.
You will have to use mri_glmfit. Look at the FSGD examples on the wiki.
doug
On 06/28/2013 03:28 AM, Sandra Preissler wrote:
> Dear freesurfer experts,
>
> we want to do longitudinal analyses for two different time points
How does the annot look on the surface (ie, intksurfer)? What is the
full terminal output of mri_label2vol?
On 06/28/2013 10:19 AM, LAOUCHEDI MAKHLOUF wrote:
> Hi
> i run mri_label2annot to get individual annot files for all
> labels, then i run mri_label2vol to get nifti volumes of my labe
Hi Jonathan
so you lose that entire gyrus? What are the intensity values of the wm in
the brain.mgz in that region? And it's not present in the wm.mgz either?
That means it's a segmentation problem not a topology one (which is what
I would have guessed)
Bruce
On Fri, 28 Jun 2013, Jonathan Ho
Hi Jonathan,
is this in cross sectional processing or in longitudinal?
One thing I notice is significant motion artifacts (ringing), which seem to
lead to underestimation of WM, also you could fine tune the skull strip.
Best, Martin
On Jun 28, 2013, at 10:19 AM, Jonathan Holt wrote:
> Hi all
Martin,
this is longitudinal processing, would you recommend a more aggressive or less
aggressive skull strip?
Bruce,
I've not seen this issue on more than a handful of subjects. They're ALS, but I
dont think that is the cause behind this. I'm unfamiliar with bias fields, but
it's more likely
oh, if it's that few then yes, but that wasn't what it looked like in the
image you sent
On Fri, 28 Jun 2013, Jonathan Holt wrote:
Martin,
this is longitudinal processing, would you recommend a more aggressive or
less aggressive skull strip?
Bruce,
I've not seen this issue on more than a hand
Yes, but do these errors show up in the cross sectional data, in the base or in
the longitudinal data (or all?)? Does it look good in the base?
I'd suggest more skull strip where the pail grabs dura.
On Jun 28, 2013, at 11:26 AM, Jonathan Holt wrote:
> Martin,
>
> this is longitudinal proce
We have 4 time points for that subject and it's an issue in all 4, to a lesser
degree in one of them, but still an issue. Same area, same hemisphere, every
time. Perhaps it is pathology based, I am not entirely sure.
On Jun 28, 2013, at 11:19 AM, Martin Reuter wrote:
> Hi Jonathan,
>
> is th
excuse me but i don't understand what you mean by "terminal of mri_label2volume"
Thank you for help
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail i
So you are not processing this with the longitudinal stream? You are just
running each image independently through freesurfer and look at the results?
Is there motion in all the 4 time points in this subject or only in the one
image that you send? With motion artifacts, surfaces are not very rel
The terminal output, ie, what gets printed to the screen after your run
the program.
doug
ps. Please remember to include all previous correspondence in your email.
On 06/28/2013 11:38 AM, LAOUCHEDI MAKHLOUF wrote:
> excuse me but i don't understand what you mean by "terminal of
> mri_label2volum
excuse me but i don't understand what you mean by "terminal of mri_label2vol"
Thank you for help
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is i
Am not too familiar with QDEC, but I though you can do a simple analysis with
one group testing where a measure (e.g. thickness, curvature) is different from
zero?
If so you can do the same here, but instead of thickness you can use the
thickness difference or the thickness percent change ( one
of thank you, the program ended without any problem and with no terminal
- Mail transféré -
De : Douglas N Greve
À : freesurfer@nmr.mgh.harvard.edu
Envoyé le : Vendredi 28 juin 2013 17h41
Objet : Re: [Freesurfer] (no subject)
The terminal output, ie, what gets printed to the screen a
The system is CentOS release 6.3.
And the package of freesufer is
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.
I wonder whether the version mismatch(centos4 vs.centos6) causes this strange
problem. I think I have to check this.
(As I remember, tksurfer of this version works well in centos5
here is the command and it's terminal :
mri_label2vol --annot G_and_S_cingul-Ant.annot --temp
/home/mlaouche/makh_free/ctr2/mri/brain.mgz --subject ctr2 --hemi lh --identity
--fillthresh 0 --o /home/mlaouche/G_and_S_cingul-Ant.nii.gz --proj frac 0 1 .1
Number of labels: 0
Annot File: G_an
my guess is it that it is, as for whatever reason temporal WM seems to
darken first in an array of disorders. I would start with a couple of
control points
cheers
Bruce
On Fri, 28 Jun 2013, Jonathan Holt
wrote:
We have 4 time points for that subject and it's an issue in all 4, to a
lesser
Hello,
I have a fairly basic question regarding the order in which I should
perform the edits. After running the full recon on all of my subjects I
have now completed the Talairach edits and the skull strip edits on my
subjects. At this point I am attempting to seek out help in terms of
performing
Dear freesurfers,
My data seems not to be T1-weighted by look (
http://www.youtube.com/watch?v=W8ZFGvGvHVc). Would you please help me
further identify by reading the following experimental description?
Images were acquired with blood-oxygen level dependent (BOLD) imaging on a
3 T Siemens Trio Sca
The MPRAGE is T1 weighted. It is probably series #1.
doug
On 06/28/2013 01:16 PM, ye tian wrote:
> Dear freesurfers,
>
> My data seems not to be T1-weighted by look
> (http://www.youtube.com/watch?v=W8ZFGvGvHVc). Would you please help me
> further identify by reading the following experimen
The MPRAGE is what you want
Bruce
On Fri, 28 Jun 2013, ye tian wrote:
Dear freesurfers,
My data seems not to be T1-weighted by look
(http://www.youtube.com/watch?v=W8ZFGvGvHVc). Would you please help me
further identify by reading the following experimental description?
Images were acquired wi
Dear Bruce and Greve,
Thank you very much. But I only have 3 images of MPRAGE though.
recon-all -s subject_directory -i /Path_to_MPRAGE finishes without error,
but gives two warnings of "input volume axes are not orthogonal"
recon-all -s subject_directory -autorecon1 exists "with ERRORS" almost
excuse me Doug.
i gathered previous correspondences (i wrote your replies are in bold) :
june, 28 at 16:41
Hi Ye
there's no way a 5 minute mprage would have only 3 slices. Or any mprage
really, since they are always 3D. You need to find the rest of the slices
(there are probably more than 128 of them)
Bruce
On Fri, 28 Jun 2013, ye tian wrote:
Dear Bruce and Greve,
Thank you very much. But I onl
Any thoughts on why this file turned out this way?
Thanks!
Emily
On Jun 26, 2013, at 8:09 AM, Emily Boeke wrote:
> Sure, here it is:
>
> # Cluster Growing Summary (mri_volcluster)
> # $Id: mri_volcluster.c,v 1.38.2.3 2009/01/16 02:26:36 greve Exp $
> # cwd
> /autofs/cluster/maury/users/gcoombs
Dear Bruce,
Thanks for the quick reply!
*What "nu" does stand for ?
*
Assaf
On Fri, Jun 28, 2013 at 4:02 PM, Bruce Fischl wrote:
> oh, it saves takes the volume nu.mgz in the directory
> $SUBJECTS_DIR/$subject/mri as input
>
> On Fri, 28 Jun 2013, Dov Sadan wrote:
>
> i meant mri/nu.mgz .
Hi Emily, what is your mri_glmfit-sim command line?
doug
On 06/28/2013 02:40 PM, Emily Boeke wrote:
> Any thoughts on why this file turned out this way?
>
> Thanks!
> Emily
>
> On Jun 26, 2013, at 8:09 AM, Emily Boeke wrote:
>
>> Sure, here it is:
>>
>> # Cluster Growing Summary (mri_volcluster)
It would be very interesting to know if this issue also happed in 5.3.
On Fri, Jun 28, 2013 at 1:28 PM, Koolschijn, Cédric <
p.c.m.p.koolsch...@uva.nl> wrote:
> Hi Martin,
>
> Unfortunately it is not a single subject, it happens to many.
> If I run FS 5.3, I also have to rerun the cross-sectio
Martin,
I hate to be noobish, but can you elaborate on the longitudinal stream? It may
be that I'm doing entirely too much work.
jon
On Jun 28, 2013, at 11:38 AM, Martin Reuter wrote:
> So you are not processing this with the longitudinal stream? You are just
> running each image independently
Hi Jon,
The longitudinal stream in freesurfer is designed to reduce variability in
situations where you have several scans from the same subject. The information,
that it is the same subject, is valuable and by initializing many steps in
recon-all with common data we can increase reliability of
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