Hi Polly
I don't know why convert wouldn't work properly with tkmedit. I guess you
could try freeview
cheers
Bruce
On Wed, 5 Jun 2013, Polly Dhond wrote:
>
> Hi Experts!
>
>I am trying to montage snapshots from tkmedit.
> the output of my tcl scripts are tiff. to save ink i am trying to cha
Hi Experts!
I am trying to montage snapshots from tkmedit.
the output of my tcl scripts are tiff. to save ink i am trying to change
the background to white before concatenating them into larger images.
the following works fine with tksurfer but does NOT work with tkmedit
generated tiffs --
I obtain /Applications/freesurfer/subjects/subject_prova
my DWI file is in Diff01, Diff02 ... that are in subject_prova folder.
Thanks,
Stefano
Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 6-giu-2013 0.42
A:
Cc:
Ogg: Re: [Freesurfer] R: Re: Tracula
What do you get when
/Applications/freesurfer/subjects/subject_prova
Stefano
Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 6-giu-2013 0.42
A:
Cc:
Ogg: Re: R: Re: Tracula
What do you get when you run "echo $SUBJECTS_DIR"?
On Thu, 6 Jun 2013, std...@virgilio.it wrote:
> Hi Anastasia,
>
> y
What do you get when you run "echo $SUBJECTS_DIR"?
On Thu, 6 Jun 2013, std...@virgilio.it wrote:
Hi Anastasia,
yes, I have check the SUBJECTS_DIR. I do not understand why all previous
configuration file start normally and this no.
Do you note some line that might be wrong additionally to sete
Hi Anastasia,
yes, I have check the SUBJECTS_DIR. I do not understand why all previous
configuration file start normally and this no.Do you note some line that might
be wrong additionally to setenv SUBJECTS_DIR line.
Stefano
Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data:
Those are the sig maps for the real and imaginary components. If you
want one sig that combines both, use the fsig (which is an F-test of the
real and imag).
dogu
On 06/05/2013 05:46 PM, dgw wrote:
> Hi,
>
> I am examining the difference in significance between different scan
> parameters in
Hi,
I am examining the difference in significance between different scan
parameters in a retinotopy experiment and analysis. I have loaded the
sig.nii.gz file in matlab using MRIread, and I am confused by the
dimensions of the "volume". I understand that this is a surface based file,
but the dimen
Hi Subha, there are tools to do this in FS. You can use mri_vol2surf to
map your time courses to the surface and save the output as a gifti (eg,
mri_vol2surf --mov f.nii.gz --reg register.dof6.dat --hemi lh --o
junk.gii --projfrac 0.5)
Or you can use the FS functional analysis stream (FSFAST).
Hi Andreas, it is not the same method but somewhat related. The method
assures that total area (or volume) is preserved when mapping between
subjects. How much detail do you need?
doug
On 06/04/2013 05:21 AM, Andreas Berger wrote:
> Hello FreeSurfers,
>
> after reading this [1] paper about me
Hi Laura, what is your command line?
doug
On 06/04/2013 09:02 AM, Laura Dekkers wrote:
>
> Dear Dr Greve,
>
> Together with Dr Hilde Huizenga I am implementing an fMRI study in
> which we would like to optimize the design by using Optseq2. We have a
> few questions. Could you please help us out?
Create a label with this vertex in it and use mri_label2label. See
subject/label/lh.cortex.label for any subject as an example.
doug
On 06/05/2013 03:43 PM, Ozranov-Palchik, Ola wrote:
> Hi Doug,
>
> Thanks for the response. I'm still a bit confused.
>
> Let's just say that I have a vertex index
Hi Doug,
Thanks for the response. I'm still a bit confused.
Let's just say that I have a vertex index that I determined on the surface of
my FS average surface (created by 'make_average_subject'). Now I simply want to
find the corresponding vertex index on all the source subjects.
How can I do
thanks Doug.
just tried, but I still got no clusters.
below is the output of perm.abs.2.sig.cluster.summary.
# CreationTime 2013/06/05-18:52:23-GMT
# cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd
GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig
GLM/osgm/perm.abs.2.sig.cluster.
Hi Ola, this probably will not work. The tal coordinate is notoriously
inaccurate in cortex. You are verylikely to totally miss the area you
are looking for. A better way is to run the MNI template through
recon-all, map your VBM result to the surface of that, then use
mri_surf2surf to map the
Hi Doug,
Thank you, again! I decided to try to use the Talairach coordinates from my
analysis for ROI extraction. I created an average subject and preprocessed the
data (mris_preproc). I obtained the vertex index based on the coordinates from
the average subject. Any ideas on how I can now fi
try
mri_glmfit-sim --glmdir GLM --no-sim perm.abs.2
doug
On 06/05/2013 02:26 PM, Glen Lee wrote:
>
>
>
>
> On Wed, Jun 5, 2013 at 12:12 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> what was your original mri_glmfit-sim command?
>
> mri_glmfit-sim --glmdir GLM
>
>
>
On Wed, Jun 5, 2013 at 12:12 PM, Douglas N Greve
wrote:
> what was your original mri_glmfit-sim command?
>
> mri_glmfit-sim --glmdir GLM --sim perm 2 2 perm.abs.2 --sim-sign abs
>> --overwrite
>>
>
>
> Then, I tried no-sim on the generated csd file with the following command:
>
> mri_
On 06/05/2013 11:49 AM, Tudor Popescu wrote:
>
> C) When running mri_surf2surf, I get an error saying
> that file
> /surf/lh.white cannot be opened. The 'average' folder
> produced
> after I ran make_average_subject does not contain a
Doug --
Sorry for asking your help again as I can't seem to resolve this on my own.
I looked up the mri_glmfit-sim --help and added the path of csd file in the
argument, but it still fails to find .csd file.
Can you let me know once again what I did wrong? (see the command line
below).
mri_glmfit
>
> C) When running mri_surf2surf, I get an error saying that file
>> /surf/lh.white cannot be opened. The 'average' folder produced
>> after I ran make_average_subject does not contain a
>> /surf/lh.white file, only a /surf/lh.white_avg file! I didn’t
>> fin
MNI space.
On Jun 5, 2013, at 11:14 AM, Douglas N Greve wrote:
what space is your VBM map in?
doug
On 06/05/2013 11:06 AM, Ozranov-Palchik, Ola wrote:
Hi Doug,
Thank you for your response! I am still a bit confused about the vol2surf
command. I have a volumetric mask with voxels of interest ba
what space is your VBM map in?
doug
On 06/05/2013 11:06 AM, Ozranov-Palchik, Ola wrote:
> Hi Doug,
>
> Thank you for your response! I am still a bit confused about the vol2surf
> command. I have a volumetric mask with voxels of interest based on a VBM
> analysis in SPM. I would like to extract
Look in the summary file as JM suggested
doug
On 06/05/2013 10:56 AM, std...@virgilio.it wrote:
> I'd like to know the effective p correlated with colour bar in a
> significant cluster.
>
> Thank you very much,
>
>
> Stefano
>
>
>
> Messaggio originale
> Da: gr...@nmr.mgh.harvard.edu
> Dat
I'd like to know the effective p correlated with colour bar in a significant
cluster.
Thank you very much,
Stefano
Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 5-giu-2013 16.31
A:
Ogg: Re: [Freesurfer] Monte Carlo simulation
what do you mean by the real
On 06/05/2013 10:17 AM, std...@virgilio.it wrote:
> Hi list,
>
> I performed Monte Carlo simulation on my cortical thickness analysis.
> Now, I have significant clusters in the map for p<0.05. Is possible to
> obstain form each significant cluster the real value of p?
>
> Thanks,
>
>
> Stefano
>
>
what do you mean by the real value of p?
On 6/5/13 10:17 AM, std...@virgilio.it wrote:
Hi list,
I performed Monte Carlo simulation on my cortical thickness analysis.
Now, I have significant clusters in the map for p<0.05. Is possible to
obstain form each significant cluster the real value of
Title
Automated segmentation of hippocampal subfields from ultra‐high
resolution in vivo MRI
Authors
Koen Van Leemput, Akram Bakkour, Thomas Benner, Graham Wiggins, Lawrence
L Wald, Jean Augustinack, Bradford C Dickerson, Polina Golland, Bruce
Fischl
Year
2009
Hippocampus
Volume
19
Issue
6
Pages
5
Hi list,
I performed Monte Carlo simulation on my cortical thickness analysis. Now, I
have significant clusters in the map for p<0.05. Is possible to obstain form
each significant cluster the real value of p?
Thanks,
Stefano ___
Freesurfer mailing li
Dear Doug,
I have re-sent the whole subject via the file drop, I think everything was
fine this time. Please let me know when you have an ide of what's going on
with it.
Cheers,
Rafa
2013/6/4 Bruce Fischl
> Hi Rafa
>
> this doesn't look like the whole subject dir, just some files from it
> (e
Is the "setenv SUBJECTS_DIR" line really commented out? You must set
SUBJECTS_DIR, see the example configuration file on the wiki and under
$FREESURFER_HOME/bin/dmrirc.example.
On Wed, 5 Jun 2013, std...@virgilio.it wrote:
Hi list and Anastasia,
I'm performing a set of data with tracula ver
yes
On Wed, 5 Jun 2013, Claudia Dacquino wrote:
Thanks.So the very first step I'll run recon-all -all, then I'll do all my
corrections and rerun just recon-all -autorecon2-cp -autorecon3 ...
Is that right?
Cheers
Claudia
2013/6/5 Bruce Fischl
Hi Claudia
recon-all -autorecon2-cp -
Thanks.
So the very first step I'll run recon-all -all, then I'll do all my
corrections and rerun just recon-all -autorecon2-cp -autorecon3 ...
Is that right?
Cheers
Claudia
2013/6/5 Bruce Fischl
> Hi Claudia
>
> recon-all -autorecon2-cp -autorecon3 ...
>
> will run everything the autorecon2-wm
Hi Claudia
recon-all -autorecon2-cp -autorecon3 ...
will run everything the autorecon2-wm and autorecon2-pial would and more,
so you can just run that.
cheers
Bruce
On Wed, 5 Jun 2013, Claudia Dacquino wrote:
Hi everyone,I'm sorry, this is a probably very basic question, but I'm a
little
Hi Oscar
the mri_mc surfaces will no in general be topologically correct. The
vertex spacing will also be less uniform
cheers
Bruce
On Wed, 5 Jun 2013, Oscar
Esteban wrote:
Thank you so much, Bruce.
Yes, I want the CSF inside the brain (e. g. the ventricles). Sorry for being
unspecific.
I
no, I haven't seen that before. Can you cat
/home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm
and send us the contents?
Bruce
On
Wed, 5 Jun 2013, huang bs wrote:
Hi All,
Sorry to take up your time.
My freesurfer now can not recognize the re-con files (such as the
Hi Wily
this looks like the relevant error:
GCAMwrite(transforms/talairach.m3z): gzip encountered error.
writing output transformation to transforms/talairach.m3z...
GCAMwrite
GCAMwrite:: m3z loop
GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z
GCAMwrite:: the popen error code
hi claudia,
do your all of your (cp, pial, wm) editing and once complete then you can
combine all three steps you have below into one step:
recon-all –s -autorecon2 –autorecon3
-robert
From: Claudia Dacquino
mailto:claudia.dacqu...@gmail.com>>
Date: Wednesday, June 5, 2013 5:45 AM
To: frees
Hi everyone,
I'm sorry, this is a probably very basic question, but I'm a little bit
confused about the recon-all correct flowchart.
I mean, the first step is
recon-all -s -all (comprising autorecon1, autorecon2 and
autorecon3), correct?
After this step if I want to add control points then I hav
Thank you for your response. Would you suggest a reference I can refer to?
2013/6/4 Juan Eugenio Iglesias
> I would probably leave out the fissure, but not the fimbria...
> Cheers,
> /Eugenio
>
> On Tue, 2013-06-04 at 14:33 +0200, Claudia Dacquino wrote:
> > Hi guys!
> > I have a dataset includ
Hi All,
Sorry to take up your time.
My freesurfer now can not recognize the re-con files (such as the .mgz
files, or .xfm files, etc).
For example, I run this command to check the talairach transform:
*tkregister2 --mgz --s linziyi --fstal --surf orig*
The terminal then reports:
*ERROR:
/home/vir
Hi list and Anastasia,
I'm performing a set of data with tracula version 3.0. I have change my dmrirc
file respect to previous analyses and now I have one problem
"set: Variable name must begin with a letter.ERROR: must specify as many DWI
dicoms as subjects".
I do not find the line that is wron
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