Hi Daniel,
What operating system are you using?
Lilla
On Tue, 28 May 2013, Barron, Daniel S wrote:
Hello,
I am trying to perform an inter-subject registration using mri_cvs_register on
version 5.3.
When I ran mri_cvs_check, my feedback was I needed to find
mri_cvs_register.settings.txt
.
Date: Tue, 28 May 2013 11:41:21 -0400
From: Z K zkauf...@nmr.mgh.harvard.edu
To: Barron, Daniel S barr...@livemail.uthscsa.edu
CC: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu,
Lilla Zollei lzol...@nmr.mgh.harvard.edu
Hello Daniel,
This is a confirmed issue with the 64bit
HI,
A patch is now available for the mris_resample : Command not found
error you encountered.
Simply download the file from the following link and place it in your
$FREESURFER_HOME/bin directory:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample
--Lilla
On Thu, 6
Hi, Can you be more specific? What files / volumes do you want to
compute a group average of?
On Sun, 9 Jun 2013, Fernando Valle-Inclán wrote:
Hi freesurfers, After doing cvs registration, how can I make a group
average? Is fsaverage OK?
Thanks
.norm.gzThanks for the
very prompt reply
F
2013/6/9 Lilla Zollei lzol...@nmr.mgh.harvard.edu
Hi, Can you be more specific? What files / volumes do you want to compute
a group average of?
On Sun, 9 Jun 2013, Fernando Valle-Inclán wrote:
Hi freesurfers, After doing cvs
Hi Marcel, You would ned at least twice as much. Also, is there a
specific reason for you to use the --m3d flag? That will result in writing
out uncompressed morph files which will take up a lot of space.
Lilla
On Tue, 9 Jul 2013, Marcel Falkiewicz wrote:
Dear FreeSurfers,
I'm trying to
diff2anat.bbr.mat
Matrix from regfile:
-0.001 0.972 -0.234 -3.311;
-0.001 0.234 0.972 69.949;
0.000 0.000 0.000 1.000;
0.000 0.000 0.000 0.000;
Best,
Matt
-Original Message-
From: Lilla Zollei [mailto:lzol...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 10, 2013 6:07 PM
It should be in your $FREESURFER_HOME/subjects directory.
Lilla
On Sun, 28 Jul 2013, SHAHIN NASR wrote:
Hi, Would you tell me where I can find cvs_avg35 brain template.
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
Hi Daniel,
You need to specify the full path to the target volume, the subject id
is not sufficient. It should be somthing like this:
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/norm.mgz
Lilla
On Tue, 6 Aug 2013, Barron, Daniel S wrote:
Hi Freesurfers (Lilla),
I'm running v5.1.0 on
Hi Marcel,
First, you will find a lot of details about the usage of mri_cvs_register
if you use the --help flag in the terminal.
See detailed responses to your questions below:
I'm trying to use mri_cvs_register (whose registration accuracy is, by the
way, jaw-dropping) for EPI images.
idea... Can you think of any solutions to this issue?
Best regards,
Marcel
2013/8/8 Lilla Zollei lzol...@nmr.mgh.harvard.edu
Hi Marcel,
First, you will find a lot of details about the usage of mri_cvs_register
if you use the --help flag in the terminal.
See detailed
Hi Jim,
Using the current FS recon pipeline with your data is indeed not feasible.
We are in the process of creating another pipeline geared towards that age
range.
Lilla
On Thu, 10 Oct 2013, Alexopoulos, Dimitrios wrote:
Just wondering if anyone has attempted to process T1-mpr data for a
Hi Liv,
What you are asking for is quite ambitious. As you have noticed, most of
the image processing tools fail on the infant data sets as they are
usually of much lower SNR, they have changing GM/WM contarst, higher noise
and a much smaller anatomy. So it is not only a question of creating
Hi Tommi,
I am preparing to CVS register 30+ subjects to improve FSL probabilistic
tractography alignment across subjects. First, thanks for a really cool
tool! Then, I have some questions:
1. mri_cvs_register step1 is spherical registration. However, I have
already run FS5.3 recon-all
mri_robust_register --help
You would need to use the --affine flag.
Lilla
On Fri, 22 Nov 2013, Nathaniel Reynolds wrote:
Hi all,
I can't find any explanation of how to perform an affine registration with
mdi_robust_register. Could someone please explain?
Thanks,
Nathaniel
It is not checked in as of now to the FS distribution. I can send it to
you.
On Fri, 22 Nov 2013, Nathaniel Reynolds wrote:
Hi again,
Does anybody know about a function called mri_mi?
I have someone else's script that seems to utilize it, but I can't seem to
access it myself.
Thanks,
Hi Andre,
I posted the below on Monday on the list:
The boost library is installed by default on CentOS platforms. If a user
gets the libboost error then they are using a different platform which
doesn't have boost installed by default. On RedHat systems libboost can be
installed by typing
Hi Caspar,
One thing you can do, if you have the label correspondences between your
lables and the FS ones, is to use mri_binarize with the --replace option
in your volumes.
--replace V1 V2 : replace voxels=V1 with V2
For label descriptions you can loook up
each label in the MNC file to a new Freesurfer
label file.
Caspar
2014/1/6 Lilla Zollei lzol...@nmr.mgh.harvard.edu
Hi Caspar,
One thing you can do, if you have the label correspondences between
your lables and the FS ones, is to use mri_binarize with the --replace option
Hi,
What is the age range of your subjects?
Lilla
On Tue, 28 Jan 2014, Mher Alaverdyan wrote:
Hi all,
I just wanted to know if it is acceptable to use the Destrieux atlas in FS
for parcellation of brain images of pre-adolescents. If not this atlas, then
which would be a recommended
I would say that for 5-8 the atlas would probably work. Below 5 I would be
skeptical. There is no alternate atlas at the moment, but we are working
on it.
-Lilla
On Tue, 28 Jan 2014, Mher Alaverdyan wrote:
They are 2 - 8 years old.
On Tue, Jan 28, 2014 at 11:46 AM, Lilla Zollei lzol
step.
Lilla
On Tue, 28 Jan 2014, Lilla Zollei wrote:
I would say that for 5-8 the atlas would probably work. Below 5 I would be
skeptical. There is no alternate atlas at the moment, but we are working
on it.
-Lilla
On Tue, 28 Jan 2014, Mher Alaverdyan wrote:
They are 2 - 8 years old
Hi,
I have some FS-style surface files that were created using outside tools
(from McGill). Due to some recent changes in FreeView they do not display
properly though as the useRealRAS bit in the header is not set to 1. Do we
have any C / Matlab code that I could use to change that?
Thanks,
guess you will need to figure
out how to get the right ras2vox matrix into them
cheers
Bruce
On Sun, 9 Feb 2014, Lilla Zollei wrote:
Hi,
I have some FS-style surface files that were created using outside tools
(from McGill). Due to some recent changes in FreeView they do not display
Doug, mris_convert does not read / write that information either.
On Sun, 9 Feb 2014, Bruce Fischl wrote:
really? I didn't realize that as I don't use them much. Doug: do you have
something like MRISread?
On Sun, 9 Feb 2014, Lilla Zollei wrote:
Those .m files only give me a set
Hi Francesco,
How old are your subjects?
Lilla
On Wed, 19 Mar 2014, Francesco Baldacchini wrote:
I have some quality problems with my scans. I'm trying to run recon-all on
pediatric brain images but, given the low contrast between cortical regions and
the white matter, I do consistently
are
in the process of creatig a pipeline for them, but it is not yet ready for
distribution.
Lilla
On Thu, 20 Mar 2014, Francesco Baldacchini wrote:
Hi Lilla,
They range from neonates to 6 years old,
Francesco
2014-03-19 19:21 GMT+01:00 Lilla Zollei lzol...@nmr.mgh.harvard.edu:
Hi
Hi Francesco,
The FS recon stream is set up for adult image analysis. In the past we
have had success with analysing data sets of children, but below the age
of 4yrs the success rate really drops and the stream is not recommended.
We are working on a separate stream for that population, but
Hi Emily,
You will need to resample them in a common space before you do group
analysis.
Lilla
On Tue, 1 Jul 2014, ebell...@uwm.edu wrote:
Hello,
I was wondering if it is better to keep the FA results from a DTI analysis in
diffusion space for group analysis or if you should warp them
Hi Andre
You can run:
mri_jacobian -tm3d 3d morph template volume output volume
--Lilla
On Thu, 10 Jul 2014, André Ribeiro wrote:
Dear Freesurfer Community,
How can I obtain the Jacobian of the deformation field estimated through
mri_cvs_register for further use like VBM analysis?
AM, André Ribeiro af...@imperial.ac.uk wrote:
Thank you! Didn't realized that function existed.
Regards,
Andre Santos Ribeiro
On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu
wrote:
Hi Andre
You can run:
mri_jacobian -tm3d 3d morph
, Lilla Zollei lzol...@nmr.mgh.harvard.edu
wrote:
Hi, You should use the final m3z file. The -tm3d flag just indicates that
the file was created by mri_cvs_register.
Lilla
On Fri, 11 Jul 2014, André Ribeiro wrote:
I got an error using the mri_jacobina
Hi Carina,
You can use the -f option (instead of -v used for volumes) when you are
calling freeview from the commandline in order to display a surface and
then append :overlay=overlay_filename after the filename to identify the
overlay that you want to use. You will need to decide which hemi
Contact Caterina Mainero, M.D. (cater...@nmr.mgh.harvard.edu) if
interested!
A full-time Research Technologist (Assistant) position is available in the
field of Neuroimaging of Multiple Sclerosis (MS) at the A. A. Martinos
Center for Biomedical Imaging of Massachusetts General Hospital (MGH).
Hi Cyrus,
You can run the following script:
compute_label_volumes.csh
It will list all the labels that are in your segmentation file (and also
tell you the number of voxels colored by this label and th etotal volume).
Lilla
On Tue, 5 Jun 2012, Sarosh, Cyrus wrote:
Hello,
I was
Hi Daniel.
i'm currently applying mri_cvs_register and I'm very happy with the nice
results. Congratulation for this very clever approach. However, some data
sets which I work on have still aseg.mgz which are not segmented
appropriately. As far as I understand aseg.mgz is not redefined
Hi Martina,
What was the command that you ran when executing mri_cvs_register. The
default outpur directory is $SUBJECTS_DIR/$subject/cvs. The help alos
explains how you can change that directory.
--Lilla
On Thu, 21 Mar 2013, Bruce Fischl wrote:
mri_vol2vol or mri_convert can apply the
Hi Maish,
You can just go to
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
and unsubscribe your email address.
Lilla
On Wed, 27 Mar 2013, Dalwani, Manish wrote:
Hello Admin,
Please unsubscribe this email address.
Regards,
Manish
Hi Josh,
We do not yet have a publicly available atlas for that population. We are
working on it though and will announce it as soon as it is ready.
Lilla
On Tue, 2 Apr 2013, Joshua Lee wrote:
The aseg has shown poor performance in my sample. Are there settings,
atlases, etc, available
Hi David,
Have you downloaded the updates of mri_cvs_register from
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes ? We found some bugs
in the orginial 5.1 release and put the fixed versions at the above.
Let me know if that still does not solve the problem.
--Lilla
On Tue, 21 Jun
:
Is this significant enough that we should re-run data processed using the
standard recon-all stream in version 5.1?
Thanks,
Peter
On Jun 10, 2011, at 3:28 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Message: 2
Date: Fri, 10 Jun 2011 12:59:34 -0400 (EDT)
From: Lilla Zollei lzol
Hi,
Yes, you should.
Lilla
On Sat, 11 Jun 2011, t...@ms36.hinet.net wrote:
lt;pgt;Dear FS expertslt;/pgt;
lt;pgt;I download CentOS5 x86-64 version (not CentOS4) of FS 5.1. should I
need to upgrade the mri_cvs_register and applyMorph for correction ?lt;/pgt;
lt;pgt;bestlt;/pgt;
Hi,
I have some diffusion scans acquired at the Childrens and when running
mri_glmfit on them to reconstrct the tensors, I get the following error.
ERROR: cannot extract sDiffusion.alBValue[1] from dwi-infodump.dat
I checked the dump file and there is a field sDiffusion.alBValue[0]. Does
Hi Constantin,
When you used tkregister2 which volume was the target? Acoording to what
you write it was the b0 volume. So when you apply the registration to the
T1 volume, you should keep it that way.
--mov T1
--targ b0image
and no -inv is necessary.
Let me know if I misunderstood what you
should
remain constant.
You mean that even if I want to register the T1 to the b0 i have to set the
b0 as target?
Thanks
Constantin
Quoting Lilla Zollei lzol...@nmr.mgh.harvard.edu:
Hi Constantin,
When you used tkregister2 which volume was the target? Acoording to
what you write
Hi Joana,
You should use the lowb volume as the moving volume for the registration
and then apply the output registration matrix to your FA volume. You can
also add the --o flag to your below command so that the resampled and
registered volume gets written out at the end. You would want that
Even though it is not ideal, manual adjustments can be useful. I would
use manual registration in a small number of cases though. If most of your
data requires it, I would try to play with the automatic registration
parameters more.
--Lilla
On Sun, 16 Oct 2011, Joana Braga Pereira wrote:
The tool to use is: track_transform
It should be distributed with the DTK / TrackVis tools.
-Lilla
On Wed, 9 Nov 2011, Douglas N Greve wrote:
Hi Paolo, I don't think we have have any tools to apply a matrix to a
trk file. Or maybe I'm wrong?
doug
paolo wrote:
Bruce, Doug, Thomas, thank
Hi Antonella,
1) I will be very grateful if you can confirm if my coding is write. First can
you please let me know if by default dt_recon is re-sample FA to talairch
space? In this case because I want to register on CVS should I add the
--no-tal flag? I am asking this question
because
.
Lilla
___
From: Lilla Zollei
, they don't live in the
same space.
--Lilla
From: Lilla Zollei lzol...@nmr.mgh.harvard.edu
To: Antonella Kis ator...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, November 15, 2011 5:11 PM
Subject: RE:[Freesurfer] dt_recon registration
Hi Antonella,
1) Why
2) The name suggests that the avg was created from 35 subjects.
Lilla
On Fri, 25 Nov 2011, Louis Nicholas Vinke wrote:
1) As long as the remaining skull/scalp is not distorting the surfaces then
it should not cause any problems with your analysis. Based on the snapshot
you sent it looks
Hi Antonella,
1) I will be very grateful if you let me know what data I should use for my
fsgd when I run the GLM group analysis: the dti data after running the dtrecon
(for example for my first control I called this directory C01_dti or the FS
data after running recon-all on the
structural
Hi Antonella,
1). I wonder if the GLM group analysis that is described on the webpage you
sent me (as instructed by Doug and Bruce, I was aware of this webpage and I
used it for my
QDEC studies but I am not sure if can be used for DTI data analysis) can be
used for a DTI group analysis.
Hi Peter,
Could you attach the log files from your process?
Lilla
On Mon, 5 Dec 2011, Peter J. Molfese wrote:
All,
I've been trying to use mri_cvs_register on a 64-bit mac and received the
following error (below). Google found a couple of hits that others are
having this problem but
Hi Antonella,
1) On the FS Diffusion Tutorial webpage I found for the Group Analysis the
following scrip: GroupAnalysis.csh with the following instruction:
# Assemble input for group analysis
set type = CVS-to-avg35# alternatively could be 'TAL-to-avg35' or
'MNI-to-avg35'
Can you
Hi Antonella,
I was running the mri_cvs_register with the flag --noaseg and no argument for
my target template so as I understood the registration was done on the cvs
template as you can see below:
mri_cvs_register--mov P01 --noaseg
Yes, that is right.
After registration I got 4
Hi Antonella,
I am trying to resample my DTI data in the CVS space and seems that after I
ran the mri_cvs_register with the flag --noaseg and no argument for my target
template (so the registration was done on the cvs template) I got the
following error:
ERROR: cannot find or read
Hi Antonella,
I will appreciate a lot if you can help me understand what is the meaning of
the results after running after running mri_cvs_register and the GLM group
analysis.
More exactly, I followed all the instructions from the webpage:
___
From: Lilla Zollei lzol...@nmr.mgh.harvard.edu
To: Antonella Kis ator...@yahoo.com
Hi Antonella,
I am doing a DTI group analysis study more exactly I am interested to see any
changes in the FA values within two groups: controls versus patients (children
with epilepsy). I introduced a white matter mask that will ensure that I am
only considering diffusion values
in the
Hi Antonella,
Can you send the log file so that we can figure out where your process
stopped?
Lilla
On Thu, 22 Dec 2011, Antonella Kis wrote:
Dear experts,
I was running the mri_cvs_register for a few times for a subject and I am
getting an error. The registration will not bwe
Hi Antonella,
I have a problem with mri_cvs_register. I am getthing the following error and
I will be very grateful if you can help me to fix it (I am don't understand
what means this errors).
I suspect that you are running out of memory on your computer. Can you
tell me the parameters of
Hi Greg,
Have you tried to just apply the bbreg transformation to your tract to
double check whether that registration is accurate?
Lilla
On Tue, 10 Jan 2012, Gregory Kirk wrote:
Hi
i am trying to transform/morph a tract created with tracula into my cvs
template subject space, using
Hi Antonella,
You should be able to just do
mri_convert
/media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.mgz
/media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.nii.gz
BTW, when resampling your FA data to CVS
mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \
$SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \
$TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz
and when it follows the resampling on the CVS space I see:
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
--m3z
map or an intensity threshol?
It really depends on your data. You might want to look at both outputs on
a couple of data sets and then decide.
--Lilla
From: Lilla Zollei lzol...@nmr.mgh.harvard.edu
To: Antonella Kis ator...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu freesurfer
___
From: Lilla Zollei lzol...@nmr.mgh.harvard.edu
___
From: Lilla Zollei lzol...@nmr.mgh.harvard.edu
To: Antonella Kis ator...@yahoo.com
___
From: Lilla Zollei lzol...@nmr.mgh.harvard.edu
To: Antonella Kis ator...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, January 18
Hi,
Could you forward the below to interested students / collaborators? I
attended this summer school both as a student and as a lecturer in the
past and I can highly reccomend it.
--Lilla
CALL FOR PARTICIPATION
You can just use the norm.mgz file.
Lilla
On Mon, 30 Jan 2012, Antonella Kis wrote:
Dear Doug,
I don't have an orig.mgz file for the cvs_avg35 and I suppose I need when I
will replace the fsaverage.In the mri file I have olny the norm.mgz
Can you please help me to get the orig.mgz for the
radialdiff.nii stands for radial diffusivity. dt_recon does not compute AD
(axial diffusivity). you could compute it on your own using the eigvals
and eigvecs files.
Lilla
On Mon, 13 Feb 2012, Antonella Kis wrote:
Dear All,
I would like to know how I can get the RD radial diffusivity and
Hi,
I would redo the processing for the Tracula processing as the FSL tools
require your data to be in a certain orientation and ours don't so you
might end up with some inconsistencies if you use the two packages
together.
Lilla
On Wed, 28 Mar 2012, Antonella Kis wrote:
Hi Anastasia,
Hi Cheol,
I am using freesurfer for patients with various neural disease. I wonder the
the
freesurfer atlas is applicable to them: dementia (with Lewy bodies, DLB),
epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some studies
already
used freesurfer for some of the diseases in the
, Lilla Zollei lzol...@nmr.mgh.harvard.edu
wrote:
Hi Cheol,
I am using freesurfer for patients with various neural disease. I
wonder the the
freesurfer atlas is applicable to them: dementia (with Lewy bodies,
DLB),
epilepsy, schizophrenia, ADHD, Alzheimer
Hi Jackie,
You will not need that file any more, so if that is the only file missing
you can go ahead with the registration. I will update the mri_cvs_check
script to reflect that.
Lilla
On Thu, 19 Apr 2012, Jackie Leung wrote:
Hi,
I'm new to Freesurfer, so this may be a silly question.
Hi Jackie,
Could you attach the log file?
Thanks, Lilla
On Thu, 19 Apr 2012, Jackie Leung wrote:
hi,
I'm trying to run mri_cvs_register and I'm getting a strange error message.
MRISread(CVS_test_26to47_1/lh.resample.white): could not open file
No such file or directory
Error reading
:37 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu
wrote:
Hi Jackie,
Could you attach the log file?
Thanks, Lilla
On Thu, 19 Apr 2012, Jackie Leung wrote:
hi,
I'm trying to run mri_cvs_register and I'm getting a strange error
message
will rerun everything overnight to see if i get the same problem.
thanks,
jackie
On Fri, Apr 20, 2012 at 3:56 PM, Lilla Zollei
lzol...@nmr.mgh.harvard.edu wrote:
Hi Jackie,
What is the size of the *resample* files? The only thing I can
think about
Hi Farras, I would be heppy to meet with you. Would some time between 12
and 2pm work?
Lilla
On Thu, 3 May 2012, farras abdelnour wrote:
Dear FreeSurfer experts,
I am in Charlestown for a short course at MGH until tomorrow, Friday,
4PM. I have a couple of questions on how to incorporate an
Hi Martin,
I thought we fixed this problem with the latest release. I am checking
into this.
--Lilla
-- Forwarded message --
Date: Fri, 15 Oct 2010 14:38:29 +0200
From: Martin Kavec martin.ka...@gmail.com
To: Freesurfer mailing list freesurfer@nmr.mgh.harvard.edu
Subject:
Hi Joakim,
I had a couple of questions regarding mri_cvs_register (which looks
terrific), and couldn't find any answers after a quick search. If I
missed an important page or pages, please don't hesitate to send me
there.
We are interested in using mri_cvs_register on a large body of
er/round4/9033b/cvs/el_reg_to9032b
/home/decharms/data/freesurfer/round4/9033b/cvs/
trace_el_reg_to9032b_9033b.txt
error executing surf2vol at
/usr/local/freesurfer//bin/elastic_registration_CVS.pl lin
e 162.
-Original Message-
From: Lilla Zollei [mailto:lzol...@nmr.mgh.harvard.edu
Thanks, I will look into this.
--Lilla
On Mon, 15 Nov 2010, Joakim Vinberg wrote:
Lilla,
Terrific! Here is the trace file.
Best,
Joakim
-Original Message-
From: Lilla Zollei [mailto:lzol...@nmr.mgh.harvard.edu]
Sent: Monday, November 15, 2010 7:37 AM
To: Joakim Vinberg
Cc
Hi Pedro Paulo,
The aparc+aseg file describes a single volume with parcellation and
segmentation information combined.
--Lilla
On Wed, 15 Dec 2010, Pedro Paulo de Magalhães Oliveira Junior wrote:
Hi,
One quick question: In the aparc+aseg file I suppose we have two volumes
(one for aparc
Hi Adam,
No, Freesurfer is not able to extract the neonatal cortical ribbon and I
am not aware of other automatic research tools that would be able to do
that.
Lilla
-- Forwarded message --
Date: Wed, 30 Mar 2011 14:38:26 -0500
From: Eggebrecht, Adam
Hi Greg,
Thanks for your note. I actually got rid of the perl script already so
in 5.1 it should not be a problem any more.
Lilla
On Thu, 19 May 2011, GREGORY R KIRK wrote:
running mri_cvs_register --mov 004 --template 003
get error executing surf2vol at
Hi,
We found a bug in the mri_cvs_register script after the
release. Please, download the new version of applyMorph and
mri_cvs_register from one of the below links for Linux Centos4,
Linux Centos4 x86 64 and Mac Leopard respectively:
for this question in advance.
Regards,
Andre Santos Ribeiro
PhD Student, Imperial College London
On Fri, Jul 11, 2014 at 4:11 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu
wrote:
Hi,
First, in the mri_cvs_register I kept all the files and therefore
] reg_IBSR_01_2_IBSR_02_brain.nii.gz
[icon_10_generic_list.png] jacobian.nii.gz
Regards,
Andre Santos Ribeiro
PhD Student, Imperial College London
On Tue, Aug 5, 2014 at 4:24 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu
wrote:
Hi Andre,
What do you mean by they do not seem to match voxel-wise
the applyMorph, and subtract the initial
virtual 4d image. The Jacobian matrix can also be calculated through this
fields.
That is definitely one way of doing it.
Best, Lilla
On Wed, Aug 6, 2014 at 3:35 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu
wrote:
Hi Andre,
The jacobian field
Hi Ben,
What version of freesurfer are you using?
Lilla
On Wed, 10 Sep 2014, bigben2...@web.de wrote:
Hey everyone,
i have tried to run the mri_cvs_register command but it returned an error in
the second step. It returned:
VolumeMorph load - failed to open input stream
I have
Could you also send the log file along?
Thanks, Lilla
On Wed, 10 Sep 2014, bigben2...@web.de wrote:
I'm using the version stable v5.3.0.
Ben
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Hi Mohammadi-Nejad,
Could you include the command that you submitted and the error message and
log file from when the process terminated?
Lilla
On Mon, 29 Sep 2014, Ali-Reza Mohammadi-Nejad wrote:
Hi
I am trying to do an mri_cvs_register for two subjects analyzed with FS-5.1.0
on a
file you can find the log of this command.
Best regards,
Mohammadi-Nejad
On Monday, September 29, 2014 2:12 PM, Lilla Zollei
lzol...@nmr.mgh.harvard.edu wrote:
Hi Mohammadi-Nejad,
Could you include the command that you submitted and the error message and
log file from when the process
Hi Piotr,
There are several tutorials that describe our standard data processing
pipeline. You can start by looking at:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial
with Introduction to Freesurfer and Analyzing the Individual Subject.
If you have any further questions, please, send
Hi Octavian,
If you have an OK aseg volume, you could try to fit a
surface over it using mris_make_surfaces with the -cover_seg flag.
Lilla
On Tue, 25 Nov 2014, Bruce Fischl wrote:
-- Forwarded message --
Date: Tue, 25 Nov 2014 08:05:55 -0600
From: Octavian Lie
Hi, Could you use a colormap for your aseg? It is really hard to see the
different ROIs on a grayscale image.
Thanks, Lilla
On Wed, 26 Nov 2014, Octavian Lie wrote:
Dear Lilla,
Here is a snapshot of the aseg volume, which rescues some gray matter not
included in the pia. I am not sure if
Hi Zach,
You would call it like the following:
applyMorph --template $t --transform $m point_list $i $o linear
wheer t is the template volume, m is the tm3d morph file, i is the input o
is the output and linear refers to the type of interepolation.
Lilla
On Wed, 4 Feb 2015, Zachary Greenberg
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