Hello all
I have a basic question. How do I create cortical thickness maps? I have been through most of the freesurfer tutorial and understand most of the commands. However, I am wondering how I can create a cortical thickness map for some of my own MRI data. Please let me know what steps I should take to do this.
Thanks! Abi
Hi Abi,
the cortical thickness maps are created as part of the recon-all process. Once you complete a reconstruction, there will be ?h.thickness maps for each hemi.
Bruce On Mon, 13 Nov 2006, Abi Gopal wrote:
Hello all
I have a basic question. How do I create cortical thickness maps? I have been through most of the freesurfer tutorial and understand most of the commands. However, I am wondering how I can create a cortical thickness map for some of my own MRI data. Please let me know what steps I should take to do this.
Thanks! Abi
Hello all
Hello all
I am trying to view my outputted images from reconstruction in tksurfer. However, there are no files in the 'surf' folder in my subject. The 'mri' folder only has the orig.mgz file. How do I get the other files, such as .wm, .filled, etc, that result from the 'tesselating' and 'smoothing and inflating' steps?
To clarify, I performed the 'recon-all' command on my data set, but I only see the orig.mgz file. I consulted the tutorial, and using the example 'bert,' it showed all the outputted files in the surf folder. However, it does not state what actions I need to perform in order to get these files. In fact, it seems to suggest that the recon-all command would take care of all these steps. I'm a little confused.
Please let me know if you can answer my questions.
Thanks! Abi
Hi Abi,
in general, we need more info than what you have supplied. As a new user, you are probably what is helpful info and what is not. To assist you, we have prepared the following web site: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting. Please look over that and supply all the information is asks for.
thanks!
doug
Abi Gopal wrote:
Hello all
Hello all
I am trying to view my outputted images from reconstruction in tksurfer. However, there are no files in the 'surf' folder in my subject. The 'mri' folder only has the orig.mgz file. How do I get the other files, such as .wm, .filled, etc, that result from the 'tesselating' and 'smoothing and inflating' steps?
To clarify, I performed the 'recon-all' command on my data set, but I only see the orig.mgz file. I consulted the tutorial, and using the example 'bert,' it showed all the outputted files in the surf folder. However, it does not state what actions I need to perform in order to get these files. In fact, it seems to suggest that the recon-all command would take care of all these steps. I'm a little confused.
Please let me know if you can answer my questions.
Thanks! Abi
-- Abilash A. Gopal Doris Duke Research Fellow, Harvard Medical School MD Candidate 2008, Tufts Medical School
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi all, below is my information.
rhinal
cat $FREESURFER_HOME/build-stamp.txt
source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/rhinal/2/users/gopal/lynch_data
which tkmedit
cd /space/rhinal/2/users/gopal/lynch_data
tkmedit lynch filled.mgz
error: loading volume filled.mgz couldn't read the anatomical volume.
TKMedit couldn't read the file you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.
Again, to clarify, I ran the 'recon-all' command on the lynch data, per the tutorial. However, as you can see from above, I did not create the ' filled.mgz' file, nor other files which I thought would have been created ( e.g. .white, .pial, and .thickness files). How do I create these files? I thought that by running recon-all I would have created them. Please let me know what you think; I believe that this is a very basic question.
Thanks Abi
On 11/13/06, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Hi Abi,
in general, we need more info than what you have supplied. As a new user, you are probably what is helpful info and what is not. To assist you, we have prepared the following web site: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting. Please look over that and supply all the information is asks for.
thanks!
doug
Abi Gopal wrote:
Hello all
Hello all
I am trying to view my outputted images from reconstruction in tksurfer. However, there are no files in the 'surf' folder in my subject. The 'mri' folder only has the orig.mgz file. How do I get the other files, such as .wm, .filled, etc, that result from the 'tesselating' and 'smoothing and inflating' steps?
To clarify, I performed the 'recon-all' command on my data set, but I only see the orig.mgz file. I consulted the tutorial, and using the example 'bert,' it showed all the outputted files in the surf folder. However, it does not state what actions I need to perform in order to get these files. In fact, it seems to suggest that the recon-all command would take care of all these steps. I'm a little confused.
Please let me know if you can answer my questions.
Thanks! Abi
-- Abilash A. Gopal Doris Duke Research Fellow, Harvard Medical School MD Candidate 2008, Tufts Medical School
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
but how did you reun recon-all and what did it output? On Tue, 14 Nov 2006, Abi Gopal wrote:
Hi all, below is my information.
rhinal
cat $FREESURFER_HOME/build-stamp.txt
source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/rhinal/2/users/gopal/lynch_data
which tkmedit
cd /space/rhinal/2/users/gopal/lynch_data
tkmedit lynch filled.mgz
error: loading volume filled.mgz couldn't read the anatomical volume.
TKMedit couldn't read the file you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.
Again, to clarify, I ran the 'recon-all' command on the lynch data, per the tutorial. However, as you can see from above, I did not create the ' filled.mgz' file, nor other files which I thought would have been created ( e.g. .white, .pial, and .thickness files). How do I create these files? I thought that by running recon-all I would have created them. Please let me know what you think; I believe that this is a very basic question.
Thanks Abi
On 11/13/06, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Hi Abi,
in general, we need more info than what you have supplied. As a new user, you are probably what is helpful info and what is not. To assist you, we have prepared the following web site: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting. Please look over that and supply all the information is asks for.
thanks!
doug
Abi Gopal wrote:
Hello all
Hello all
I am trying to view my outputted images from reconstruction in tksurfer. However, there are no files in the 'surf' folder in my subject. The 'mri' folder only has the orig.mgz file. How do I get the other files, such as .wm, .filled, etc, that result from the 'tesselating' and 'smoothing and inflating' steps?
To clarify, I performed the 'recon-all' command on my data set, but I only see the orig.mgz file. I consulted the tutorial, and using the example 'bert,' it showed all the outputted files in the surf folder. However, it does not state what actions I need to perform in order to get these files. In fact, it seems to suggest that the recon-all command would take care of all these steps. I'm a little confused.
Please let me know if you can answer my questions.
Thanks! Abi
-- Abilash A. Gopal Doris Duke Research Fellow, Harvard Medical School MD Candidate 2008, Tufts Medical School
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I ran recon-all as follows: recon-all -i asl_12slices_180/1024.dcm -s lynch
it outputted 001.mgz
what are the steps i need to follow in order to create the 'filled.mgz' file and the other files (e.g. .white, .pial, and .thickness files)? I thought that recon-all would have taken care of the remaining steps and created these files.
Thanks abi
On 11/14/06, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
but how did you reun recon-all and what did it output? On Tue, 14 Nov 2006, Abi Gopal wrote:
Hi all, below is my information.
rhinal
cat $FREESURFER_HOME/build-stamp.txt
source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/rhinal/2/users/gopal/lynch_data
which tkmedit
cd /space/rhinal/2/users/gopal/lynch_data
tkmedit lynch filled.mgz
error: loading volume filled.mgz couldn't read the anatomical volume.
TKMedit couldn't read the file you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.
Again, to clarify, I ran the 'recon-all' command on the lynch data, per
the
tutorial. However, as you can see from above, I did not create the ' filled.mgz' file, nor other files which I thought would have been
created (
e.g. .white, .pial, and .thickness files). How do I create these
files? I
thought that by running recon-all I would have created them. Please let
me
know what you think; I believe that this is a very basic question.
Thanks Abi
On 11/13/06, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Hi Abi,
in general, we need more info than what you have supplied. As a new
user,
you are probably what is helpful info and what is not. To assist you,
we
have prepared the following web site: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting. Please look over that
and
supply all the information is asks for.
thanks!
doug
Abi Gopal wrote:
Hello all
Hello all
I am trying to view my outputted images from reconstruction in
tksurfer.
However, there are no files in the 'surf' folder in my subject. The
'mri'
folder only has the orig.mgz file. How do I get the other files, such
as
.wm, .filled, etc, that result from the 'tesselating' and 'smoothing
and
inflating' steps?
To clarify, I performed the 'recon-all' command on my data set, but I
only
see the orig.mgz file. I consulted the tutorial, and using the example 'bert,' it showed all the outputted files in the surf folder. However,
it
does not state what actions I need to perform in order to get these
files.
In fact, it seems to suggest that the recon-all command would take care
of
all these steps. I'm a little confused.
Please let me know if you can answer my questions.
Thanks! Abi
-- Abilash A. Gopal Doris Duke Research Fellow, Harvard Medical School MD Candidate 2008, Tufts Medical School
Freesurfer mailing list Freesurfer@nmr.mgh.harvard
.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Abi Gopal -
Bruce Fischl -
Doug Greve