Hi,
I copied the default average subject from $FREESURFER_HOME/subjects dir to my analysis dir.
Then, I make a FSGD file and some contrast matrices and put them into my analysis dir.
After that, I start to run group analysis.
But, when I type the following commands:
mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh --meas thickness --out lh.noise_0.5-1-5.thickness.00.mgh
The terminal shows:
ERROR: flag -- not recognized
Now, I have two problems want to ask.
1) What's wrong about the commands that I type? And, how to solve the problem?
2) I found this commands from the FreeSurfer web. And, I'm confused about that two ways to do analysis. One is cached (qcached) data, and the other is uncached data. What's way is suitable to my subjects? (My subjects is one factor and three levels, had run QDEC before, but QDEC is not good job to analysis, and, I want to change the analysis method from QDEC to DODS) So, which way do I choose to analysis my subjects?? Idon't understand the differences from them.
Thank you in advance!
Feng-Xian
On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote
in general, it is not necessary to run make_average_subject prior to performing an analysis. using the default average subject that freesurfer provides, named 'fsaverage', is sufficient for most cases, because it doesnt affect the analysis, its only used as a target upon which to project results. the 'fsaverage' subject is in the $FREESURFER_HOME/subjects dir, and you should copy it to your own SUBJECTS_DIR prior to performing any group analysis.
Nick
On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote:
Hi,
I know I wont to do QDEC now, so I want to change the method of group analysis from QDEC to the web you tell me. But, I did QDEC before.
Before I do DODS, should I do make_average_subject to view the result of
my
subjects? Or, I have another method to view the results??
Thank you in advance!
Feng-Xian
On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote
Feng-xian,
I should also mention that i dont think creating your own average subject will solve the problem you describe, where you need to work
with
three levels in your group. for that, you wont be able to use qdec, but will need to run things manually. these pages give examples:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
and note one of them is 1 Factor, 3 Levels.
Nick
On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote:
Feng-Xian,
It appears that you do not have permission on your system to change
the
limits. So you will have to edit the scripts make_average_volume, make_average_surface and make_average_subject to comment out
the 'limit'
line, so that it looks like this:
#limit descriptors unlimited
Nick
On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote:
Hi,
I have a problem with make_average_subject.
After running all commands (including ln -s $FREESURFER_HOME/subjects/fsaverage and recon-all -s <subjid> -qcache for all my subjects) about
running
QDEC, I
found that QDEC could not analysis my group.
Because the group have 1 factor and three levels, QDEC can't run.
So, I want to change the method of analysis from QDEC to DODS.
I had a fsaverage file when I running QDEC, but the fsaverage did
not
use my
subjects to make.
So, can I use the fsaverage file to run DODS?
If not, I should make a new fsaverage with my subjects.
But, I encounter the problem about make_average_subject.
When I type:
make_average_subject --subects <subjid1> <subjid2> ...
the terminal show that:
limit: descriptors: Can't remove limit
What's wrong about the command I type? And, how to solve the
problem?
Thank you in advance!
Feng-Xian
Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)
------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)
Is there a space between "--" and "hemi"?
caching is just a way to speed some analyses by pre-smoothing and sampling to the standard space.
doug
Feng-Xian wrote:
Hi,
I copied the default average subject from $FREESURFER_HOME/subjects dir to my analysis dir.
Then, I make a FSGD file and some contrast matrices and put them into my analysis dir.
After that, I start to run group analysis.
But, when I type the following commands:
mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh --meas thickness --out lh.noise_0.5-1-5.thickness.00.mgh
The terminal shows:
ERROR: flag -- not recognized
Now, I have two problems want to ask.
What's wrong about the commands that I type? And, how to solve the problem?
I found this commands from the FreeSurfer web. And, I'm confused about that two ways to do analysis. One is cached (qcached) data, and the other is uncached data. What's way is suitable to my subjects? (My subjects is one factor and three levels, had run QDEC before, but QDEC is not good job to analysis, and, I want to change the analysis method from QDEC to DODS) So, which way do I choose to analysis my subjects?? Idon't understand the differences from them.
Thank you in advance!
Feng-Xian
On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote
in general, it is not necessary to run make_average_subject prior to performing an analysis. using the default average subject that freesurfer provides, named 'fsaverage', is sufficient for most cases, because it doesnt affect the analysis, its only used as a target upon which to project results. the 'fsaverage' subject is in the $FREESURFER_HOME/subjects dir, and you should copy it to your own SUBJECTS_DIR prior to performing any group analysis.
Nick
On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote:
Hi,
I know I wont to do QDEC now, so I want to change the method of group analysis from QDEC to the web you tell me. But, I did QDEC before.
Before I do DODS, should I do make_average_subject to view the result of
my
subjects? Or, I have another method to view the results??
Thank you in advance!
Feng-Xian
On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote
Feng-xian,
I should also mention that i dont think creating your own average subject will solve the problem you describe, where you need to work
with
three levels in your group. for that, you wont be able to use qdec, but will need to run things manually. these pages give examples:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
and note one of them is 1 Factor, 3 Levels.
Nick
On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote:
Feng-Xian,
It appears that you do not have permission on your system to change
the
limits. So you will have to edit the scripts make_average_volume, make_average_surface and make_average_subject to comment out
the 'limit'
line, so that it looks like this:
#limit descriptors unlimited
Nick
On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote:
Hi,
I have a problem with make_average_subject.
After running all commands (including ln -s $FREESURFER_HOME/subjects/fsaverage and recon-all -s <subjid> -qcache for all my subjects) about
running
QDEC, I
found that QDEC could not analysis my group.
Because the group have 1 factor and three levels, QDEC can't run.
So, I want to change the method of analysis from QDEC to DODS.
I had a fsaverage file when I running QDEC, but the fsaverage did
not
use my
subjects to make.
So, can I use the fsaverage file to run DODS?
If not, I should make a new fsaverage with my subjects.
But, I encounter the problem about make_average_subject.
When I type:
make_average_subject --subects <subjid1> <subjid2> ...
the terminal show that:
limit: descriptors: Can't remove limit
What's wrong about the command I type? And, how to solve the
problem?
Thank you in advance!
Feng-Xian
Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)
Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Thank you for your response! I solve this problem of mris_preproc. The next step is to do mri_glmfit.
And, when I type the following command: mri_glmfit --y lh.noise_0.5-1-5.thickness.10.mgh --fsgd noise_0.5-1-5.fsgd dods --C noise_0.5-1.mtx --surf fsaverage lh --cortex --glmdir lh.noise_0.5- 1.glmdir
The terminal shows: ERROR: Option --cortex unknown
Would you tell me what’s wrong? And how do I do to solve this error?
Thank you in advance!
Feng-Xian
On Tue, 07 Jul 2009 11:49:32 -0400, Douglas N Greve wrote
Is there a space between "--" and "hemi"?
caching is just a way to speed some analyses by pre-smoothing and sampling to the standard space.
doug
Feng-Xian wrote:
Hi,
I copied the default average subject from $FREESURFER_HOME/subjects
dir
to my analysis dir.
Then, I make a FSGD file and some contrast matrices and put them into my analysis dir.
After that, I start to run group analysis.
But, when I type the following commands:
mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh --
meas
thickness --out lh.noise_0.5-1-5.thickness.00.mgh
The terminal shows:
ERROR: flag -- not recognized
Now, I have two problems want to ask.
What's wrong about the commands that I type? And, how to solve the problem?
I found this commands from the FreeSurfer web. And, I'm confused
about
that two ways to do analysis. One is cached (qcached) data, and the other is uncached data.
What's
way is suitable to my subjects? (My subjects is one factor and three levels, had run QDEC before, but QDEC is not good job to analysis,
and, I
want to change the analysis method from QDEC to DODS) So, which way do I choose to analysis my subjects?? Idon't
understand
the differences from them.
Thank you in advance!
Feng-Xian
On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote
in general, it is not necessary to run make_average_subject prior to performing an analysis. using the default average subject that freesurfer provides, named 'fsaverage', is sufficient for most cases, because it doesnt affect the analysis, its only used as a target upon which to project results. the 'fsaverage' subject is in the $FREESURFER_HOME/subjects dir, and you should copy it to your own SUBJECTS_DIR prior to performing any group analysis.
Nick
On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote:
Hi,
I know I wont to do QDEC now, so I want to change the method of
group
analysis from QDEC to the web you tell me. But, I did QDEC before.
Before I do DODS, should I do make_average_subject to view the result
of
my
subjects? Or, I have another method to view the results??
Thank you in advance!
Feng-Xian
On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote
Feng-xian,
I should also mention that i dont think creating your own average subject will solve the problem you describe, where you need to work
with
three levels in your group. for that, you wont be able to use qdec, but will need to run things manually. these pages give examples:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
and note one of them is 1 Factor, 3 Levels.
Nick
On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote:
Feng-Xian,
It appears that you do not have permission on your system to change
the
limits. So you will have to edit the scripts make_average_volume, make_average_surface and make_average_subject to comment out
the 'limit'
line, so that it looks like this:
#limit descriptors unlimited
Nick
On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote:
> Hi, > > I have a problem with make_average_subject. > > After running all commands (including ln -s > $FREESURFER_HOME/subjects/fsaverage > and recon-all -s <subjid> -qcache for all my subjects) about >
running
QDEC, I
> found that QDEC could not analysis my group. > > Because the group have 1 factor and three levels, QDEC can't run. > > So, I want to change the method of analysis from QDEC to DODS. > > > I had a fsaverage file when I running QDEC, but the fsaverage did >
not
use my
> subjects to make. > > So, can I use the fsaverage file to run DODS? > > If not, I should make a new fsaverage with my subjects. > > But, I encounter the problem about make_average_subject. > > > When I type: > > make_average_subject --subects <subjid1> <subjid2> ... > > the terminal show that: > > limit: descriptors: Can't remove limit > > > What's wrong about the command I type? And, how to solve the >
problem?
> > > Thank you in advance! > > Feng-Xian > > > ------------------------------------------------- > Chang Gung University Mail Server Web Mail system > By Chang-Gung University Information Center > (http://www.cgu.edu.tw/ic/) > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)
Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)
You probably have an older version that does not recoginze --cortex. Try --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label instead
Feng-Xian wrote:
Hi, Thank you for your response! I solve this problem of mris_preproc. The next step is to do mri_glmfit.
And, when I type the following command: mri_glmfit --y lh.noise_0.5-1-5.thickness.10.mgh --fsgd noise_0.5-1-5.fsgd dods --C noise_0.5-1.mtx --surf fsaverage lh --cortex --glmdir lh.noise_0.5- 1.glmdir
The terminal shows: ERROR: Option --cortex unknown
Would you tell me what’s wrong? And how do I do to solve this error?
Thank you in advance!
Feng-Xian
On Tue, 07 Jul 2009 11:49:32 -0400, Douglas N Greve wrote
Is there a space between "--" and "hemi"?
caching is just a way to speed some analyses by pre-smoothing and sampling to the standard space.
doug
Feng-Xian wrote:
Hi,
I copied the default average subject from $FREESURFER_HOME/subjects
dir
to my analysis dir.
Then, I make a FSGD file and some contrast matrices and put them into my analysis dir.
After that, I start to run group analysis.
But, when I type the following commands:
mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh --
meas
thickness --out lh.noise_0.5-1-5.thickness.00.mgh
The terminal shows:
ERROR: flag -- not recognized
Now, I have two problems want to ask.
What's wrong about the commands that I type? And, how to solve the problem?
I found this commands from the FreeSurfer web. And, I'm confused
about
that two ways to do analysis. One is cached (qcached) data, and the other is uncached data.
What's
way is suitable to my subjects? (My subjects is one factor and three levels, had run QDEC before, but QDEC is not good job to analysis,
and, I
want to change the analysis method from QDEC to DODS) So, which way do I choose to analysis my subjects?? Idon't
understand
the differences from them.
Thank you in advance!
Feng-Xian
On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote
in general, it is not necessary to run make_average_subject prior to performing an analysis. using the default average subject that freesurfer provides, named 'fsaverage', is sufficient for most cases, because it doesnt affect the analysis, its only used as a target upon which to project results. the 'fsaverage' subject is in the $FREESURFER_HOME/subjects dir, and you should copy it to your own SUBJECTS_DIR prior to performing any group analysis.
Nick
On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote:
Hi,
I know I wont to do QDEC now, so I want to change the method of
group
analysis from QDEC to the web you tell me. But, I did QDEC before.
Before I do DODS, should I do make_average_subject to view the result
of
my
subjects? Or, I have another method to view the results??
Thank you in advance!
Feng-Xian
On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote
Feng-xian,
I should also mention that i dont think creating your own average subject will solve the problem you describe, where you need to work
with
three levels in your group. for that, you wont be able to use qdec, but will need to run things manually. these pages give examples:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
and note one of them is 1 Factor, 3 Levels.
Nick
On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote:
> Feng-Xian, > > It appears that you do not have permission on your system to change > >
the
> limits. So you will have to edit the scripts make_average_volume, > make_average_surface and make_average_subject to comment out > >
the 'limit'
> line, so that it looks like this: > > #limit descriptors unlimited > > > Nick > > On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote: > > >> Hi, >> >> I have a problem with make_average_subject. >> >> After running all commands (including ln -s >> $FREESURFER_HOME/subjects/fsaverage >> and recon-all -s <subjid> -qcache for all my subjects) about >> >>
running
QDEC, I
>> found that QDEC could not analysis my group. >> >> Because the group have 1 factor and three levels, QDEC can't run. >> >> So, I want to change the method of analysis from QDEC to DODS. >> >> >> I had a fsaverage file when I running QDEC, but the fsaverage did >> >>
not
use my
>> subjects to make. >> >> So, can I use the fsaverage file to run DODS? >> >> If not, I should make a new fsaverage with my subjects. >> >> But, I encounter the problem about make_average_subject. >> >> >> When I type: >> >> make_average_subject --subects <subjid1> <subjid2> ... >> >> the terminal show that: >> >> limit: descriptors: Can't remove limit >> >> >> What's wrong about the command I type? And, how to solve the >> >>
problem?
>> Thank you in advance! >> >> Feng-Xian >> >> >> ------------------------------------------------- >> Chang Gung University Mail Server Web Mail system >> By Chang-Gung University Information Center >> (http://www.cgu.edu.tw/ic/) >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >>
Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)
Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Feng-Xian