Dear Nick Schmansky
I am a beginner of freesurfer,and now I'm in trouble.
I have install the VirtualBox to run freesurfer,but the disk space is not
enough (11.0G).So I need to mount a disk to the system.
And now I want to know how to change the working path of freesurfer such as
Hi BoBO, use the setenv command to change/set the SUBJECTS_DIR or
FREESURFER_HOME. If that command does not mean anything to you, then I
think there is a linux primer on our web site.
doug
bowan...@mail.ustc.edu.cn wrote:
Dear Nick Schmansky
I am a beginner of freesurfer,and now I'm in
Hi Mahinda, try demeaning and normalizing the ICV values (ie, subtract
the mean and divide by the stddev).
doug
Mahinda Yogarajah wrote:
Dear Experts,
I am trying to carry out a simple 2 group (conrol and patient)
analysis with ICV as nuisance factor, and thickness as the dependent
Hi Lin, look at this page
http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V
and let me know if you still have questions
doug
林鄞 wrote:
Dear all
I have a question about the design of matrix. I have one group of two
levels ( patient and control) and two continous variables (age and
weight).
Hi All,
I am trying to figure out the contrasts to use for a study. I am comparing
age matched patients and controls (all female). The FSGD file has 4
columns, but I'm not sure how to make an appropriate contrast matrix. I
can't seem to find an applicable example on the wiki.
Any guidance would
Hi Allison, have you looked at
http://www.freesurfer.net/fswiki/PairedAnalysis ?
doug
Allie Rosen wrote:
Hi All,
I am trying to figure out the contrasts to use for a study. I am
comparing age matched patients and controls (all female). The FSGD
file has 4 columns, but I'm not sure how to
Dear all,
I've some fsl niftii MPRAGE images converted by MRIConverter. They look
fine in fslview and I can open them by freesurfer as well (tkmedit -f
*.nii.gz) , but when I compare the images between fslview and tkmedit they
look slightly different. It seems that the orientation is the same in
It works like this:
setenv SUBJECTS_DIR /path/to/your/data
setenv FREESURFER_HOME /path/to/freesurfer
The primer Doug is referring to can be found on this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/April2012CourseSchedule
The Unix slides, online practice, and Processing your own
what do you want to test?
doug
Allie Rosen wrote:
Hi Doug,
I have. I think that I have two groups (patients/controls) with one
covariate (age), so the following is my situation:
http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V
Thank you again,
Allison
On Mon, Feb 27, 2012 at 10:31
tkmedit will re-align to scanner space. The pixel data are not affected.
tkmedit is not used to process any data, only to view it, so it won't
affect stats.
dougt
Gabor Perlaki wrote:
Dear all,
I've some fsl niftii MPRAGE images converted by MRIConverter. They
look fine in fslview and I
Octavian, recon-all does not use --save_distance by default. You can
have it add --save_distance to the mris_volmask command line using the
expert options. Run recon-all with -help to get more info.
doug
octavian lie wrote:
Dear all,
to follow up on my prior message below, I must say that
yes, this is a know issue. It has been fixed for the next version, but
you can upload a fixed linux program from
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol
copy this to $FREESURFER_HOME/bin
doug
David Grayson wrote:
Hi,
I am noticing that when I use
Dear FS experts
I am trying to produce surface models with a higher resolution than 1x1x1mm
from T1-w. images acquired on a 7T scanner (0.75x0.75x0.75 mm). I have run
the following commands so far:
recon-all -autorecon1 -cm -noskullstrip -s subject
cd subject/mri
mri_convert -cs 1 nu.mgz
Could you explain why please ? I'm following this :
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On Fri, Feb 24, 2012 at 18:51, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote:
Oh, the problem may be in your label2vol cmd. Try this one
mri_label2vol --seg
Sorry, I think you did have the right command originally. If everything
looks good in tkmedit but bad in fslview, then I think you'll need to
talk to the FSL people (or at least tell us exactly what FSL commands
you are running on the data).
doug
Jimmy Ghaziri wrote:
Could you explain why
Hi Kristine, unfortunately we're not set up for that. Sorry.
doug
Kristine Beate Walhovd wrote:
Hi,
we´re running FS 5.1 and have a data set with a lot of missing values.
There are different subsets of persons missing different values of
interest, and we´re running analyses on concat
Just to clarify, you can do this analysis in FS, but not in QDEC. You'll
have to create an FSGD file. Do a search for FSGD on our wiki to get
examples that you can generalize from.
doug
MCLAREN, Donald wrote:
Charlotte,
There is no difference, from a statistical perspective, of nuisance
Kristine/Doug,
Are you missing Dependent Variable values or Independent Variable Values?
If you are missing some IV values, there are two potential solutions:
(1) Drop the subject;
(2) Impute the value of that subject given other variables and
relationships of those variables and the variable
Hi Martijn,
Which pathway does it fail on? Is the pathology of your subject affecting
the structures in the aparc+aseg that surround that pathway?
a.y
Dear all,
I'm running Tracula on a brain with some pathology. During the preproc
phase it fails with the following error:
INFO: Rejected
Hi,
I was wondering if I am doing something wrong when doing step 3 of the
longitudinally process.
The error I get is:
ERROR: Template/base ID cannot be the same as a time point ID
(in /shared/subjects/subjects/a-aut-v510/10022/base-tps)
Here is the environment:
Could someone please explain to me the difference between mri_binarize
and mri_extract_label?
I had been using mri_extract_label to create ROI masks of cerebral white
matter (2 and 41). I recently became aware that this would give me a
label with 0 and 128. I tried mri_binarize (with the same
Hi Doug,
Thanks for the response. I have had a read about demeaning on the forum. I
had a couple of questions:
1) If I want to include age as well as ICV as nuisance variables in a DODS
analysis comparing thickness between patients and controls, should I demean
(+ ? normalise) the age as well
Hi freesurfer experts:
i'm using qdec to perform statistical analysis in Freesurfer 5.0.0,
within 'Measure' menu in 'Design' tab, the default is 'thickness', however,
there are other measurements such as 'area' and 'area.pial'. the latter seems
meaning area in pial surface. what does
That is the area of the white surface. But don't use this unless you
have updated to the new version of mris_preproc.
doug
On 2/27/12 8:15 PM, ZhiLiangLong wrote:
Hi freesurfer experts:
i'm using qdec to perform statistical analysis in Freesurfer
5.0.0, within 'Measure' menu in
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