Hello,
I just downloaded and installed Freesurfer onto a new computer, and after
going through all the steps outlined on the download and installation page,
I get the following error when trying to run recon-all:
sudo recon-all -s bert -all
FREESURFER_HOME: Undefined variable.
However, I have s
Hi,all:
I have several problems about the qdec in freesurfer 5.0.
Firstly,can somebody explain the function of the buttons in the qdec's third
step (display),such as Set using FDR in the False Discovery Rate ,Monte Carlo
Null-Z simulation.If I just let these buttons as the default ,is it ri
One more thing that might be useful: for my current dataset, everything was
processed in FreeSurfer 4.3.1.
Thank you,
Jeff
On Mon, Mar 7, 2011 at 12:41 PM, Jeff Sadino wrote:
> Hello,
>
> I have a question about the effects of FreeSurfer's resampling algorithms.
> The way our pipeline goes is t
Hello,
I have a question about the effects of FreeSurfer's resampling algorithms.
The way our pipeline goes is that we convert our DICOM images into .nii.gz
format using FSL tools. One of the commands we use is FSLCPGEOM. I was
never sure why, but our script would always break without it. Look
Hi Gonzalo,
the ii) and iii) produce directories that look like this:
.long. and
.long.
These two directories are full subject-directories for time point 1 and
time point 2. So if you are familiar with the cross sectional freesurfer
subjects directory structure, you can find all kinds of informati
yes, mri_binarize can work on .mgz files.
cheers
Bruce
On Mon, 7 Mar 2011, Ritobrato
Datta wrote:
> Hi All,
>
> I am looking for a way to binarize MGH files.
>
> I took a mask I made in volumetric space to surface space, and I want to
> binarize it so it doesnt contain decimal values. What is t
Hi Martin:
I processed a patient (with two MRIs in different dates) using the
instructions in the web page that you told me, but I didn't understand
very well the results that I got...
Which values I got in aseg.stats with:
i) recon-all -base -tp -tp -all
ii) recon-all -long -all
Hi All,
I am looking for a way to binarize MGH files.
I took a mask I made in volumetric space to surface space, and I want to
binarize it so it doesnt contain decimal values. What is the command?
Will mri_binarize work on mgh files ? I need to manipulate MGH files, with the
same output type.
Helen,
the Release Notes page describes the differences between versions:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
but more importantly, we will be releasing a new version, v5.1, within
the next couple weeks. primarily the big difference between 5.1 and 4.5
are improvements to the
Hello Bruce and All,
Here are some new questions to an ongoing issue.
1. What are advantages of version 5.0 over the former version? I have
processed 82 scans so far in the former version and am debating whether to
re-run them all in 5.0. We will eventually have a total of 560 scans, so we
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