Hi Nick,
Apologies, I should have looked at the recon-all.log file
myself. It says that there was an error with mris_topo_fixer:
it couldn't allocate memory (malloc error). So I guess that
the brainmask is still not correct. I will try to fix that with
the option -wsmore.
Cheers,
Ed
On 9 May
Dear all,
Is TRACULA able to handle 4D FSL niftii as input for DTI images? Are
bves/bvalues extracted by dcm2nii and MRICro accurate for TRACULA? I think
TRACULA needs the bvecs in the image coordinate system, which is not the
same as scanner coordinate system in case of oblique acquisition. Do I
the memory requirements of the topo fixer are quadratic in the convex
hull of the largest defect, so check the lh.orig.nofix and see if there is
a connection to the skull or the cerebellum. You will probably need to fix
it in the wm.mgz
cheers
Bruce
On Thu, 10 May 2012, Ed
Gronenschild
Hi Gabor - The input DWIs can be in any format that can be read by
mri_convert, including the NIfTI format. The gradient directions should be
in voxel coordinates, like the ones used by FSL. I don't have experience
with dcm2nii, but if you have original DICOM files, you can pass those as
the
Dear Anastasia,
I've the original DICOM files, but it is acquired with the standard Siemens
DTI ep2_diff, and not with the MGH-DTI sequence. Is DTI images acquired
with the standard DTI accurate and TRACULA able to extract the bvals and
bvecs from the dicom files?
Thanks,
Gabor
2012/5/10
You can specify them by setting bvecfile and bvalfile in your
configuration file.
On Thu, 10 May 2012, Gabor Perlaki wrote:
Dear Anastasia,
I've the original DICOM files, but it is acquired with the standard Siemens
DTI ep2_diff, and not with the MGH-DTI sequence. Is DTI images acquired
Hi Gabor,
dcm2nii's default setting for VB17 DICOMs should be to rotate the bvecs
that it returns into the voxel/image axes if you have a modern version of
it.
See item 8 under Sample Datasets of
http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html
for some notes on this issue and a
Hi Lilla,
Is it possible to use our own sample to build an atlas and than start group
comparisons based on that, even though the backengine is still based on an
adult atlas?
I ask this question, because my sample is of kids from 6-16 years
Any suggestions?
Thank you
Best regards,
Felipe Picon, MD
anson,
check the terminal output after you press the 'generate stats table'
button. it gives a more succinct error message. when this function
fails, its almost always because an aseg.stats file for one of the
subjects is missing or corrupt. you can regenerate the aseg.stats for a
subject by:
Hi Reem,
#1. Is this from mri_glmfit-sim? If so, you can ignore it
#2. You do not need both contrasts. Use abs to get a double sided test
#3. The first contrast will be positive for ControlPatient. If you
specify neg, it will only show clusters where ControlPatient
#4. Depends on what you mean
Hi,
I am a research assistant and I'm new to Freesurfer. I am using Windows and
downloaded the VirtualBox and Freesurfer. I was able to get through the steps
on the website for Testing Freesurfer. However, I get stuck when I am trying
to download the sample data for the tutorials. In the
Small unix lesson
A period . is shortcut for the current directory
df is a utility for seeing how much free space is left on a file system.
Unless quotas are involved which I am pretty sure they are not on the
VirtualBox image distributed. At the Martinos Center quotas are involved
with home
Thank you very much for your help. I am able to see that my curent directory
has a total of 11G and only 1.6G are available.
FreeSurfer:~ df -h .
Filesystem Size Used Avail Use% Mounted on
/dev/sda1 11G 8.3G 1.6G 85% /
When I try to use the quota command it says
Hi Rayna
disks that are over 800G or even a couple of TB are very cheap these
days. You need to find more disk space!
Bruce
On Thu, 10 May 2012, Trietsch, Rayna
wrote:
Thank you very much for your help. I am able to see that my curent directory
has a total of 11G and only 1.6G are
Assuming you have the free space on your Windows computer's disk,
you would need to create a virtual disk big enough in VirtualBox and
format it and mount it (at for example /data) in the Linux system. Then
put the data there.
That is the basic concept. The details on doing it are not
isxavg-fe-sess is an out-dated program that won't give you what you
want. If you do the -per-run option, you are sort of on your own in that
you'll have to run mri_glmfit, then that the results from that and
concatenate across subject. A different question is why do you want to
do this?
doug
Hello,
I have created a region in the left hemisphere by selecting my own set of
vertices (based on functional data). I would like to also create a region
as similar as possible in the right hemisphere. Does Freesurfer provide any
functions to create a right-hemisphere region (label) using a
I have successfully installed and launched the virualbox freesurfer image,
but I am unable to update it and I need to install smbfs in order to access
my data. The address that this installation points to appears to no longer
supported ubuntu. We have replicated this problem on two local PCs.
Is
Hi Doug
Thank you very much for answering all my questions, I hope it's okay that I ask
for further clarification on one point clusterwise correction is probably more
reliable at higher voxel-wise thresholds.
Can I clarify what is meant by 'higher' in this context i.e.
Higher = more
Hi Reem,
higher meaning more significant (ie, lower p-value)
doug
On 5/10/12 8:06 PM, Reem Jan wrote:
Hi Doug
Thank you very much for answering all my questions, I hope it's okay
that I ask for further clarification on one point clusterwise
correction is probably more reliable at higher
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