Dear freesurfer experts,
I download freesurfer CentOS 6 version and my PC is CentOS 6.5 version. When
I decompression it, I get error message:
gzip: stdin: invalid compressed data--format violated
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: e
usually that means you ran out of disk space while writing some file
cheers
Bruce
On Tue,
1 Jul 2014, tulu wrote:
Dear freesurfer experts,
I download freesurfer CentOS 6 version and my PC is CentOS 6.5 version. When I
decompression it, I get error message:
gzip: stdin: invalid compresse
Sorry, we don't have atlases to do that. I don't know of others either.
doug
On 06/30/2014 01:47 PM, Gonzalo Rojas Costa wrote:
>
> Hi:
>
> How can I segment the pons and midbrain using freesurfer ?... or any
> other segmentation software that do such task ?...
>
> Sincerely,
>
> Gonzalo Rojas C
I don't know about the first step but 2 and 3 look ok. But why are you
using the aseg? It will just give you the lh and rh cerebral WM
On 06/30/2014 03:11 PM, Alshikho, Mohamad J. wrote:
>
> Hi Fs Experts,
>
> In order to calculate the mean diffusivity MD in my DTI data I did the
> following:
Can you send the log file (or the full terminal output)?
On 06/30/2014 03:11 PM, angela.fav...@unipd.it wrote:
> Hi all,
> I have a problem with 'Surface-based Interhemispheric Registration'
>
> I followed the instructions and all seem to work, but the command:
> 'surfreg --s $subject --t fsaverage
Why not just write a little program that will create a color table with
random colors?
On 06/30/2014 05:00 PM, pavit...@nmr.mgh.harvard.edu wrote:
> Hi Freesurfer Team,
>
> I'd like to view a multicolored quilt of individual cortical icosahedron
> subdivisions.
> I have labels for these subdivis
The problem is that the dpsd is 0.5 which means that you want to perform
an FIR analysis to reconstruct the hemodynamic response at a temporal
resolution of 0.5 sec. This is probably not what you want to do. But you
need 0.5 because your TR is 2.5 and your stimulus is 3.5. A way around
this is
The slice is displayed in native (scanner) coordinates so the talairach
y can change. This is probably the case even for fsaverage since that is
in MNI305 space
doug
On 06/30/2014 01:09 PM, DeCross, Stephanie N. wrote:
> Hi,
>
> In FreeSurfer 5.3, when I click around in a coronal view slice, t
Can you upload the orig.mgz to me using our filedrop?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 06/30/2014 03:51 PM, Remy Wahnoun wrote:
> Thanks Douglas,
> orig.mgz looks fine to me. Do you know if there is any detailed log i
> could look into? Or maybe process tasks one after the other
sure! thank you
> Can you send the log file (or the full terminal output)?
> On 06/30/2014 03:11 PM, angela.fav...@unipd.it wrote:
>> Hi all,
>> I have a problem with 'Surface-based Interhemispheric Registration'
>>
>> I followed the instructions and all seem to work, but the command:
>> 'surfreg
Hi Kristina, sorry for the delay. Each of these stats files represents a
different atlas. The aparc.area.stats is from the Desikan-Killiany
atlas, the a2005s is from the Destrieux atlas. The DK atlas has larger
ROIs (too large for some) and is build from 39 subjects. The Destrieux
atlas has man
Chris,
This is why we no longer actively support CUDA development in freesurfer
and instead have focused on openmp to reduce overall runtime. The
complexity of the CUDA programming coupled with the required
libraries/driver matching of various builds with various OSes is simply
beyond the reso
I'm not sure why this is failing. Are there other things in the xhemi
folder? What version of FS are you using?
doug
On 07/01/2014 11:06 AM, angela.fav...@unipd.it wrote:
> sure! thank you
>
>
>> Can you send the log file (or the full terminal output)?
>> On 06/30/2014 03:11 PM, angela.fav...@u
Hi Doug
I am using the 5.0, but I have followed the instructions and downloaded
the new files as indicated.
the xhemi folder has some folders that are empty (bem, label, src, stats,
tmp), while the others include files (mri, scripts, surf, touch)
Is it possible that the script fails to copy files
Thanks Doug,
Actually I want to calculate the MD just for the right and left hemispheric
white matter.
The output of dt_recon doesn't include anything about the mean diffusivity (i.e
we have just the eignvals.nii ) so what is the best way to generate the MD as a
nifty file? Is it by using fslspl
Dear experts,
I am new to freesurfer, and please forgive me if this is not the right way
to present my issue.
I drew a ROI in QDEC, in the left hemisphere of a template and saved it as
a Label file (a .txt file)
I would like to flip this ROI to the right hemisphere.
Does anybody know an easy way
Hi Bryan,
Re: 1a) Did you run the case all the way through recon-all? Even if the
skullstripping looks poor, it's possible that the surfaces will turn out
ok and might only require some pial edits. Otherwise, this site has some
helpful info on rerunning the skullstripping step:
https://surf
Hi James,
Freeview has a "Write Movie Frames" option which will grab multiple
screenshots throughout a volume. I recently requested a commandline
option for this. I've run into the "no X11 on cluster" limitation as
well, and I don't have a work-around at this point.
The snapshot-to-html scr
Hi Max,
Could you send a snapshot of an area where your wm edits did not have an
effect? Keep in mind the wm voxels you add to the wm.mgz should be well
connected to the rest of the wm mask, or else it will tend to get pruned
off. You can look at the ?h.orig.nofix surfaces to see if the
intia
it does use an atlas. Check out the help in mri_watershed - there is a
switch that turns off the atlas usage.
cheers
Bruce
On Fri, 27 Jun 2014, Teo Gelles
wrote:
Hi Everyone,
I am trying to skullstrip an mri image without using an atlas. Does the
following command use an atlas at any point
The mean diffusivity is the same as the apparent diffusion coef (ADC);
there should be an adc volume in the output of dt_recon
doug
On 07/01/2014 12:38 PM, Alshikho, Mohamad J. wrote:
> Thanks Doug,
> Actually I want to calculate the MD just for the right and left hemispheric
> white matter.
>
Cool !
Thanks
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, July 01, 2014 3:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Mean diffusivity (MD)
The mean di
Hi,
I have been following the steps for longitudinal processing from here (
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), and
was hoping for some advice on how to setup the GLM.
I have a set of data where I have 2 time points for all subjects, have run
recon-all, qcache, t
When following the longitudinal qdec tutorial (
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), does
using the generate Stats Data Tables option extract data for the difference
between time point1 and 2, or something else?
Thank you.
Salil Soman, MD, MS
_
Hi
I don't know what you mean. The word 'generate' does not appear on that web
page.
Best Martin
Sent via my smartphone, please excuse brevity.
Original message
From: Salil Soman
Date:07/01/2014 9:50 PM (GMT+01:00)
To: free surfer
Subject: [Freesurfer] question about q
Hi salil, the command for that are on the wiki. You'd do a one sample group
mean (-osgm) . This asks if the variable of interest is significantly different
from zero. Since you ran long mris slopes, that variable would be for example
the rate of change or the percent change (one measure per subj
Hello,
I was wondering if it is better to keep the FA results from a DTI analysis in
diffusion space for group analysis or if you should warp them into standard
space as you would typically do with functional MRI data.
Emily
___
Freesurfer mailing lis
hello,
I was wondering if it was possible to use mris_divide_parcellation on white
matter labels.
Thanks,
Corinna
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information i
Hi Corinna
not really, as that is a surface-based utility. You could divide the
cortical labels and then recrate the wmparc from it, which might do what
you want.
cheers
Bruce
On Tue, 1 Jul 2014, Corinna
Bauer wrote:
> hello,
> I was wondering if it was possible to use mris_divide_parcellat
Hi Anastasia,
I created bvals.txt and bvecs.txt using dcm2nii.
These original files were text files and set in dmrirc profile as
"set bvalfile = /path/to/bvals.txt".
I checked word count for these files
# wc -w bvals.txt bvecs.txt
65 bvals.txt
195 bvecs.txt
260 total
However, when I run "t
Hi Emily,
You will need to resample them in a common space before you do group
analysis.
Lilla
On Tue, 1 Jul 2014, ebell...@uwm.edu wrote:
> Hello,
>
> I was wondering if it is better to keep the FA results from a DTI analysis in
> diffusion space for group analysis or if you should warp them
I understand about matching all the different combination of driver versions
with linux distros. My plan is to use a centos 6.5 distro and just install the
CUDA 5.5 library. I will try and replicate what there is already with CUDA 5.0
with the new library.
I will let you know how it goes.
I un
There are probably some empty spaces at the end of the lines of the
original files that confuses it into introducing those zeros. If you
attach the original files, I can take a look at them.
On Wed, 2 Jul 2014, Jun Shinozaki wrote:
> Hi Anastasia,
>
> I created bvals.txt and bvecs.txt using dc
Hi Emily - Depends on what you're doing. If you're doing an ROI-based or
tractography-based analysis, where you extract average FA in a part of
white matter, there is no need to warp. If you're doing a voxel-based
analysis, obviously all the subjects need to be in a common space to
compare the
34 matches
Mail list logo
