Dear dr. Fischl,
I was wondering if you've had any chance to look at our images (image 3 and
4 are attached to a second e-mail with the subject: Anterior Temporal Lobe
/ Pial Reconstruction Troubles - part 2)?
Sincerely,
Las
2014-07-11 16:06 GMT+02:00 Las Blawimo :
> Dear Dr. Fischl,
>
> Than
Thank you for your Help. I figured out that it was a problem with the data
which caused this error.
On Wed, 04 Jun 2014 12:00:08 -0400
Douglas N Greve wrote:
>
> This is a strange error that I cannot figure out from the terminal
> output. What version of FS are you using? Here's something
Hello Doug,
Ideally, I am trying to take subject tstat maps from FsFast (stable3
environment) and register these native structural space maps to the
MNI152_2mm standard brain.
The t_000.bfloat file is what was generated relative to my contrast that
was set up in FsFast stable3. There are a series
Hi pfannmoe
this is a bug in mri_label2label that we fixed a while ago. Zeke: can
post a new version and let people on the list know where it is?
thanks
Bruce
On Fri, 18 Jul 2014,
pfannmo...@uni-greifswald.de wrote:
> Dear Experts,
>
> I am working with freesurfer 5.3 on Mac OSX. I applied re
It would be very helpful for me.
On Fri, 18 Jul 2014 09:18:15 -0400 (EDT)
Bruce Fischl wrote:
> Hi pfannmoe
>
> this is a bug in mri_label2label that we fixed a while ago. Zeke: can
> post a new version and let people on the list know where it is?
>
> thanks
> Bruce
>
> On Fri, 18 Jul 2014,
Hi Las
it's tough to tell from just those images. Can you upload the entire
subject directory?
cheers
Bruce
On Fri, 18 Jul 2014, Las Blawimo wrote:
Dear dr. Fischl,
I was wondering if you've had any chance to look at our images (image 3 and
4 are attached to a second e-mail with the subj
Dear Freesurfer-Experts,
I am currently trying to measure Cortical Thickness of a
Volume-defined ROI in a patient measured at 4 timepoints.
Basically, I am interested in a ROI resulting from fMRI activation
measured on Timepoint 1.
I would then like to get thickness values in the same ROI for all
You can use mri_convert to change the orientation in the header. If you
run mri_convert without options it will give you lots of documentation
doug
On 7/18/14 9:17 AM, Fan, Qiuyun wrote:
> Hi Doug,
>
> I think I figured it out. It's the angulation of the image plane.
> ImageOreintation (should
not that I know of. When I have to do this, I save the data to a file,
then call mri_surf2surf with a system call, then load the result back
into matlab
On 7/18/14 1:12 AM, Reza Rajimehr wrote:
> Hi,
>
> For a simulation purpose, I want to load a surface into Matlab, assign a
> random value (ta
Hi Fs Experts,
In order to calculate the global white matter fractional anisotropy FA I used
(wm.mgz ) the output of recon-all as a mask in the following command line
mri_segstats --seg $SUBJECTS_DIR/015601/mri/wmparc.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --mask wm.mgz --i fa.anat
Thanks Doug! I need to do this procedure 100 times, so I have to automate
it. Do you have an example C-shell script for this? Or is there a way to
call mri_surf2surf inside a "for loop" of Matlab?
Thanks,
Reza
not that I know of. When I have to do this, I save the data to a file,
then call mri_s
Hi Arman,
Thanks for your suggestion. Sadly, the command
source /usr/share/fsl/5.0/etc/fslconf/fsl.sh
doesn't work and I've got the error:
FSLDIR=/usr/share/fsl/5.0: Command not found.
POSSUMDIR=/usr/lib/fsl/5.0: Command not found.
Bad : modifier in $ (/).
Do you think removing FSL altogether
Hello,
This shell script may do close to what you want it to do, so you could
modify it. It does it within AFNI using converted freesurfer surfaces.
http://faculty.fiu.edu/~adick/links/alphasurface.tcsh
If you see any errors please let me know.
Anthony
On 7/18/14, 12:39 PM, Douglas Greve wrot
Dear Freesurfer experts,
We are trying to convert a volume created in SPM and saved as a .nii file into
a label to overlay on a Freesurfer surface. We are using a template surface
found online, colin (http://mindboggle.info/data.html). We are able to display
our .nii in freeview successfully. T
Hello Anastasia,
I have just converted pathstas.overall.txt files to a table for group analyses.
Now, I am trying to convert pathstats.byvoxel.txt files to a table for group
analyses using the command:
trac-all -stat -c
I am receiving the error message: ERROR: flag -stat unrecognized
I am work
Hi Tudor,
yes, it can of course happen that neither group is significantly
different from zero, but the groups are different from each other. For
example one group mean is slightly above zero, the other slightly below,
then they would not differ from zero, but maybe the distance is large
enou
Hi Paul,
yes, take a look here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
should be similar to what you want to do (base and long are in the same
space), you would not need the lta_convert command, I think as you are
going to brainmask, not the rawavg.
Best, Martin
On 0
Dear Anastasia,
Another quick question:
We found significant differences in two subject groups for the AD_AVG as well
as the AD_AVG_Weight, which is stated as the "weighted average over the entire
path distribution'. Could you tell me how the average weight is calculated and
why it would be be
Hi Bastian,
use the longitudinal base for it. Also, once your ROI is in that space
you can simply apply it in each long as they are in the same space as
the base. The registration of base >> TP1.long etc. probably only
changes results very little.
Best, Martin
On 07/18/2014 10:45 AM, Bastian
Do you have the latest version of Tracula? There was an update posted
after FS 5.3 came out.
On 07/18/2014 04:48 PM, Cat Chong wrote:
Hello Anastasia,
I have just converted pathstas.overall.txt files to a table for group
analyses. Now, I am trying to convert pathstats.byvoxel.txt files to a
Thanks Chris,
I will try that right now!
> On Jul 18, 2014, at 2:37 PM, Chris Watson
> wrote:
>
> Do you have the latest version of Tracula? There was an update posted after
> FS 5.3 came out.
>
>> On 07/18/2014 04:48 PM, Cat Chong wrote:
>> Hello Anastasia,
>>
>> I have just converted path
Hi Cat - AD_AVG_Weight weighs the AD value at each voxel with the
probability value of the tract going through that voxel. So it's the
proper definition of the expected (mean) value from probability theory.
a.y
On Fri, 18 Jul 2014, Cat Chong wrote:
Dear Anastasia,
Another quick question:
Thank you for clarification, Martin!
Will do so and also try registration of base >> TP1.long etc.
Does FS create registration files (.dat) for this purpose
automatically? I found some *.lta files in the /mri/transfers folder
of the base image but am not sure how to apply them (maybe
tkregister2
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