Hi everyone, I'm getting the follow error and it's jus started happening
after updating Xquartz.. any ideas what I can do? Also, i dont have a
.debug_tkmedit file, when tkmedit was running normally the first line would
say could not create debug file.
Many thanks,
Hugh
ERROR: A segfault has
Hi Emily,
1. That's fine because the BET-based mask is not used by default in the
the tractography. The brain mask from the freesurfer segmentation of the
structural scan is used instead.
2. To check the diffusion-to-anatomical registration, you can look at the
aparc+aseg registered into
Hi Elijah
This is happening because the columns of your Qdec table file are separated by
tabs or something else. You need to use simple spaces instead or properly
modify fReadQdec to support tabs. This is something I need to fix on github:
https://github.com/NeuroStats
Best
-Jorge
Hi Anastasia,
Thank you so much, this is really helpful.
I have one other question. So, at the bedpost stage, the no_dif_brain mask is
used correct (looking at the fsl webpage), or at this stage the freesurfer
segmentation is used as well?
If in addition to using tracula, lets say if I also
Hi Knut
Thank you very much for your contribution. I'll take a look at it and apply the
patches as soon as I have time (probably next weekend) on github:
https://github.com/NeuroStats
Best
-Jorge
De: Knut J Bjuland knut.j.bjul...@ntnu.no
Para: jorge luis
Hi Elijah
You are getting NaNs
because the rows of your Qdec variable (except the first) are already
numeric values instead of strings. You just need to do this:
Qdec
= Qdec(2:end,:);
The variable Y has
the data that you already read with:
[Y, mri] =
fs_read_Y('lh.thickness_sm10.mgh');
Sorry, you need to do:
M = Qdec(2:end,:);
Best
-Jorge
De: jorge luis jbernal0...@yahoo.es
Para: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Enviado: Lunes 14 de julio de 2014 10:06
Asunto: Re: [Freesurfer] LME Longitudinal QDEC Table
Hi
i've tried reinstalling xquartz (this is on a mac by the way) and now I'm
getting this error when trying to run tkmedit, any ideas would be hugely
appreciated!
Thanks,
Hugh
Couldn't create output file .xdebug_tkmeditGLUT: Fatal Error in
tkmedit.bin: could not open display:
Hi Jorge,
Thank you again. It works! Now, the M variable only contains the numeric
data, without the column headers.
For the last step (sorting the data), I am met with the following error
command:
[M,Y,ni] = sortData(M,1,Y,sID)
Error using sort
Input argument must be a cell array of strings.
Hi Emily - When a mask is used as input to bedpostx, all voxels outside
that mask will be zero in all bedpostx output volumes. So it makes sense
to use the same mask for any subsequent processing. Is the mask that
you're referring to a symbolic link to another volume? You can run ls -l
to see
Hi Eileen - That step is run with the program epidewarp.fsl, which you can
run on the command line to see the available options. The input phase map
volume is expected to have either 2 frames (2 separate phase maps) or 1
frame (the difference phase map). This error from trac-all means that it
Hi Anastasia,
So probtractx uses the output from the bedpost stage (which I ran in Tracula).
I noticed that the bedpost stage (in the dmri.bedpostx folder) also outputs a
no_dif_brain mask. I guess what I am worried about is that if bedpost creates
this no_dif_brain mask, that is what will be
Hi Emily - Sorry for the confusion. The mask in the bedpostx output
directory is a copy of whichever mask was input to bedpostx. By default,
tracula uses the anatomical mask for this. If that mask doesn't cover the
brain well, I would check for diffusion-to-anatomical miregistration.
Another problem now is that my terminal is not recognising the freesurfer
folder.. it's just saying that the directory doesn't exist even though i
can see and interact with all the files through the finder.. any ideas what
might have happened/how I can check for the problem would be much
Hugh,
Can you provide some examples of the problem with the terminal having
issues detecting the FreeSurfer folder (ls pwd etc.)? And describe
where the folder is installed on your computer in the Finder?
Thanks,
D
On Mon, Jul 14, 2014 at 12:54 PM, Hugh Pemberton
hughpembert...@gmail.com
I think that there must be a problem with your FSL install. I hate to
pass the buck, but did you contact the FSL list?
doug
On 07/13/2014 01:36 PM, Alan Lee wrote:
Hi Doug,
When I run the following:
/usr/lib/fsl/5.0/bin/bet2
it gives me the following error:
bet2: error while loading
what is your command line? Or otherwise, how are you visualizing it?
On 07/14/2014 08:09 AM, car...@van-vlodrop.de wrote:
*Gesendet:* Sonntag, 06. Juli 2014 um 22:48 Uhr
*Von:* car...@van-vlodrop.de car...@van-vlodrop.de
*An:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hi Alan,
I can guess there are several problems here with your fsl installation. Are
you on Neurodebian? For some historical reasons fsl5.0-command format for
usual fsl commands were used so that when people wanted to use both fsl 4
and 5 at the time there wouldn't be any confusion. Anyway you
Hello Freesurfer,
I am attempting to take label files generated in fsaverage surface space
and transform them into MNI152 volume space.
Using the commands below, I am able to view the final output image with
fslview in the the same space as the MNI brain. However, the registration
is very off.
Hi Fs Expert,
I have a group of kids subjects (4-15) year old. I want to do cortical
reconstruction process using Freesurfer. My question is:
is still correct to use the command line recon-all -all -subjid in this age
group? Do I need to use the flag -noseg ? (i.e can I use aseg for this range
Hugh,
it looks like the new XQuartz v2.7.6 is breaking tkmedit, and we don't
know why. You will have to revert to using v2.7.5:
http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.5.dmg
Nick
On Mon, 2014-07-14 at 15:25 +0100, Hugh Pemberton wrote:
i've tried reinstalling xquartz (this is
When viewed on the inflated surface in tksurfer, we are seeing “holes” in annot
files we created defining our own ROIs. We first created 6 label files on
fsaverage then mapped these 6 label files to 5 different subjects using
mri_label2label. Once the 6 label files were mapped to each subject,
can you send a picture?
On 07/14/2014 02:38 PM, April Clausen wrote:
When viewed on the inflated surface in tksurfer, we are seeing “holes” in
annot files we created defining our own ROIs. We first created 6 label files
on fsaverage then mapped these 6 label files to 5 different subjects
Try this instead
mri_vol2vol --inv --targ M4_LH_orig.mgz --mov
$FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o M4_LH_orig_MNI152.nii.gz
--interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat
On 07/14/2014 02:07 PM, jaco...@nmr.mgh.harvard.edu wrote:
Hello Freesurfer,
I am
Thank you Doug, that seems to solve the issue!
Try this instead
mri_vol2vol --inv --targ M4_LH_orig.mgz --mov
$FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o M4_LH_orig_MNI152.nii.gz
--interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat
On 07/14/2014 02:07 PM,
Dear TRACULA experts
I am writing to ask about an error in pre-processing in TRACULA.
After making FSL radiological header of dwi_orig_flip.nii.gz, an error
occurs.
When the name of file is changed from dwi_orig_flip.mghdti.bvals to bvals,
I can't find the file dwi_orig_flip.mghdti.bvecs.
So an
Dear All,
For longitudinal data sets, is there a way that the lh.pial surface from the
Base can be transformed into the brainmask.mgz space of a Cross so that it can
be viewed with tkmedit on the Cross brainmask.mgz?
Thanks,
Paul
___
Freesurfer
Hi Andrew
What does the ?h.orig look like? And what is the intensity volume in the
background?
Cheers
Bruce
On Jul 14, 2014, at 4:18 PM, Andrew Schoen schoen.andr...@gmail.com wrote:
Hi All,
I am currently running freesurfer on a group of subjects, some of which have
some bright areas
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