Ack. Can't believe I missed that. Thank you. I'll run it again and see how
that turns out.
On Thu, Dec 11, 2014 at 2:07 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Thomas - No bother at all! If you search for the word error in your
trac-all.log, you'll see that it couldn't
Hi Thomas - No bother at all! If you search for the word error in your
trac-all.log, you'll see that it couldn't find the MNI template, which
means that some of the pre-processing steps did not complete. You can
either remove the mnitemp line from your configuration file (so that it
uses the
Hi Nawaf - The first error occured much earlier in the log file. Your
gradient table file could not be found. Did you set the bvecfile variable
in your configuration file?
a.y
On Fri, 29 Mar 2013, Nawaf Yassi wrote:
Hi Anastasia
Thanks for your reply
Here is the file attached (I have
Hi Nawaf - Can you please send your trac-all.log? It's possible that the
problem started at an earlier step.
Thanks,
a.y
On Thu, 28 Mar 2013, Nawaf Yassi wrote:
Dear mailing list
I am encountering an error at the trac-all –path stage of a tracula analysis
(the
first two stages on
Hi Stefano - What are the contents of the bedpostX output directory? In
your case, that'd be this directory:
/Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX
a.y
On Mon, 11 Feb 2013, std...@virgilio.it wrote:
Hi list,
I'm running trac-all -path -c
Hi list,
I'm running trac-all -path -c $FREESURFER/dmrirc_single_subject but I have this
error:
Loading mask from
/Applications/freesurfer/subjects/subject_prova/Con02/dlabel/diff/aparc+aseg_mask.bbr.nii.gzLoading
BEDPOST parameter samples from
Wonderful - thank you. That seemed to fix the problem.
Kiely
On Fri, May 18, 2012 at 3:25 PM, Priti Srinivasan
rspr...@nmr.mgh.harvard.edu wrote:
Hi Kiely,
In your terminal (after sourcing the freesurfer environment) type the
following:
gedit $FREESURFER_HOME/bin/trac-preproc (use pico
That seemed to fix the registration issue, but I'm still unable to
reconstruct the tracts using trac-all -path. I'm getting the same error
that the control points are not within the mask. THis happens for all
tracts.
Thanks,
Kiely
On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
Were the old .mat files replaced with the new ones?
On Fri, 18 May 2012, Kiely Madhavan wrote:
That seemed to fix the registration issue, but I'm still unable to
reconstruct the tracts using trac-all -path. I'm getting the same error that
the control points are not within the mask. THis
I only created a diff2anat.flt.mat file which replaced the old one. Do they
all need to be recreated? If so, is that something I add to the command
line?
On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Were the old .mat files replaced with the new ones?
The other registration files depend on diff2anat. For example, diff2mni is
composed of diff2anat and anat2mni. If you're using the old diff2mni,
it's like you didn't change anything.
The -intra step creates all these. You need to edit the command that
generates the diff2anat in your version
OK - Can you point me in the direction of the trac-preproc file that I
should edit?
On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
The other registration files depend on diff2anat. For example, diff2mni is
composed of diff2anat and anat2mni. If you're
This is a script, it's in the directory where all freesurfer scripts are.
You can find it by doing which trac-preproc.
On Fri, 18 May 2012, Kiely Madhavan wrote:
OK - Can you point me in the direction of the trac-preproc file that I should
edit?
On Fri, May 18, 2012 at 12:18 PM,
That's where I looked, but all I see is the following (I don't see the
command line that creates the diff2anat for me to edit):
Last login: Fri May 18 13:45:47 on ttys000
/Applications/freesurfer/bin/trac-preproc ; exit;
Kielys-MacBook-Air:~ kielydonnelly$
This is the help text that you get when you run the script. You need to
open the script in a text editor.
On Fri, 18 May 2012, Kiely Madhavan wrote:
That's where I looked, but all I see is the following (I don't see the command
line that creates the diff2anat for me to edit):
Last login:
Hi Kiely,
In your terminal (after sourcing the freesurfer environment) type the
following:
gedit $FREESURFER_HOME/bin/trac-preproc (use pico if you're using mac, you
can also use other editors like vi or emacs)
This will open up trac-preproc script in a text editor.
you can scroll through to
Hi Priti - Thanks for your help. The inter-subject registration seems to
have run OK, but there must be something wrong with the intra-subject
registration. When I try to view it using freeview, it's completely dark -
I don't see a brain at all. Is there a way to troubleshoot this?
Thanks,
Kiely
Hi Kiely - Looks like you used flirt for the intra-subject registration,
so you can look in trac-all.log for the flirt command line that registers
diffusion to anatomical and play around with the parameters.
You can also use bbregister instead of flirt for the intra-subject
registration -
Kiely, For flirt, try using corratio, cost function instead of mutualinfo
(which is the default in trac-all) to see if that solves your registration
problem.
Hi Kiely - Looks like you used flirt for the intra-subject registration,
so you can look in trac-all.log for the flirt command line that
Is this something I can change in my dmrirc file or do I need to run flirt
on it's own?
Thanks,
Kiely
On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan
rspr...@nmr.mgh.harvard.edu wrote:
Kiely, For flirt, try using corratio, cost function instead of mutualinfo
(which is the default in
No, this is something you have to try yourself on the command line. If you
want to make the change permanent, you can edit the relevant line in
$FREESURFER_HOME/bin/trac-preproc.
On Wed, 16 May 2012, Kiely Donnelly wrote:
Is this something I can change in my dmrirc file or do I need to run
you have to run flirt commandline separately to check if it solves your
problem.
Is this something I can change in my dmrirc file or do I need to run flirt
on it's own?
Thanks,
Kiely
On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan
rspr...@nmr.mgh.harvard.edu wrote:
Kiely, For
I tried using corratio and it seems to have fixed the registration issue.
I'm very new to this so just want to make sure I did it correctly before I
move forward. Should the command line look something like this if I am
running it in this individuals dmri directory:
flirt -in dwi_orig.nii.gz
The .mat registration matrix should be saved under dmri/xfms/.
On Wed, 16 May 2012, Kiely Donnelly wrote:
I tried using corratio and it seems to have fixed the registration issue.
I'm very new to this so just want to make sure I did it correctly before I
move forward. Should the command line
Hi Kiely,
Have you checked your inter and intra subject registrations? The control
points going off the dwi is not only for one paths but for all the paths.
If the registration goes terribly wrong, this can happen. You can take a
look at
/dmri/lowb_brain_anat.flt.nii.gz (For intra subject
Hi, I'm getting the same error as before; merged_ph1samples.nii.gz
isn't getting created, I think. This is after I ran bedpostx on its own,
per your instructions from this thread.
Here are the last few lines of output from trac-all -path:
Loading BEDPOST parameter samples from
Hi Chris,
The diff_slices folder is still there, which means that bedpostX probably
did not finish processing. That folder usually gets deleted after bedpostX
processing completes. It's strange that you have merged_ph2samples.nii.gz
and not merged_ph1samples.nii.gz.
Did you accidentally run
Yes, I figured out that I had previously run trac-all -bedp and it
created data_slice_0002. I deleted this directory, and bedpostx
finished, but now I get this error from trac-all-path:
Segmentation fault (core dumped)
/parietal/freesurfer/current/bin/dmri_mergepaths --indir
So I'm assuming that you don't have any issues merged_ph* files anymore?
As far as the error below is concerned, this is typically the last step in
trac-paths, where it should merge all the 18 tracts to create a 4D tract
volume for visualization. The input for this should be all the 18
posterior
Hello, I successfully ran trac-all -bedp, and when I run the next step I
get the following error:
Loading BEDPOST parameter samples from
/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX
niiRead(): error opening file
What's in the diff_slices directory? That's a temporary directory that
bedpostx creates and that gets deleted after the results get merged. So
my guess would be that bedpostx didn't finish processing.
On Fri, 23 Mar 2012, Chris Watson wrote:
Hello, I successfully ran trac-all -bedp, and when
[freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/
dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz
mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz
th1samples.nii.gz
Come to think of it, when I ran bedpostx, it only output 1 slice
processed,
Oh, ok. That's a known issue, it has to do with changes in the command
line of the latest version of bedpostx. We've updated trac-all and it'll
be working in our next release but for now you'll have to run bedpostx by
itself and not through trac-all. Sorry for the inconvenience!
On Fri, 23
Ok. Do I run it with the defaults?
# fibers per voxel = 2
ARD weight = 1
burn-in period = 1000
# jumps = 1250
sample every = 25
On 03/23/2012 01:22 PM, Anastasia Yendiki wrote:
Oh, ok. That's a known issue, it has to do with changes in the command
line of the latest version of bedpostx. We've
Yes.
On Fri, 23 Mar 2012, Chris Watson wrote:
Ok. Do I run it with the defaults?
# fibers per voxel = 2
ARD weight = 1
burn-in period = 1000
# jumps = 1250
sample every = 25
On 03/23/2012 01:22 PM, Anastasia Yendiki wrote:
Oh, ok. That's a known issue, it has to do with changes in
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