ignorance again.
I have now downloaded FSL on VMplayer I also have FS running on Oracle
VM.So my question is if I run dti_recon,will freesurfer automatically
detect FSL,which is running on a different VM.-
Many thanks for your help,
Chikku
On 4 February 2013 16:39, Anastasia Yendiki
You mean the exact command line to delete a folder? It's rm -rf.
On Tue, 5 Feb 2013, std...@virgilio.it wrote:
Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
(/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I have
data.nii.gz bvecs bvals MPRAGE.nii.gz
If I write
Why do you want to rerun recon-all after trac-all? You just need to run it
before trac-all.
On Tue, 5 Feb 2013, std...@virgilio.it wrote:
No, I 'm sorry. I try to reformulate my question.
I have a folder called Diff01 in
my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova)
You could just move the recon-all output directories from the location
where they was originally generated into the Diff01 directory. For the
purposes of running trac-all this should not make a difference.
On Tue, 5 Feb 2013, std...@virgilio.it wrote:
Because initially I have run recon-all
It's looking for files in
/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion
Does this directory actually exist?
On Tue, 5 Feb 2013, std...@virgilio.it wrote:
Thank you very much Shantanu and Anastasia.Now I'm running trac-all but I
have an error:
niiRead(): error opening
I'm guessing that there's some confusion about the instructions in the
tracula tutorial and that you are settin the trainfile variable in your
configuration file to look for a file in that directory. If so, just
delete that line from your configuration file.
On Tue, 5 Feb 2013,
Yes.
On Mon, 4 Feb 2013, Varghese Chikku wrote:
Dear Team,
I tried to run dt_recon and the systems says cannot find
eddy_correct,Make sure FSL is installed. So ,do I need to install the
whole FSL package to run this.
In Thanks
Chikku
___
Do you have a freesurfer recon of your subject's T1 in the $SUBJECTS_DIR?
On Sun, 3 Feb 2013, std...@virgilio.it wrote:
I think that I have resolved the bvecs error by using sudo nano option but
now in the next step I visualize this error:
ERROR: fio_pushd:
Hi Stefano - Are the original bvecs (that you specify in your
configuration file) arranged in 3 rows or 3 columns?
a.y
On Thu, 31 Jan 2013, std...@virgilio.it wrote:
Hi list,
I'm running trac-all -prep -c
but I have this error
dtifit -k
You're very welcome. You can send me your data.nii.gz and I'll try to see
if I can replicate the error. You can send it through here:
http://gate.nmr.mgh.harvard.edu/filedrop2/
On Fri, 1 Feb 2013, std...@virgilio.it wrote:
Yes Anastasia. To check it, I'm attaching the last
Hi Cat - What's the runlist variable set to in the configuration file?
a.y
On Wed, 30 Jan 2013, Cat Chong wrote:
Hello Experts,
Unfortunately I am currently only able to run tracula on a personal
computer, System Version: Mac OS X 10.6.7 (10J869)
Kernel Version: Darwin 10.7.0.
I
Hi Catherine - Yes, for now treat each time point as a different subject
for trac-all purposes. (You can pass the time points' recon-all
directories either before or after longitudinal processing.) However,
there may also be a longitudinal version of tracula coming soon - but you
didn't hear
to run before an analysis can be
added
# to this file.
#
# Original Author: Anastasia Yendiki
# CVS Revision Info:
# $Author: ayendiki $
# $Date: 2010/12/15 08:36:00 $
# $Revision: 1.1 $
#
# Copyright (C) 2010
# The General Hospital Corporation (Boston, MA).
# All rights reserved
values must be specified.
#
# Any other commands that you might want to run before an analysis can
be
added
# to this file.
#
# Original Author: Anastasia Yendiki
# CVS Revision Info:
# $Author: ayendiki $
# $Date: 2010/12/15 08:36:00 $
# $Revision: 1.1
Hi Stefano - The argument of the -c option is a configuration file, not a
directory. For more info on trac-all and setting up the configuration
file, please see the trac-all wiki page:
http://www.freesurfer.net/fswiki/trac-all
and tracula tutorials:
Hi Stefano - Type which trac-all to find out where trac-all lives on
your computer, then copy the updated version over it.
a.y
On Mon, 28 Jan 2013, std...@virgilio.it wrote:
Thank you very much for you kindness Anastasia.
The folder that contains .nii.gz file is correct?
I'm looking the
values must be specified.
#
# Any other commands that you might want to run before an analysis can be
added
# to this file.
#
# Original Author: Anastasia Yendiki
# CVS Revision Info:
# $Author: ayendiki $
# $Date: 2010/12/15 08:36:00 $
# $Revision: 1.1 $
#
# Copyright (C) 2010
Hi Cat - I hope this helps:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25987.html
a.y
On Tue, 22 Jan 2013, Cat Chong wrote:
Hello Experts,
I am running bedpost x through fsl on the dmri directory (as advised in a
previous post). I receive the fsl error message: “child
Hi Salil - It's a well-known (see email archives) compatibility issue with
the newer version of bedpostx, that has different command-line arguments
than it used to. You can run bedpostx directly on the command line for
now. This is solved in the next version of trac-all.
a.y
On Sat, 19 Jan
Hi Cat - Can you please send along your dmrirc file? It's hard to tell
without looking at it.
a.y
On Mon, 14 Jan 2013, Cat Chong wrote:
Hello Experts:
I am running the first pre-processing step in Tracula and come across the
error:
set: Variable name must begin with a letter.
Below
get
this error message.
Thank you very much,
Catherine
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Cat Chong cavecreekcut...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Sent
Hi Cat - 1 out of 18 is the left CST. That one usually isn't hard to
initialize b/c it's not a part of the brain where it's especially
difficult to align a typical individual to the atlas. I'd wait to see the
final outcome before declaring defeat, but is there any chance that the
top of the
have any resources on this?
Thank you again for your help,
Allison
Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu:
Hi Allison - The mri_convert command at the top of your log file is
trying to convert the directory /Users/Desktop/Tracula/diffusion_DTI to
a nifti file. From the name
Hi Allison - The mri_convert command at the top of your log file is trying
to convert the directory /Users/Desktop/Tracula/diffusion_DTI to a nifti
file. From the name of that nifti file, it looks like it's expecting to
find a field map and not finding it.
Hope this helps,
a.y
On Tue, 8 Jan
, or is it
better to delete all folders?
Thanks for you help,
Alessia.
2013/1/6 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
That shows you how many subjects were included in the atlas.
There's a total of 33 subjects in the atlas, and for a general
purpose study there's no reason
That shows you how many subjects were included in the atlas. There's a
total of 33 subjects in the atlas, and for a general purpose study there's
no reason not to use all of them. Did you change the trainlist parameter
in the configuration file at any point?
On Sun, 6 Jan 2013, Alessia
Hi Gerit - The bvecs file that's fed into dtifit has commas instead of
dots as the decimal mark. I'd try setenv LANG en_US.UTF-8 in your unix
environment and rerun to see if that fixes the problem.
Hope this helps,
a.y
On Fri, 4 Jan 2013, Gerit Pfuhl wrote:
Dear all,
despite reading the
Note: Nick's response does not apply to tracula code, where changes can be
expected until the night before the official release.
On Thu, 3 Jan 2013, Nick Schmansky wrote:
Hi,
A beta of the upcoming v5.2 is available here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
that. Is there any
information on that somewhere I could look up?
best wishes,
Prerona
On 21 December 2012 15:47, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
This doesn't look right. Are you certain that your gradient table is
correct? Have you looked at the eigenvectors of the tensor fit
like the pathstats? I knew the tractstats2table
will do the jobs, but it is binarized and hard-coded.
ping
On Thu, Dec 20, 2012 at 5:30 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Ping - The total number of paths that were sampled doesn't enter the
picture. Of these sampled
=jet:isosurface=0,0:color='Red'
)
Here is a screenshot attached. Should I also email you my files?
best wishes,
Prerona
On 20 December 2012 16:44, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Prerona - As I've mentioned to others, you can ignore the Degenerate
spline segment message.
I
meant how to calculate path length based
on path.pd.nii.gz, and the Center and Weight Average of the scalar
images?
Thanks.
On Fri, Dec 21, 2012 at 3:45 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Ping - Are you asking how you can produced the stats? You could use
fslstats
, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Path length: that's independent of any external scalar images.
Weighted average: you multiply with the actual value in path.pd.nii.gz, then
average.
Center average: you average only over the voxels in path.map.nii.gz.
On Fri, 21 Dec 2012
Hi Bryon - I was able to reconstruct the forceps major in your subject
after tweaking some of the 7 control points for the initialization. I'm
attaching the text file with the corrected control points - just drop it
in dlabel/diff and rerun the path reconstruction (don't use reinit,
though!)
control point didn't help. Therefore I
uploaded remaining
images. It would be great if you could have a look again.
All the best,
Arman
On Sat, Dec 1, 2012 at 1:45 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Arman - One more thing. Do you mind sending me the original
it?
Thank you so much for your help!
best wishes,
Prerona
On 12 December 2012 11:57, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
1) Can't hurt to delete.
2) Yes.
3) Yes.
On Wed, 12 Dec 2012, s0675204 wrote:
Hello,
thank you for your help with the first steps of running Tracula
, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
1) Can't hurt to delete.
2) Yes.
3) Yes.
On Wed, 12 Dec 2012, s0675204 wrote:
Hello,
thank you for your help with the first steps of running Tracula.
I was trying to run trac-all step 3 (paths), but was getting an error
Hi Yaniv - What results did you anticipate and what results did you get?
a.y
On Thu, 20 Dec 2012, Yaniv Kaufman wrote:
Dear Freesurfers,
I am not very experienced with Freesurfer and would like to construct a
Diffusion Tensor Image. I have the .bvecs, .bvals and .img files which I
Hi Maia - It would still be probabilistic global tracrography, you'd just
run it without anatomical priors since you don't have any prior knowledge
of what areas your pathway goes through.
For each subject you'd need to define the two end ROIs of the pathway and
(this is the trickier part) an
Hi Andi - I managed to track this down by looking at the complete data set
that you sent me. Your bvals file has no b=0, there's only b=2075 with
some b=5 interspersed. The b=5 volumes must be your baseline volumes but
unfortunately there's no way for the program to know this right now.
As
on the list to run bedpost as:
bedpostx /usr/local/freesurfer/subjects/C001/dmri
is this the same dmri folder as created by tracula step 1 (for each subject)
Thank you so much for your help with this - I really appreciate it
best wishes
Prerona
On 10 December 2012 19:54, Anastasia Yendiki
ayend
wishes,
Prerona
On 8 December 2012 13:38, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
In your dmrirc, you define multiple subjects, but only one bvecfile and one
bvalfile that are used for all subjects.
On Sat, 8 Dec 2012, s0675204 wrote:
the values are the same but each subject
that don't have default values must be specified.
#
# Any other commands that you might want to run before an analysis can be added
# to this file.
#
# Original Author: Anastasia Yendiki
# CVS Revision Info:
#$Author: ayendiki $
#$Date: 2011/05/24 06:47:12 $
#$Revision: 1.3.2.3 $
#
# Copyright
Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Great, I love easy problems :)
On Fri, 7 Dec 2012, s0675204 wrote:
Thank you! It's chugging away now
best wishes,
Prerona
On 7 December 2012 13:46, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Prerona - You need to uncomment
-0.56895911693573 -0.02196817658841 0.51983833312988 0.83259600400924
0.99861049652099 0.85606354475021 0.36184993386268
On 7 December 2012 14:08, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Great, I love easy problems :)
On Fri, 7 Dec 2012, s0675204 wrote:
Thank you! It's chugging
?
best wishes,
Prerona
On 7 December 2012 23:38, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Yes, I can see that each of the bvecs/bvals files is one long line. Was that
the case for the original files that you specified in the dmrirc?
On Fri, 7 Dec 2012, s0675204 wrote:
Hi
-boun...@nmr.mgh.harvard.edu] En nombre de Anastasia Yendiki
Enviado el: 28 November 2012 15:30
Para: Fernando Ventrice
CC: freesurfer@nmr.mgh.harvard.edu
Asunto: Re: [Freesurfer] FW: TRACULA some fiber volumes being too small
Hi Fernando - I looked at your data and changing the sign of the z
28, 2012 at 7:34 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Arman - Have you ruled out any issues with the gradient directions? In
situations where the
problem is wide-spread, this seems to be the usual suspect. If you've
checked the eigenvectors
and they're
Hi Bryon - It does look like this individual and the tract atlas are not
in good alignment. The one step that requires good alignment is for
choosing an initial guess for the pathway. If the fmajor from all or most
of the subjects that are included in the tract atlas goes through the
Hi Arman - Have you ruled out any issues with the gradient directions? In
situations where the problem is wide-spread, this seems to be the usual
suspect. If you've checked the eigenvectors and they're ok, can you send
an example case where the problem persists? You can use this page to
Hi Fernando - I looked at your data and changing the sign of the z
coordinate in your gradient table gave me eigenvectors that looked fine in
both fslview and freeview. Why you would get eigenvectors that look
different in freeview and fslview before flipping z but not after is still
a
Hi Alessia - I'm not sure what you're referring to as the dti mask. Can
you give me the file name of the image that you're displaying in the
screehshot? It does look like noise.
Thanks,
a.y
On Wed, 21 Nov 2012, Alessia Sarica wrote:
Dear Freesurfer Users,I'm a Ph.D. Student and I'm
On Wed, 21 Nov 2012, Alessia Sarica wrote:
Hi Anastasia,thanks for your fast reply.
I mean the file named dtifit_FA.nii
I've re-run twice recon-all and tracula both, but it doesn't change the result.
Best regards,
Alessia.
2012/11/21 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Hi Alessia
Hi Joy-Loi,
You can edit the bedpostx script (make sure you figure out which version
of that script trac-all is calling). Find this line and delete the
@fmrib.ox.ac.uk part:
mailto=`whoami`@fmrib.ox.ac.uk
Hope this helps,
a.y
On Tue, 20 Nov 2012, Loi wrote:
Hello FreeSurfer
Hi Jon - The path.pd volumes are indeed the posterior probability
distributions of each pathway. They are not normalized to a sum of 1
though b/c they're estimated by a sampling algorithm (drawing sample paths
from this unknown distribution and adding up the sample paths, instead of
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Tuesday, October 30, 2012 1:24 PM
To: Fernando Ventrice
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FW: TRACULA some fiber volumes being too small
See screenshot now :)
On Tue, 30 Oct 2012, Anastasia
Hi Fernando - Thanks for uploading your data. Looking at the primary
directions from tensor fit on the data that you sent me (see screenshot),
they seem to be off by a 90 degree angle from what you'd expect them. This
means that your gradient table is probably off as well.
Hope this helps,
Hi Andi - The most common problem that would cause all or almost all
pathways to fail is an incorrect gradient table. You can do a sanity check
on that by looking at the primary eigenvectors from your tensor fit
(dmri/dtifit_V1.nii.gz). See also my answer to Fernando earlier today.
Hope
Hi Crystal - This is because of the way the B0 dewarping script is called
during the pre-processing. It assumes that you have 2 phase images instead
of the difference of 2 phase images (which is what you have). The next
version actually accommodates both cases but for now you have 2 options:
Hi Verena - Which version of freesurfer are you using? In the public
release of 5.1 the CVS registration option in trac-all is disabled.
a.y
On Tue, 23 Oct 2012, Verena Gramse wrote:
From: Verena Gramse
Sent:
Hi Fernando - Thank you for your kind words. You can indeed try the reinit
option as Christofer suggested when one of the pathways looks like a
single curve and not like a volume.
However, because some of your other pathways in the screenshots look a bit
funky too, I would also check that
Hi Joy-Loi - No, all updates that happened since the 5.1 release are
listed here:
http://www.freesurfer.net/fswiki/Tracula
For now it's assumed that all your subjects were scanned with the same
protocol, which is usually the case, unless you're comparing different
protocols. If you
(from Neurodebian)
The first problem I had was with the first command: trac-all -prep -c dmrirc_file gave
an error about not finding the 'job' command. This was solved (thanks to Anastasia Yendiki) using:
set runlist=(1) in the 'dmrirc_file'.
Then, I had some problems with the second command: trac
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Thursday, October 11, 2012 1:50 PM
To: Fernando Ventrice
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA trac-all -path ERROR
Hi Fernando - Can you please send your scripts/trac-all.log file? My guess
in your configuration file, even if you want to process all
subjects on your list. So if you have 5 subjects for example:
set runlist = (1 2 3 4 5)
Hope this helps,
a.y
On Fri, 5 Oct 2012, Fernando Ventrice wrote:
Dear Anastasia Yendiki,
I have been trying to use TRACULA and I think I'm
that the first time I run trac-all (without
specifying the bvecs and bvals), the bval file generated seems to list
the values twice. ie:
0
0
7
7
7
7
0
0
7
7
7
7
I hope this make sense. Thank you,
Joy-Loi
On 9/27/12, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote:
Thanks
lateralized in most
of our analyzed data. Here is the post about this issue:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024541.html
Is it also OK with Tracula?
Thank you in advance,
Gabor
2012/9/27 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu:
Hi Gabor - Tracula
tried removing the empty lines and rerunning trac-all -prep,
but the error persists.
Joy-Loi
On 9/28/12, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote:
There are 10 empty lines at the end of your Tbvecs.txt file. Can you try
removing those and reruning?
Hope this helps,
a.y
Hi Juke - I apologize for the late response. I was away and I'm still
catching up on email.
It looks like it fails while it's loading the atlas data (here the 4th out
of 33 atlas subjects). Does this happen in other cases? Are the cases that
fail running on a machine with less memory than
Hi Akvile - Sorry for the late response, I was out of town for a bit.
At first glance it looks like all the tracts are stuck where they're
initialized. This might happen occasionally for a tract if initializing it
is tricky (i.e., if the subject is not well aligned to the atlas, if the
brain
Hi Clare - Sorry for responding late to any email that was sent while I
was away.
The fmajor and slft are sometimes tricky in their initialization b/c of
their high curvature. The initial guess for the path is chosen from the
atlas and if it's not well-aligned and veers off the subject's
Hi Gabor - Tracula doesn't use the BA labels, only the labels in the
aparc+aseg. I hope this answers your question.
a.y
On Sun, 16 Sep 2012, Gabor Perlaki wrote:
Dear Anastasia,
Earlier I was posted an issue about BA44/pars triangular:
Hi Joy - How were your bvecs and bvals files generated? In the past some
people have had problems with files exported from Excel b/c it generates
text files with Windows-specific end-of-line characters that cannot be
read properly on Linux. Do the files look normal when you run more on
them
and gradient tables I make (I originally didn't
specify these, and got the same error message), new bvecs and bvals
are generated in the trac-all -prep process, leading to the error.
Thank you,
Joy-Loi
On Thu, Sep 27, 2012 at 7:30 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Joy
, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Natalia - This is an error that will occur if lowb_brain_mask
does not exist. The command that generates lowb_brain_mask is
bet - can you find that line in the log file and run it
directly on the command line and see if you
, Aug 23, 2012 at 1:48 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Natalia - I'd need to see at which point in the processing
the error occurs, since this is a very generic error message.
Can you please include your trac-all.log and dmrirc?
Thanks,
a.y
Chicago, IL 60611
On Thu, Aug 23, 2012 at 2:08 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Can you please check that the x-y-z dimensions of the bedpostx
output files are the same as the dimensions of the DWIs?
On Thu, 23 Aug 2012, Natalia Sánchez wrote
Hi Knut - Does merged_ph1samples.nii.gz exist in your dmri.bedpostX
directory? It's one of the bedpostx output files. If not, it means
bedpostx did not finish running properly. You can try running bedpostx
directly on the dmri directory, not through trac-all -bedp.
Output files of bedpostx
Hi Richard - In the listing you sent below I do see the a
nodif_brain_mask.nii.gz and a control.dat, although I have no idea what
control.dat is. As for data.nii.gz, it should be created as a symbolic
link to dwi.nii.gz, since bedpostx indeed expects it to be called data.
I have not seen
running bedpostx. Then everything should run normally.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki
[ayend...@nmr.mgh.harvard.edu]
Sent: Thursday, August 16, 2012 4:24 PM
To: Richard
of the above.
Thanks for your help eveyone
Richard
On Thu, Aug 16, 2012 at 2:24 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
The symlinks are actually created in the -bedp step, not the
-prep step. If you're running bedpostx outside of trac-all, you
need to create them
Hi Chris - That's probably the corpus callosum forceps major or minor.
It's the highest-curvature path and that makes it harder to initialize the
tractography. If it looks right visually, and it took 90 tries to do that,
then it's doing its job as it's supposed to :)
a.y
On Mon, 13 Aug 2012,
There will not be any intermediate releases of trac-all before the
freesurfer 5.2 release. A few different things are being changed at the
same time and releasing a half-tested version would possibly cause more
problems than it'd solve. ETA of 5.2 is within the next few months but I
can't
Do these files that it's trying to load exist? If not, the actual error
happened earlier, when they were being generated. Looking at the entire
trac-all.log instead of just the end might shed some light on this.
On Fri, 10 Aug 2012, Natalia Sánchez wrote:
Hi!I am running tracula for the
Ave, Suite 1100
Chicago, IL 60611
On Fri, Aug 10, 2012 at 4:28 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
dtifit_FA.fl
t.nii.gz
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu
Hi Juke - The end ROIs are obtained by dilating the end points of the
training streamlines from the tract atlas and finding their intersection
with the cortex of the test subject.
Hope this helps,
a.y
On Thu, 9 Aug 2012, Juke Cha wrote:
Hi,
I'm wondering if I can get any information
Costa
On Mon, Jul 30, 2012 at 5:36 PM, Anastasia Yendiki ayendiki@nms
r.mgh.harvard.edu wrote:
Hi Gonzalo - This has come up a few times recently. Please see here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23064.html
Hope this helps,
a.y
will. Thanks for your help! :)
Sergio.
2012/7/30 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Hi Sergio - Sorry, if this occurs independently of
trac-all, whenever you run bedpostx directly, you're
better off asking for help on the FSL list. We've never
run
as before :(
2012/7/27 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
The monitoring script that bedpostx runs and tells you if things
have or haven't finished properly can't always be trusted. So if
that's the only error message you see, I wouldn't worry about
it. Have the *ph1
Hi Gonzalo - This has come up a few times recently. Please see here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23064.html
Hope this helps,
a.y
On Mon, 30 Jul 2012, Gonzalo Rojas Costa wrote:
Hi:
I ran trac-all -prep -c dmrirc and it finished ok... Then, when I
tried
, so I run the script that checks that: bedpostx_datacheck, the
output (n3-bedpostx-datacheck.txt) doesn't show any signs of errors so I
would like to assume everything is ok with the input data...
Any idea?
Thanks, once again.
Sergio.
2012/7/27 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Hi Sergio - Thank you for your kind words, and also thank you for taking
the time to search the archives for answers!
The first problems you had with running bedpostx through trac-all have to
do with trac-all assuming an older version of FSL than the current one,
and this'll be fixed in the
-9678
kjyo...@uchicago.edu
On Fri, Oct 7, 2011 at 10:04 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Judit,
1. If you can run bedpostx directly then you should do:
bedpostx /usr/local/freesurfer/subjects/C001/dmri
Note that this dmri directory
Hi Gonzalo - You'll find some recent emails on this in the archives. In
short, you can try deleting a few lines from the file:
$FREESURFER_HOME/trctrain/trainlist.txt
For every line you're deleting, you're removing a subject from the tract
atlas that tracula uses. There are currently 33
Hi Rui - You can ignore the message about spline segments, it's fine.
For the directory structure and where to find your files, I'll refer you
to the trac-all wiki page (see section Outputs from trac-all -path):
http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all
Hope this helps,
a.y
Hi Michael and Jürgen - This issue has been resolved, see Updates:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
It had to do with the original mac executables having been compiled on an
older version of MacOS, which was not smart about utilizing all the memory
on your computer. If
-- Forwarded message --
From: Rui Lavrador ruilavra...@gmail.com
Date: 2012/7/16
Subject: Re: [Freesurfer] Memory allocation problem trac-all
-prior
To: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Hi Anastasia,
Each diffusion
Hi Rui - How many voxels are in your diffusion volume? How many of them
are inside the mask?
a.y
On Thu, 12 Jul 2012, Rui Lavrador wrote:
Hi all,
I'm running tracula and when doing the step:
trac-all -prior -c single_subject
After some time it gives this error:
MRIalloc(218, 182,
Hi Torben - I'm looking at all the invocations of trac-all -prep in your
log file, and they've both exited with an error (the same bvecs error).
grep prep trac-all.log
-prep -c /Users/torben/Desktop/tracon/tracon
New invocation of trac-preproc
Hi Minjie - These commonly used measures are provided for your
convenience. You can always use the reconstructed path distribution volume
path.pd.nii.gz, thresholded or not, as a mask to average your measurement
of choice.
a.y
On Thu, 28 Jun 2012, Minjie Wu wrote:
Dear TRACULA Developer
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