much.
Minjie
On Thu, Jun 28, 2012 at 11:05 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
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
Not sure if this is the simplest way but mri_convert --split, followed by
mri_concat, should do it. You'll also have to remove the respective
gradient directions from the gradient file.
Hope this helps,
a.y
On Wed, 27 Jun 2012, Drottar, Marie wrote:
I have a DTI dataset with 10 b0 and
Hi Torben - I just scrolled to the end of your log file. The last
invocation of trac-all -prep is the one that failed b/c of the bvecs
error. Did you rerun trac-all -prep after you fixed the bvecs?
Thanks,
a.y
On Tue, 26 Jun 2012, Torben Prokscha wrote:
Hi Priti,
thank you for your reply,
Hi Maria - Do you at any point get the following warning?
WARN: CVS template is not unavailable in the current version
Thanks,
a.y
On Wed, 20 Jun 2012, Maria Gemzicka wrote:
Hi,
I run -corr and -intra with no errors. -inter finishes without errors if
does not use doregcvs.
When I
Oops, that's a typo, meant is unavailable. In any case something like
this should show up early in the logs.
On Wed, 20 Jun 2012, Bruce Fischl wrote:
not unavailable
On Wed, 20 Jun 2012, Anastasia Yendiki wrote:
Hi Maria - Do you at any point get the following warning?
WARN: CVS
and bval from the DICOM
header?
thank in advance.
Xiangzhen Kong
From: Anastasia Yendiki
Date: 2012-02-04 00:52
To: Xiangzhen Kong
CC: freesurfer
Subject: Re: [Freesurfer] /path/to/dmri/dwi_orig_flip.mghdti.bvecs
This is going to be updated in the next version of freesurfer. There have
been some compatibility issues with the latest version of bedpostx that
we've had to fix. For now please run bedpostx by itself. Thanks!
On Fri, 25 May 2012, Gabor Perlaki wrote:
Dear Priti
The bedpostx works fine
. THis happens for all tracts.
Thanks,
Kiely
On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
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
, 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?
On Fri, 18 May 2012, Kiely Madhavan wrote:
That seemed to fix the registration issue
, 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 using the old diff2mni, it's like you didn't change anything.
The -intra step creates all these. You need
of this script and exit
-help : print full contents of help
logout
[Process completed]
On Fri, May 18, 2012 at 1:59 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
This is a script, it's in the directory where all freesurfer scripts are. You
can find it by doing which
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 -
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
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 Gabor - The input DWIs can be in any format that can be read by
mri_convert, including the NIfTI format. The gradient directions should be
in voxel coordinates, like the ones used by FSL. I don't have experience
with dcm2nii, but if you have original DICOM files, you can pass those as
the
with
the standard DTI accurate and TRACULA able to extract the bvals and bvecs
from the dicom files?
Thanks,
Gabor
2012/5/10 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Hi Gabor - The input DWIs can be in any format that can be read
by mri_convert, including the NIfTI format
Hi Carolina - Tracula is not an exploratory method for tractography from
any seed region of your choice. It reconstructs a specific set of 18
tracts.
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
http://www.frontiersin.org/neuroinformatics/10.3389/fninf.2011.00023/abstract
a.y
On Fri, 4
Hi Andi - I'm pretty sure we were already planning to change some of the
mutualinfo's to corratio's in the next release, so no, this is in no way
an official endorsement!
a.y
On Tue, 1 May 2012, Andi Heckel wrote:
Dear Tracula Team,
i noticed that TRACULA uses fsl's flirt with mutualinfo
Hi Knut - If I understand correctly, your modification was replacing
fsl_sub_seychelles with fsl_sub?
a.y
On Fri, 27 Apr 2012, Knut J Bjuland wrote:
Hi
I am trying to run Trac-all on a cluster with PBS/torque. The trac-all
scripts was modified to run with qsub, but
the second stage in
, Anastasia Yendiki wrote:
Hi Knut - If I understand correctly, your modification was replacing
fsl_sub_seychelles with fsl_sub?
a.y
On Fri, 27 Apr 2012, Knut J Bjuland wrote:
Hi
I am trying to run Trac-all on a cluster with PBS/torque. The trac-all
scripts was modified
, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Viviana - I cannot replicate this on our systems but I think
I know what your system may be fussy about and I'll amend it.
For now, if you don't get any outputs can you please try running
bedpostx directly on
/media
On Wed, Apr 18, 2012 at 1:18 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Viviana - I suspect it may be b/c you're using the 2mm-resolution MNI
template brain, and our atlas was built using the 1mm one. From your
dmrirc file:
# MNI template (the only option
Hi Richard - I'd check your bedpostx output files, run mri_info on them to
make sure they have the right number of slices. The monitoring script that
produces the slices processed messages checks only every once in a
while, so you won't see a separate message for each slice.
The warnings
Hi Fabricio - You can only use the formats supported by mri_convert:
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert
Dicom or nifti is recommended.
Hope this helps,
Anastasia.
On Thu, 19 Apr 2012, fabricio feltrin wrote:
Hi Anastatia.
Is it possible to use REC/PAR images from philips
:03:33 CEST 2012
2012/3/27 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu:
Ciao Sarina - The problem is here fslorient: Command not found. You have
to make sure that FSL is properly installed and the FSL executables are in
your path, as trac-all calls a few of them.
Hope this helps,
a.y
On Tue
anything wrong!
Thank you!
Viviana Siless
--
Parietal Team, INRIA Saclay
Neurospin, Centre CEA de Saclay
91191 Gif sur Yvette – FRANCE
On Thu, Apr 5, 2012 at 7:38 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Viviana - If you upload this data set I'm happy to look
Hi Juke - Impossible to tell without looking at the output for the
specific cases. Could you send the entire trac-all.log file for one of
them?
Thanks,
a.y
On Thu, 5 Apr 2012, Juke Cha wrote:
Hi all,
Running TRAC-ALL - PATH, I've got a error. Strangely trac-all reports all
jobs done
Hi Viviana - If you upload this data set I'm happy to look at it.
Also, I strongly recommend getting the updated version of trac-all from
the wiki (I'm guessing from the log file that you're probably not using
that?) See 2012/01/09 update here:
Hi Gabor - If you provide the DWI dicoms directly, tracula uses
mri_convert to convert them to nifti, and mri_convert doesn't read
directions from the header, it looks them up from:
$FREESURFER_HOME/diffusion/mgh-dti-seqpack/
This should be fine assuming you use the same standard
Note that tracula doesn't extract from the atlas the exact spatial
location of the tracts. It only extracts which anatomical labels are the
neighbors of the tract at each point along its trajectory. So it's not as
sensitive to misregistration as a voxel-based analysis would be. Our paper
Trackvis does deterministic tractography, not probabilistic.
Which previous results do you want to use and why?
On Wed, 28 Mar 2012, Antonella Kis wrote:
Dear FS experts,
I would like to know if for a Diffusion tensor imaging (DTI) tractography
study
with TRACULA I can use my previous
Ciao Sarina - The problem is here fslorient: Command not found. You have
to make sure that FSL is properly installed and the FSL executables are in
your path, as trac-all calls a few of them.
Hope this helps,
a.y
On Tue, 27 Mar 2012, Sarina Sacco wrote:
quando avvio il trac-all (relase
Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as
input to freesurfer.
a.y
On Mon, 26 Mar 2012, Johnson wrote:
Hi FS expert
I need to know the transformation matrix itself since I will do the
transformation in matlab.
I successfully transformed white matter fibers
, Anastasia Yendiki wrote:
Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as
input to freesurfer.
a.y
On Mon, 26 Mar 2012, Johnson wrote:
Hi FS expert
I need to know the transformation matrix itself since I will do the
transformation in matlab.
I
used ?
JG
On 03/26/2012 12:24 PM, Anastasia Yendiki wrote:
Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used
as
input to freesurfer.
a.y
On Mon, 26 Mar 2012, Johnson wrote:
Hi FS expert
I need to know
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
, it only output 1 slice processed,
but repeated 70 times, or however many slices there are. The data is from a
Siemens 3T, by the way.
On 03/23/2012 01:16 PM, Anastasia Yendiki wrote:
What's in the diff_slices directory? That's a temporary directory that
bedpostx creates and that gets deleted
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
Hi Martijn - You could check how the ILF of the atlas subjects aligns with
your subject's anatomical segmentation. These files are all in MNI space
here:
dlabel/mni/aparc+aseg.nii.gz
dlabel/mni/aparc+aseg_mask.nii.gz (dilated version used as a brain mask)
dlabel/mni/lh.ilf_*_histo.nii.gz
Hi Andi - Thanks for your kind words!
As explained on the trac-all wiki page (and also the help text you get
from trac-all --help), the part about not submitting trac-all with
pbsubmit is specific to our local Martinos Center users.
That's b/c we've modified fsl_sub (and bedpostx) to work
Hi Minjie - There was no attachment to your email. The fmajor issue that
you're describing sounds like an initialization issue. That single curve
that you describe is where the algorithm starts at and b/c something is
wrong with it, it doesn't move from there. Does the curve seem to go into
a
16 11:45:26 CET 2012
I run TRACULA on Mac OS X 10.6.8, and I have 4GB of memory. Is it
really a memory error or something else?
Thank you,
Tanja.
On Wed, Feb 15, 2012 at 8:02 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
When I look at them with the more command on a linux
ok to me. I can't find the problem.
I attach the files, could you please take a look on them?
Thank you very much,
Tanja.
On Tue, Feb 14, 2012 at 7:31 PM, Tetiana Dadakova tetian...@gmail.com wrote:
I see, thank you :)
On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki
ayend
Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first
guess, too. Does this lowb.nii.gz actually exist? Anything looks strange
when you run mri_info/freeview/fslview on it?
a.y
On Wed, 15 Feb 2012, Chris Watson wrote:
Hello, in running trac-all -prep, I get an error saying
Anastasia Yendiki wrote:
Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first
guess, too. Does this lowb.nii.gz actually exist? Anything looks strange
when you run mri_info/freeview/fslview on it?
a.y
On Wed, 15 Feb 2012, Chris Watson wrote:
Hello, in running
0.400017.8426
0. 0. 0. 1.
It looks normal in fslview/freeview.
Chris
Anastasia Yendiki wrote:
Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my
first
guess, too. Does this lowb.nii.gz actually exist
.
I attach my configuration file and the command I use is trac-all
-prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc
.
I also attach a picture of my file tree and a track-all.log file.
Thank you for your time and help,
Tanja.
On Fri, Feb 3, 2012 at 2:21 AM, Anastasia
and a track-all.log file.
Thank you for your time and help,
Tanja.
On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Tanja - The file is supposed to be created under
$dtroot/$subjectname/dmri/bvecs. If it's trying to create it as
/dmri/bvecs
On Fri, Dec 23, 2011 at 2:42 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Kiely - It's strange that bepostx would create ph2samples
and not
ph1samples. These are the orientation angles for the 2
anisotropic
!
2012-02-04
Xiangzhen Kong
·¢¼þÈË£º Anastasia Yendiki
·¢ËÍʱ¼ä£º 2012-02-04 00:48:58
ÊÕ¼þÈË£º Xiangzhen Kong
³ËÍ£º freesurfer
Ö÷Ì⣺ Re: [Freesurfer] What does trac-all do on the file 'bvecs'?
When the DWIs are transformed to LAS and processed with eddy_correct, the
same
When the DWIs are transformed to LAS and processed with eddy_correct, the
same transformations are applied to the respective bvecs.
On Fri, 3 Feb 2012, Xiangzhen Kong wrote:
Hi, all~
I use trac-all with .nii data, not dicom. So I have to specify the bvecs and
bvals in the config file.
Unless your dicoms came from the same acquisition as the default
MGH/Siemens one, you'll have to set bvecfile and bvalfile and provide
those files yourself.
On Fri, 3 Feb 2012, Xiangzhen Kong wrote:
Hi all
Now I am learning the trac-all using with DICOM data, but came across a
problem.
+++
Hi there - First of all, let me clarify that the new and old trac-all have
no differences in terms of usage, so all of this applies to both.
1. Yes, we did come across the issue of jot not being part of some
platforms. It'll be fixed in the next release. If you're getting this
error,
Hi Tanja - The file is supposed to be created under
$dtroot/$subjectname/dmri/bvecs. If it's trying to create it as
/dmri/bvecs, this means that something wasn't defined correctly. What is
the exact trac-all command line that you're using? And your configuration
file if you're using one?
a.y
See: mris_divide_parcellation --help
On Wed, 18 Jan 2012, Ritobrato Datta wrote:
Is there a way to divide a surface label like V1 into equal parts (say 10
parts) either along its length or width and save each part as a separate
label ? Drawing them in tkmedit is quite crude and not very
Hi Kiely - It's strange that bepostx would create ph2samples and not
ph1samples. These are the orientation angles for the 2 anisotropic
compartments, so if there's a 2nd there should be a 1st. Have you asked
about it on the FSL list?
a.y
On Thu, 22 Dec 2011, Kiely Donnelly wrote:
Hi
Hi Scott - Are there any files created directly under dmri.bedpostX?
a.y
On Fri, 16 Dec 2011, Scott Hayes wrote:
Hi,
After I run step 2 of tracula (trac-all -c config_DTI_B.txt -bedp), I
am missing multiple bedpost output files (e.g., mergedph1samples.nii).
Examining the output, it looks
nodif_brain_mask.nii.gz
bvecs diff_slices monitor xfms
--Scott
Anastasia Yendiki
Fri, 16 Dec 2011 09:43:47 -0800
Hi Scott - Are there any files created directly under dmri.bedpostX?
a.y
On Fri, 16 Dec 2011, Scott Hayes wrote
file -t
ERROR: Could not open image -t
Image Exception : #22 :: Failed to read volume -t
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
On Fri, Dec 9, 2011 at 12:44 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Scott - Here are the tracula executables
Ok, I just checked the 4.1.4 version of fslstats, and indeed it doesn't
have the -t option. We're using version 4.1.5.
On Mon, 12 Dec 2011, Scott Hayes wrote:
Hi,
I'm using FSL 4.1.4
On Mon, Dec 12, 2011 at 12:43 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Scott - Which
Hi Catherine - Sorry, no hidden options there! We currently have the 18
pathways listed in the tutorial and in our paper. To add another pathway,
it'd have to be labeled manually in the subjects that are part of our
atlas.
a.y
On Thu, 8 Dec 2011, Cat Chong wrote:
Hello Experts,
I would
Nope, sorry about that. The reason for keeping them separate is that the
middle step is running bedpostx. It's the lengthiest step and we typically
run it on a cluster. When run on a cluster it's parallelized by slice, and
the other 2 steps are parallelized by subject. One could try to queue
Hi - It's $FREESURFER_HOME/trctrain/trainlist.txt. Note the underscore. In
any case this is the default, so you don't have to specify trainfile in
your dmrirc unless you're using something else.
a.y
On Tue, 6 Dec 2011, C. Paula de los Angeles wrote:
Hi,
I am using TRACULA for the first
Oh yeah, that too. Tracula came out in 5.1.
On Tue, 6 Dec 2011, Nick Schmansky wrote:
i dont think those files are in v5.0.0. you will need to download v5.1.
n.
On Tue, 2011-12-06 at 17:12 -0500, C. Paula de los Angeles wrote:
Hi,
I am using TRACULA for the first time, and I am having
and a more generous bet threshold. Even with these changes I still
saw the problem with the bbregister version of a tract. Is there anything
else I should check/change?
Thanks again,
-Tyler
On Nov 30, 2011, at 4:00 PM, Anastasia Yendiki wrote:
Hi Tyler - Sometimes this happens if the brain
else I should check/change?
Thanks again,
-Tyler
On Nov 30, 2011, at 4:00 PM, Anastasia Yendiki wrote:
Hi Tyler - Sometimes this happens if the brain mask (which will come
either from the FS recon or from the DWIs themselves, depending on your
settings) is missing part of that tract (usually
generous bet threshold. Even with
these changes I still saw the problem with the bbregister version of a
tract. Is there anything else I should check/change?
Thanks again,
-Tyler
On Nov 30, 2011, at 4:00 PM, Anastasia Yendiki wrote:
Hi Tyler - Sometimes this happens if the brain mask (which
Hi Alex - It looks like your bvecs/bvals files were saved from a windows
program? The end-of-line characters are not recognized by linux (try
running the more command on them, for example, to see the problem).
Re: your other question, I don't know what files your other processing has
created.
Hi Tyler - Sometimes this happens if the brain mask (which will come
either from the FS recon or from the DWIs themselves, depending on your
settings) is missing part of that tract (usually one of the end region).
Have you checked your brain masks?
a.y
On Wed, 30 Nov 2011, Tyler Blazey
Hi Peter - The format for the bvec and bval files is explained in:
$FREESURFER_HOME/bin/dmrirc.example
If you've structured your dmrirc following this example file and you're
still getting this error, please send the following so I can debug this:
- your exact trac-all command
Hi Peter - Each of the volumes in your DWI series was acquired with a
certain b-value and a certain diffusion gradient direction. These have to
be in the bvals and bvecs files, respectively, in the same order. This
means for every volume in the DWI series, there'll be 1 number in bvals
and 3
1. Currently trac-all uses only the MNI template, not CVS. So yes, all
steps apply.
2. See the tracula tutorial, section outputs from tracula, to see where
to find the MNI-space outputs.
3. What clusters are you talking about? Do you want to do a voxel-based
analysis? If so, why are
FSLv4.1.4. I take it that we are due for an upgrade? Is there a
minimum version number that we should be using in order for
bedpostx to run smoothly?
Thanks again,
~SB
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Wednesday
this step? We are fairly in
the dark with this function over here, so any help / hints you can provide
would be wonderful. Please let me know if you need more information.
Thanks again for your help and patience,
~Shannon B.
-Original Message-
From: Anastasia Yendiki [mailto:ayend
Hi Shannon - Does the original bedpostx run fine on your cluster? You'd
probably have to edit that to get it to work, it's not made to work on
every possible cluster. Bedpostx_seychelles is the modified version that
tracula calls that I've modified from the original FSL version so that it
:07 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Ansgar - Most likely everything is fine. Sometimes the script that's
built into bedpost
to monitor its progress gives this error but in fact everything has ran
fine. You should
check that all the outputs
FLIRT seem OK.
It appear the problems are not simply due to the poor segmentation
from the T1 recon-all.
Any further suggestions?
BR,
Ping
On Fri, Oct 14, 2011 at 11:04 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Ping-Hong,
Yes, you can set usemaskanat = 0 in your dmrirc
.
ping
On Wed, Oct 19, 2011 at 2:52 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Ping - Do the corresponding brain masks in diffusion space
(dlabel/diff/aparc+aseg_mask.bbr.nii.gz and aparc+aseg_mask.flt.nii.gz) now
cover the entire brain well, after the aparc+aseg fixes?
a.y
Hi all - Since a few of you have inquired about a TRACULA reference in the
past, here's one:
http://www.frontiersin.org/neuroinformatics/10.3389/fninf.2011.00023/abstract
There's a link on the right where you can download the PDF. Happy reading!
a.y
(by setting
usemaskanat = 0? ) so I get around the T1 segmentation problem from
FS recon?
It seems that there is no quick answer on fixing the aparc+aseg?
Thank you,
p
On Tue, Oct 11, 2011 at 10:35 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
I'll have to refer you back
Hi Joana - You can try our in-house tool for within-subject registration,
bbregister, with the --dti option.
a.y
On Thu, 13 Oct 2011, Joana Braga Pereira wrote:
Dear FreeSurfers,
I'm trying to coregister FA images pre-processed with FSL to Freesurfer,
however i'm having a few problems and
Sent: Friday, September 23, 2011 12:31 PM
To: Anastasia Yendiki
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Tracula Memory Requirements
Hi - The voxel dimensions are 1.0156 x 1.0156 x 2.6 mm in the merged_f1
bedpost output and the total number of voxels in the nodif_brain_mask
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 and the one you tried to run
bedpostx_single_slice.sh on are different, so I'm not sure which location
is the right one where your data is, but in
Hi Shige - See $FREESURFER_HOME/FreeSurferColorLUT.txt.
a.y
On Fri, 7 Oct 2011, Shigetoshi Takaya wrote:
Dear FreeSurfers,
In aparc+aseg file, each segmented or parceled region seems to be labeled by
its own intensity (e.g. the intensity is 53 in the right hippocampus, 10 in
the left
Hi Lena - When you say the most recent stable version, did you by any
chance download the snow leopard executables?
a.y
On Sat, 1 Oct 2011, Lena Palaniyappan wrote:
Dear Anastasia Team
I am running trac-all on 5.1 but my recons were processed using 4.5.
I am on 10.5.8 Darwin MAcOSX
I
Hi Joana - Can you please send your dmrirc file too?
Thanks,
a.y
On Fri, 30 Sep 2011, Joana Braga Pereira wrote:
Dear Freesurfers,
I'm pre-processing my DTI data with Tracula and i found the following error
while running trac-all -prep -c dmrirc_H_P01:
dtifit -k
.
Ping
On Thu, Sep 22, 2011 at 1:18 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Ping - There are 2 possibilities:
1. You can try to fiddle with the initialization points yourself to make
sure they're well in the CST. The point coordinates are saved in a text file
- look
process DOES NOT appear
to have successfully completed. Please examine your
results carefully.
/usr/local/freesurfer/bin/bedpostx_seychelles: line 281: kill: (12792) - No
such
process
===
On Thu, Sep 22, 2011 at 5:17 AM, Anastasia Yendiki
ayend
Hi Shanqing - You can cite this for now:
A Yendiki, P Panneck, A Stevenss, L Zo ̈llei, J Augustinack, R. Wang, D.
Salat., S. Ehrlich, T. Behrens, S. Jbabdi, R. Gollub, B, Fischl, Automated
probabilistic reconstruction of white-matter pathways in health and
disease using an atlas of the
Hi Judit - It's hard to know where the problem occurs without knowing what
was going on right before it. Does this happen in the very beginning
before any other output? Can you send your dmrirc and trac-all.log?
Thanks,
a.y
On Fri, 23 Sep 2011, Judit Haasz wrote:
Hi,
I have been running
Hi Ammar - Are these macos or linux machines and what is the size of your
diffusion images?
a.y
On Fri, 23 Sep 2011, Moiyadi, Ammar wrote:
Hi Freesurfers,
I've been getting a memory allocation error (below) when running trac
prep and trac paths on my computer with 6 gb ram. Since I was
Hi Ri - Tracula reconstructs 18 specific tracts, listed in step 14 here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Just like you cannot use freesurfer to find a region that's not included
in the freesurfer atlas, you canot use tracula to find a tract that's not
included in
On Fri, 23 Sep 2011, Moiyadi, Ammar wrote:
Hi Anastasia,
These are both linux ubuntu 10.04 lts machines. The DICOM images are 1300
slices each 140 KB.
Thanks,
Ammar
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Friday, September
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Friday, September 23, 2011 11:41 AM
To: Moiyadi, Ammar
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Tracula Memory Requirements
Hi Ammar - Can you check the voxel dimensions of one
Hi Ansgar - Currently there's no way to specify multiple scans for the
same subject as dicom files, sorry. You can concatenate the DWIs from the
2 scans in one nifti file, and also concatenate the bvecs/bvals from the
two scans, and pass the concatenation to dmrirc.
As for your error, it
Hi Ping - It looks like the path initialization may have failed. The
algorithm needs an initial guess for the path and iterates from there.
This initial guess is chosen based on the tracts in the atlas and if your
subject is not perfectly aligned with the atlas this initial guess might
end up
Hi Sandra - Bedpost is an FSL program, so your question would be best
answered on the FSL list. But yes, I do believe there were changes to it
since 2008. For sure there are more outputs saved in the output dir now
than before. Not sure if there were changes to the algorithm beyond this.
a.y
Hi Judit - Hard to tell what could've gone wrong but you can try running
the postprocessing yourself as follows:
bedpostx_postproc.sh /path/to/subject/dmri
Hope this helps,
a.y
On Thu, 8 Sep 2011, Judit Haasz wrote:
Hi,
I am running bedpostx within Freesurfer Tracula with default
Hi Bill - You should not have a problem at all with the 24 hour limit.
Tracula runs independently of the main FS stream (actually has to be run
after the main FS stream). Times vary with different configuration
parameters and data size, and we should get around to posting some nominal
Hi Antonella - There's functional data, and then there's diffusion data.
You don't need one to analyze the other. If you want to analyze functional
data with FSL, you use FEAT. If you want to analyze diffusion data with
FSL, you use this:
http://www.fmrib.ox.ac.uk/fsl/fdt/index.html
a.y
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