Hi Kate - There is an example configuration file for tracula in your
freesurfer distribution ($FREESURFER_HOME/bin/dmrirc.example). The same
file is also here:
http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
If you attach your configuration file and the log file
(scripts/trac-all.log), we can
it
into FSL's probtrackx viz bb register. If so, how might I go about doing that?
Thanks so much for your help,
Emily
From: freesurfer-boun...@nmr.mgh.harvard.edu
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki
ayend
Hi Ludy - If your gradient table is formatted in 3 rows you need to
either:
1. Convert it to 3 columns so you can use it with the 5.3 version of
tracula, which requires the gradient table to be formatted in columns
OR
2. Download the tracula update that can use gradient tables formatted in
it and sorry for the confusion! And I stand by
my statement on the model user - it's not about not ever running into
problems but about not being afraid to troubleshoot them! :)
a.y
On Wed, 20 Aug 2014, Kirstie Whitaker wrote:
On 20 August 2014 14:27, Anastasia Yendiki ayend
Hi Robby - It looks like in your config file setbveclist is one word,
instead of set bveclist. This may be why you're getting the Badly
placed ()'s. error at the very beginning of your trac-all output. And it
would explain why it can't find the files.
Hope this helps,
a.y
On Thu, 21 Aug
Hi Robby - Which version of tracula are you using? In general it's hard to
guess what's going on just by seeing the error message. Please attach the
entire log file (scripts/trac-all.log).
a.y
On Mon, 25 Aug 2014, Robby De Pauw wrote:
Hi Anastasia
Thanks for your quick reply. I’ve
Hi Kirstie - This was a glitch related to yesterday's storage cluster
maintence. It's been fixed now, so please try again.
a.y
On Wed, 20 Aug 2014, Kirstie Whitaker wrote:
Hi,
I apologise if this is only on my end but I can't seem to download any of the
updates from
Thanks a lot, Kirstie. Nice job on finding solutions in the archives! You
are a model user :)
On Wed, 20 Aug 2014, Kirstie Whitaker wrote:
Hi Anastasia and the freesurfer list,
I've been working on getting the latest version of tracula to run and I
thought I would post here the errors
Hi Lau - There is a scheduled outage of the Martinos Center storage
cluster all day today. Please try again later, it has nothing to do with
your system.
a.y
On Tue, 19 Aug 2014, Lau Møller Andersen wrote:
Dear List
I get the following error: „550 Failed to change directory.”
I tried on
that this is likely to happen soon
with additional features and bug fixes. If so, I think it would be worth the
wait.
Thank you!
Yoon
On May 22, 2014, at 5:37 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
wrote:
Hi Yoon - If you are getting an error from longitudinal tracula, do check
fasiculous.
I am just getting a better sense of what to look for in terms of bad vs. good
tracts.
Emily
- Original Message -
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 16, 2014 4:54:29 PM
Hi Tommi - The input reference volume (--inref) should be in the same
space as the input .trk file, i.e., your individual's diffusion space. It
seems that you're using the individual's T1 space instead?
a.y
On Fri, 25 Jul 2014, r...@nmr.mgh.harvard.edu wrote:
Hi,
I am attempting to morph
Hi Rotem - It's hard to tell without zooming into some key areas, like
corpus callosum and cingulum for example. The colors look ok (red and
green, respectively) but it's hard to see how the lines look.
a.y
On Mon, 28 Jul 2014, Rotem Saar wrote:
Dear Anastasia,
I followed your
Hi Shantanu - It's stuck trying to initialize one of the tracts. You can
check which tract it is, and then check the data to see if there's
something wrong that would affect that particular tract (for example, if
part of the brain that this tract goes through is cut off in the mask).
a.y
On
Hi Emily - The weighted average is the most reliable in practice, and it
is also the proper statistical definition of mean (expected) value. It
weighs the value of FA etc at each voxel with the probability of the tract
going through that voxel.
The cases that are missing stats may need to be
Weighted average recommended, see my previous email.
On Tue, 5 Aug 2014, Emily Louise Belleau wrote:
Hello all,
I was just wondering if in publications/papers it is more common to report the
average FA statistics, the weighted average statistics, or the center statistics
(the average of
Hi Yoon - Sorry, the config file is necessary for anything that doesn't
use default settings for trac-all, and that includes running it in
longitudinal mode.
What kind of cluster do you have? I'm working on making running trac-all
easier on clusters that are not currently supported, as part
Hi Wynn - There is a scheduled outage of the Martinos Center storage
cluster today and tomorrow.
a.y
On Mon, 18 Aug 2014, Wynn Legon wrote:
Hi,Trying to
download freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz. Link
gives 550 error and terminal error is:
No such directory
PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Cat - Just install the update and run trac-all -qa. This will produce
the motion measures. Check the tutorial for where to find the output.
a.y
On Mon, 21 Jul 2014, Cat Chong wrote:
Hello Anastasia,
I ran Tracula on Freesurfer
Hi Emily - Actually, there is a bug in the 5.3 version of freeview in that
specific feature. But you can use fslview - you select the V1 file, click
on the (i) button and choose Display as: Lines.
a.y
On Tue, 22 Jul 2014, ebell...@uwm.edu wrote:
Hi all,
I was wondering how you go about
Hi Sarina - It's linear interpolation.
a.y
On Wed, 23 Jul 2014, Sarina Sacco wrote:
Hi all freesurfer experts ,
I have a question about the command trac-all-stat-c ,what is the
interpolation that uses?
___
Freesurfer mailing list
Hi Rotem - The FA values are actually invariant to a rotation of the
gradient vectors. You can test that yourself. If, however, you get
different FA maps with the different gradient tables, then something else
is going on and not a simple rotation.
a.y
On Wed, 23 Jul 2014, Rotem Saar
this capability, then it would be ideal.
Shantanu
On Tue, July 22, 2014 2:35 am, Anastasia Yendiki wrote:
Hi Shantanu - What do you mean by compatible? Are you trying to import an
output from the other software into tracula or vice versa?
a.y
On Mon, 21 Jul 2014, Shantanu Ghosh wrote:
Hi FS
Hi Elia - Have you searched for the libnetcdf error in the archives? I do
believe that a few people were getting that error when 5.3 was first
released.
a.y
On Tue, 22 Jul 2014, Elia S. wrote:
Dear Freesurfer Community,
Running Tracula preprocessing produces this error:
ERROR: Could not
It'd be nice if things were that simple, but!
Although the pre-processing is done with FSL tools, tractography is done
with locally written code. Some gradient sets may appear to work with FSL,
but they won't work for us. For example, some dicom converters may perform
a L-R flip as
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:
for me to do epidewarp manually and then follow through with the
remaining steps using trac-all?
Thanks,
Eileen.
Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT)
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] trac-all -prep error field map error
Hi Emily - This is not necessarily a problem. To make sure, you can check
the output path.pd.nii.gz file from that specific tract. If it got stuck
somewhere (e.g., because the brain mask is missing a bit of brain that
this tract should go through) then the path.pd.nii.gz will look like a
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
mask since it was used in the bedpost
stage? I planned on using the output from the bedpost stage in tracula into
FSL's probtractx to also try some local probablistic tractography.
Emily
- Original Message -
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Freesurfer support
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
am sorry. I know I am making this confusing!
Thanks,
Emily
- Original Message -
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Monday, July 14, 2014 10:18:11 AM
Subject: Re: [Freesurfer] Tracula
Hi Emily
files have 65 entries (bval with 65 for each one of the three
sequences).
Can you spot the error?
Regards
Pedro Rosa
On Thursday, July 3, 2014 at 3:05 AM, Anastasia Yendiki wrote:
Hi Pedro - Have you specified not to do eddy current compensation? It
looks like it's being skipped. In that case, you
-2422.100.13~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Fri Jul 4 07:04:02 BRT 2014
Pedro Rosa
On Friday, July 4, 2014 at 5:18 AM, Anastasia Yendiki wrote:
The error message is data and bvals/bvecs do not contain the same
number
of entries. This doesn't necessarily mean
!
Regards,
Jun Shinozaki
2014-07-02 15:21 GMT+09:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu:
There are probably some empty spaces at the end of the lines of the
original files that confuses it into introducing those zeros. If you
attach the original files, I can take a look at them
-07-01 15:56 GMT+09:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu:
Hi Jun - By a simple word count on these files:
% wc -w bvals bvecs
65 bvals
198 bvecs
263 total
As you can see, there are 3 extra entries in the bvecs file. If you then
open the file, you'll see
Hi Emily - Depends on what you're doing. If you're doing an ROI-based or
tractography-based analysis, where you extract average FA in a part of
white matter, there is no need to warp. If you're doing a voxel-based
analysis, obviously all the subjects need to be in a common space to
compare
had 65 images.
Also, I checked bvals and bvecs in the dmri folder, and they have 65 counts.
It seems consistent.
I attach bvals and bvecs. These files were created by freesurfer
automatically.
Regards,
Jun Shinozaki
2014-06-30 18:38 GMT+09:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Hi Jun - It's failing at the point where it tries to extract the low-b
images from the DWI series. I suspect that the number of frames in the 4D
DWI volume that is extracted from your dicom does not match the number of
frames that it expects to find based on how many gradient vectors or
Hi Durai - You cannot run all 3 steps of trac-all at the same time. The 3
steps need to be run separately. Please check the tutorial on the wiki for
more details.
a.y
On Tue, 24 Jun 2014, Durai Arasan wrote:
Hi Freesurfer experts,
I tried running trac-all with my config file and received
Hi Elia - This could very well be the case. Does the epidewarp.fsl command
give you any specific error message, or does it just not create an output?
a.y
On Tue, 17 Jun 2014, Elia S. wrote:
Hi Anastasia,
Yes, launching the same command line from terminal produced the same error, but
at
Check the email archives for a recent message about epidewarp.fsl from
Doug, there is a newer version that works with FSL 5.
On Tue, 17 Jun 2014, Elia S. wrote:
Hi Anastasia,
The epidewarp.fsl gives me the following output:
FSLVersion 5.0.6
FSLVerMaj 5
FSL Version is 5.0.6, must be 3.X or
Hi Elia - It looks like this file didn't get created:
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
The command that was supposed to create it was epidewarp.fsl. You can find
the command line that begins with epidewarp.fsl in the log file that you
sent
multiple bval files is not shown.
Thank you
Yoon
On May 22, 2014, at 5:37 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
wrote:
Hi Yoon - If you are getting an error from longitudinal tracula, do check
the tracula updates at the link that I gave you in my previous email.
As for 5.2
Hi Shantanu - The -qa flag was added in the update to tracula that was
posted after the 5.3 release.
http://freesurfer.net/fswiki/Tracula/#Updates
Martinos Center users can simply switch to the dev version of freesurfer
to take advantage of these updates, in which case you don't need
Hi Kathryn - The -stat option was added in the latest tracula update, see
here:
http://freesurfer.net/fswiki/Tracula/#Updates
You need to download this update, after installing freesurfer 5.3, to be
able to do what is described in the tutorials.
a.y
On Wed, 4 Jun 2014, Kathryn Cullen
Hi Sal - There is no way to do this through trac-all, sorry.
a.y
On Fri, 6 Jun 2014, Salil Soman wrote:
Hi,
I noticed in the output for tracula -prep I am currently running using
cvsreg it mentions openmp=1, I was wondering if there is a way to enable
more than 1 core for openmp for
changes to my .tcshrc to access the dev version?
Thanks in advance.
Shantanu
On Fri, June 13, 2014 12:02 pm, Anastasia Yendiki wrote:
Hi Shantanu - The -qa flag was added in the update to tracula that was
posted after the 5.3 release.
http://freesurfer.net/fswiki/Tracula/#Updates
Hi Yoonho - Tracula did not change at all between the 5.2 and 5.3
releases. It was recon-all that changed, and in fact 5.3 was released to
correct a bug in 5.2, so it is not recommended to use 5.2 recon-all.
For info about tracula versions, see:
which is used, and if these differences can be ignored?
Thanks and best wishes,
Colm.
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: 11 March 2014 00:39
To: McGinnity, Colm
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA
Hi Elia - This issue was fixed in the last update:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates
FYI, there will be another tracula update soon (after ISMRM) that will
further improve the longitudinal stream specifically.
a.y
On Fri, 9 May 2014, Elia S. wrote:
Dear
Hi Satra - Sorry, no.
a.y
On Fri, 25 Apr 2014, Satrajit Ghosh wrote:
hi a.y.,
is there any part of tracula that currently benefits from openmp or mkl
availability?
cheers,
satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Bonsoir Emilie - Tracula draws a large number of path samples, which in
the end are added up to produce the path probability distribution. FA
shows the values of FA at each point along the path sample with the
greatest probability, i.e., along a single 1D curve. FA_Avg averages the
FA from
comparisons, but still the
difference worries me.
My questions are:
(1) Do our values look valid to you?
(2) Are there any article that reported SNR as mean low-b / sd in the white
matter aseg mask?
Thank you in advance!
Yuko Yotsumoto
Mar 18, 2014 1:26 PM、Anastasia Yendiki ayend...@nmr.mgh.harvard.edu の
Hi Vincent - I suspect that this problem would be fixed by some recent
changes that I've implemented for the longitudinal stream of tracula, and
that I'm in the process of testing. As soon as we can get a new dev
version built, I'll let you know so you can test it.
Thank you for your
Hi Satra - We've been talking about a 5.3.1, yes. On my end, it would
include the tracula updates that are currently available and possibly some
more (I've been working on some improvements to longitudinal tracula).
Not sure about libnetcdf but this is a good time to add things to the wish
the
longitudinal analysis of weighted average variables (overall not
byvoxel along the MAP) and now I fear that results are maybe not correct
because after all the MAP is a part of all sampled paths.
Best, Vincent
Am 4/4/2014 11:49 AM, schrieb Anastasia Yendiki:
Hi Vincent - I suspect
Hi Janosch - The December 9th tracula update is just that, an update to
the tracula code without any changes to the rest of freesurfer.
a.y
On Tue, 1 Apr 2014, Janosch Linkersdörfer wrote:
Hi all,
I am a little confused about what the latest Freesurfer version is.
I thought that v5.3.0
no?
Thanks,
Emily
- Original Message -
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Monday, March 31, 2014 6:32:17 PM
Subject: Re: [Freesurfer] SEEDING in Tracula
Hi Durai - Tracula is not for exploratory tractography, i.e
I just always do this instead and then continue with
trac-all -path? Or do I need to use trac-all -bedp specifically?
Many thanks in advance,
Best wishes,
Colm.
Colm McGinnity
King's College London
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent
Hi Yuko - Option 3, using the same FA threshold to create a mask for all
measures makes sense.
a.y
On Wed, 19 Mar 2014, Yuko Yotsumoto wrote:
Hello FreeSurfer experts,
I have a question regarding DTI analysis.
I understand that FA values ranges 0-1, and the values are often thresholded
Hi Yuko - You can use the low-b images and compute the SNR of those images
inside a mask of the white matter. Because dt_recon computes a
registration from the diffusion to the structural data, you can use that
registration to map the white matter label from the freesurfer
segmentation
groups.
Is it correct to say that the higher mean values indicate larger SNR?
Yuko
On Mar 18, 2014, at 12:53 AM, Anastasia Yendiki wrote:
Hi Yuko - You can use the low-b images and compute the SNR of those images
inside a mask of the white matter. Because dt_recon computes a registration
Hi Stefano - Our SLFt was indeed labeled as defined in Wakana et al, so it
is frontotemporal.
a.y
On Fri, 14 Mar 2014, std...@virgilio.it wrote:
Hi list,
in Wakana et al., 2007, the SLF was divided in parietal and temporal
components. As I understand it, the same subdivision has been made
Hi Ruth - These parameters are described in Benner 2011 (cited in our
paper). The -T threshold is mostly what you might need to change,
depending on your scanner. You should look at the low-b images and find a
rough lower threshold for the image intensities of brain voxels. It
doesn't have
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Ruth Carper rcarper...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Sent: Friday, March 14, 2014 4:46 PM
Subject: Re: [Freesurfer
How is the format different? Is it in 3 rows instead of 3 columns? If so,
it should be straightforward to convert it yourself from 3 rows to 3
columns.
On Thu, 13 Mar 2014, Gennan Chen wrote:
Hi! All,
Is there an utility to extract bvals and bvecs from GE’s DTI dicom files
into the format
-
From: ebell...@uwm.edu
To: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, March 5, 2014 3:25:00 PM
Subject: Re: [Freesurfer] Running Tracula on a cluster
Hi Anastasia,
We use SLURM.
I have not personally yet run bedpost off
Hi Francesco - If this registration is done with bbregister, which is the
default option in tracula, then it uses the lh.white and rh.white surfaces
from the freesrufer reconstruction of the structural. The low-b diffusion
images are aligned to those surfaces by optimizing the contrast of the
Hi Sarah - The best way to troubleshoot the configuration file is to
source it, make sure that there are no errors, and then echo each variable
to make sure it contains what you intended.
For example once you run source Tracula_config you'll get an error, and
you'll find that you have to
Hi Colm - Note that the information in the tutorial (particularly the part
where gradient tables can be formatted in 3 rows or 3 columns) pertains to
the latest tracula update:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
You're using an older version that only supports
Hi Emily - Which job management system does your cluster run on? Have you
ever tried to run any of the FSL parallelized programs, like bedpostx, on
your cluster?
a.y
On Wed, 5 Mar 2014, ebell...@uwm.edu wrote:
Hello,
I plan on running a batch of subjects (around 80) on a computer
Hi Celine - This command assumes that --intrc is a tracula output
directory, containing all the files that tracula saves in such a
directory. What are you trying to get stats from?
a.y
On Mon, 3 Mar 2014, Celine Louapre wrote:
Hi Anastasia
I have finally managed to coregister and resample
Hi Francesco - The pathways that tracula reconstructs are only the ones
included in its atlas. To add a new pathway to this atlas, it would have
to be labeled manually in a set of subjects, just as we have done with
the other 18 pathways.
Hope this helps,
a.y
On Tue, 4 Mar 2014, Francesco
Mar 2014, Francesco Baldacchini wrote:
Ok, thanks. And if I want to add a new pathway which is the file I've to
modify and where can I find it?
Francesco Baldacchini
2014-03-04 17:28 GMT+01:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu:
Hi Francesco - The pathways
I concur. If this is the lowb.nii.gz from trac-all and brainmask.mgz from
recon-all, they will be in their respective native spaces, and thus I
wouldn't expect them to be registered to each other.
On the other hand, any brain masks that trac-all saves under dlabel/diff/
are in diffusion
, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Gari - You're talking about thresholding the probtrackx maps, right?
Yes
If so the 20% at which the tracula maps are thresholded by default is
probably too high for
probtrackx, I'd try something like 2%. (Tracula
your.ecclog --bval your.bvals --out
output.txt
as well as trac-all -qa -c dmrirc_file with location of bval specified and
trac-all -prep -c, respectively
On 20 February 2014 21:16, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
wrote:
Then it's no surprise that the error doesn't occur in 5.2
/fastfs/igis/MRI_fs_rec_dti/64-23-145-1/dmri/bval for reading
) = 84
exit_group(1)
I just tried it again. Any way to specify bvals elsewhere?
Thanks
Gerit
On 21 February 2014 18:04, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
wrote:
Hi Gerit - When I run dmri_motion on the files
Does the error in trac-all -prep with 5.3 occur when dmri_motion is run
or at a different step?
On Thu, 20 Feb 2014, Gerit Pfuhl wrote:
Dear Tracula Experts,
after careful checking we still cannot run trac-all -qa or dwri-motion as the
command always returns: could not
open bvals but the
loading the *.nii file (see attachment) or
when run as
dmri_motion --dwi dwi_orig.nii.gz --mat dwi.ecclog --bval dmri/bvals --out
dwi_motion.txt immediately.
On 20 February 2014 17:08, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
wrote:
Does the error in trac-all -prep with 5.3 occur
--dwi yourDWIs.nii.gz --mat your.ecclog --bval your.bvals --out
output.txt
as well as trac-all -qa -c dmrirc_file with location of bval specified and
trac-all -prep -c, respectively
On 20 February 2014 21:16, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
wrote:
Then it's no surprise
Hi Gerit - There's no difference in tracula between 5.2 and 5.3.
a.y
On Mon, 17 Feb 2014, Gerit Pfuhl wrote:
Dear Freesurfer experts,
we are curious whether we can run trac-all -qa in 5.3. and use it as
regressors with our results from tracula 5.2.
I.e. is it advisable or shall we run the
, Feb 14, 2014 at 10:20 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Alan - The gradient table is not saved in the nifti header.
Are you using a standard MGH diffusion sequence?
a.y
On Fri, 14 Feb 2014, Alan Francis wrote:
Hi Anastasia
,
or the tracula tutorial.
Hope this helps,
a.y
On Fri, 14 Feb 2014, Francesco Baldacchini wrote:
Hi Anastasia,
I've just rerun trac-all path and got the same error. In attach there is the
trac-all.log. Thanks,
Francesco Baldacchini
2014-02-13 20:30 GMT+01:00 Anastasia Yendiki ayend
Hi Alan - The gradient table is not saved in the nifti header. Are you
using a standard MGH diffusion sequence?
a.y
On Fri, 14 Feb 2014, Alan Francis wrote:
Hi Anastasia:
Hope all is well. I have DTI data for 65 brains. They are in nifti format.
However, they do not have the bvecs and
GMT+01:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu:
Hi Francesco - The decimal separator should be dot, not comma. Can you
send me the bvecs/bvals that you get
after you change from row to column format? (Both the ones that you feed
into trac-all and the ones that get
Hi Sal - This is the command that trac-all will call if you specify field
maps, you can see here what inputs it can take:
http://surfer.nmr.mgh.harvard.edu/fswiki/epidewarp.fsl
Hope this helps,
a.y
On Thu, 13 Feb 2014, Salil Soman wrote:
Hi,
Could someone point me to an example for
Hi Celine - If the lesion mask is already in the space of the freesurfer
recon, you can pass to mri_vol2vol the dmri/xfms/anatorig2diff.bbr.dat
transform. That's the one generated by bbregister for the
anatomical-diffusion registration.
Hope this helps,
a.y
On Thu, 13 Feb 2014, Celine
the GLM matrix.
Best,
Clive
On Tue, Feb 11, 2014 at 8:29 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Clive - These are not stats in the volume or on the surface, so
mri_glmfit doesn't apply. If you want to do
group analyses along a tract on a table produced
is only 4 rows long.
2014-02-06 1:18 GMT+01:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu:
Hi Francesco - Which version of tracula are you running? To be able to
use bvecs files that are in 3 rows
instead of 3 columns, you need to make sure that you have the latest
update
and you
can see it from the bvecs file I found in the dmri directory which is
only 4 rows long.
2014-02-06 1:18 GMT+01:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu:
Hi Francesco - Which version of tracula are you running? To be able to
use bvecs files that are in 3
rows
Hi Jeff - Questions about bedpostx output files are best addressed to the
FSL list, as it's an FSL program that is not developped by us. The
appropriate info to provide them is the FSL (rather than freesurfer)
version numbers.
a.y
On Tue, 11 Feb 2014, jwa...@nmr.mgh.harvard.edu wrote:
Hi Celine - That's an interesting question. There's nothing implemented in
there right now that would allow you to skip part of the tract in the
along-the-tract stats. One (not very elegant) way to try to do something
like this is:
1. Set the lesion voxels in the dmri/dtifit_FA.nii.gz volume
Celine - You're very welcome!
If this particular motion measure is identical for pretty much all your
subjects, there is no point in including it. So you can just use the other
3 motion measures.
a.y
On Wed, 12 Feb 2014, Celine Louapre wrote:
Hi Anastasia
Thanks a lot for your very nice
Wow, that's interesting. In both cases it's called with the default
settings, without specifying any special options on the command line. You
could verify this by running the respective versions of bedpostx
independently of tracula and looking at the outputs. Unless of course
something has
generated by QDEC) to do the glm?
Thanks
Clive
On Mon, Feb 10, 2014 at 6:13 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Clive - Yes, you can use the recent tracula update on top your already
processed data. The new update only
adds new functionality to trac-all
and lo res, making this realignment difficult
thanks again!
JOn
- Original Message -
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, February 6, 2014 3:16:16 PM
Subject: Re: [Freesurfer] Fwd: trac-all
Hi Clive - Yes, you can use the recent tracula update on top your already
processed data. The new update only adds new functionality to trac-all,
without changing any of the existing functionality in 5.3.
Did you try downloading the update from here?
: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, February 6, 2014 11:00:25 AM
Subject: Re: [Freesurfer] Fwd: trac-all -path error
So there's your culprit. You need to fix the intra-subject
(diffusion-to-T1
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