Try mri_annotation2label.
On Wed, 25 Sep 2013, std...@virgilio.it wrote:
For FSL guide:
I should transforms a group of labels into a surface
Usage:
label2surf -s surface -o outputsurface -l labels
Compulsory arguments (You MUST set one or more of):
-s,--surf input surface
Hi Gari - Sorry, right now the assumption is that the gradient vectors are
the same for all subjects. How different are they?
a.y
On Wed, 25 Sep 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Anastasia,I am setting up the dmrirc file to run Tracula. I am using
Siemens Dicoms, so I did not
Hi Lucia - The error occurs when the text file with the gradient vectors
is being processed. Can you please attach that file?
Thanks,
a.y
On Fri, 20 Sep 2013, Lucia Billeci wrote:
Dear Madam/Sir,
I am trying to applying TRACULA on my data but when I run the following
command:
trac-all
Hi Alan - Glad to hear that you have an interesting finding! Can you
describe what type of thing you want to visualize a bit more? If it's not
on the surface, freeview will more likely do the trick rather than qdec.
a.y
On Fri, 13 Sep 2013, Alan Francis wrote:
Hi Anastasia and FreeSurfers:
if
possible.
thanks again,
Alan
On Fri, Sep 13, 2013 at 10:53 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Alan - Glad to hear that you have an interesting finding! Can
you describe what type of thing you want to visualize a bit
more? If it's
in these tracts.
thanks,
Alan
On Fri, Sep 13, 2013 at 11:37 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Alan - Are you looking at average AD over the whole tract, or
AD along the tract?
a.y
On Fri, 13 Sep 2013, Alan Francis wrote:
Hi
analysis and show mean differences on a single inflated brain.
thanks,
Alan
On Fri, Sep 13, 2013 at 11:43 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
I see, then it's an ROI analysis, where the tract is the ROI.
Isn't it sufficient for you to visualize the tracts
Hi Sean - Do you mean that the streamlines go through non-brain voxels?
You could you a slightly dilated version of the aparc+aseg as a mask. You
can use bbregister to map it to the subject's DWI space.
a.y
On Mon, 9 Sep 2013, Sean Hatton wrote:
Hello FS Gurus,
I would like to export FS
I'd probably try GM plus a (DWI-sized) voxel or so into the WM.
On Mon, 9 Sep 2013, Sean Hatton wrote:
Great, I will give that a shot. In the seeding ROI should I combine the gm and
wm labels or is the GM sufficient to encapsulate, say, the superior temporal
gurus GM and WM?
Anastasia
...@childrens.harvard.edu
Indeed. It's actually really easy to set up, too.
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Monday, September 02, 2013 3:46 PM
To: Watson, Christopher
Cc: Joana Braga Pereira
looks like the most likely to me. For sure the gradient table is wrong.
On Thu, 5 Sep 2013, Joana Braga Pereira wrote:
Thanks!
I've uploaded those files as well as dmrirc and bvecs and bvals.
Let me know what you think.
2013/9/5 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Indeed
this? Perhaps by modifying
any of the previous steps?
Thanks!
2013/9/5 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Hm, this looks uniformly bad. Have you checked that the gradient
directions are correct? You
can check that by looking at the eigenvectors from the tensor fit
Hi Celine - The path.pd.nii.gz file contains the full probability
distribution without any thresholding. This distribution, as with any
probabilistic tractography method, expresses the amount of uncertainty in
which is the path of most coherent diffusion between the two end regions.
(In
Hi Joana - What system are you running this on?
a.y
On Mon, 2 Sep 2013, Joana Braga Pereira wrote:
Dear Anastasia and FreeSurfers,
I was preprocessing some data using tracula and found this error after
running trac-all -bedp -c dmrirc:
INFO: SUBJECTS_DIR is /data-02/joana/Last
INFO:
Thanks for the pointers, Chris. I'd call it an opportunity for FSL
customization rather than an FSL problem per se :o)
On Mon, 2 Sep 2013, Watson, Christopher wrote:
This is an FSL problem. You can try the FSL list, and check out some links:
https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge
Nope, there's no flipping in tracula. But, *both* the gradient vectors and
the DWIs are converted to LAS orientation as the first step in the
preprocessing. This makes the FSL tools that are run later in the
preprocessing (dtifit and bedpostx) run smoothly without any flipping.
On Mon, 26
to get all
messages.
Thank you so much for your big help.
I hope I didn't cause you much trouble with my problems and questions.
Sincerely,
Florian
Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 20.08.13 17.56 Uhr
This is an Ubuntu-related error that has surfaced recently because in
Ubuntu /bin
Hi Sal - Sorry but I don't know what the interaction of dcm2nii and GE
dicom headers is. If anyone else on the list uses dcm2nii on GE dicoms,
they can chime in.
To make sure the gradient table is right, I'd always check the primary
eigenvector directions (overlaying dmri/dtifit_V1.nii.gz
Definitely age. You don't need to adjust for volume since these are not
volume/area/length measures that you're comparing. You should also check
for any group differences in motion before you proceed and make sure your
groups are matched in terms of motion. If you do separate t-tests for each
/bedpostx_mgh: 131:
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected. I also
attached the the logfile. I was reading
about this error in the mail archive. Would I have to run bedpostx outside of
tracula ?
Sincerely,
Florian
Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 19.08.13
/bash on the first line of those two scripts.
On Tue, 20 Aug 2013, Borsodi Florian wrote:
Hi Anastasia,
Yes, i am running this on ubuntu 12.04.
Sincerely,
Florian
Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 20.08.13 17.38 Uhr
Hi Florian - Are you running this on an ubuntu system
Hi Francesco - There's a list of bedpostx output files here:
http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html
The best way to determine if bedpostx finished running properly is to
check if those files were created in the dmri.bedpostX directory.
a.y
On Mon, 19 Aug 2013,
a dpath folder with summary statistics? I
have all of the bedpostx output files, however, I seem to be missing the dpath
folder as well as a script confirming that -path was completed.
Thanks,
Francesco
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu
1.
http://www1.imperial.ac.uk/medicine/people/d.soto/
On 16/08/13 16:13, Anastasia Yendiki wrote:
mri_info dmri/dwi.nii.gz
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Is it really autofs without the '/' in front?
On Thu, 15 Aug 2013, Alan Francis wrote:
Hi Anastasia:
Sorry to bother you again. I am trying to extract trac stats from the FS
data. When I run the following script, it gives me an error message:
Can you please attach the file Forceps_Major_CC.list.txt?
On Thu, 15 Aug 2013, Alan Francis wrote:
Hi Anastasia:
Yes the '/' is really there before the autofs. It is puzzling.
thanks,
Alan
On Thu, Aug 15, 2013 at 3:15 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
I
Hi Alan - I'm not sure where the output from the one subject ends the the
other starts. For future reference, it's best to attach the entire
trac-all.log files instead of copying and pasting parts of them into your
message.
I see two error messages here:
1. ERROR: must specify as many
Hi Ana - If you notice the release notes, this was relevant to an old
version of tracula. You should now be using the latest version of tracula
that's included in freesurfer 5.3, in which case you don't need any extra
downloads.
a.y
On Wed, 14 Aug 2013, ana ;osp wrote:
hi'm trying to
14, 2013 at 11:06 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Alan - I'm not sure where the output from the one subject ends the the
other starts. For future
reference, it's best to attach the entire trac-all.log files instead of
copying and pasting parts of them
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: setenv
SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons
FreeSurfer_Data: Undefined variable.
thanks,
Alan
On Wed, Aug 14, 2013 at 1:08 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Where did you
Why do you want to use a '$'?
On Wed, 14 Aug 2013, Alan Francis wrote:
Hi Anastasia:
Yes the path that you pointed out is the one I presently use. Is there no way
to use the '$' as a substitute?
thanks,
Alan
On Wed, Aug 14, 2013 at 1:46 PM, Anastasia Yendiki
ayend
?
thanks
On Wed, Aug 14, 2013 at 11:11 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Ana - If you notice the release notes, this was relevant to an old
version of tracula. You should now
be using the latest version of tracula that's included in freesurfer 5.3
Hi Alan - This appears to be the same error message as the one for subject
118 that you sent yesterday. So I'd try here whatever you did to fix that
one.
a.y
On Wed, 14 Aug 2013, Alan Francis wrote:
Hi Anastasia:
Sorry to bother you again. Another of my brains gave an error message. I
/
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 09 August 2013 22:44
To: Soto, David
Subject: Re: [Freesurfer] trac-all inquiry
Are you rotating the gradient vectors accordingly? This is done in
trac-all after running eddy_correct.
On Fri, 9 Aug 2013
in trac-all
would this be fine? I dont think the bet I run will affect the image
cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 09 August 2013 23:15
To: Soto, David
Cc: freesurfer
/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh:
Syntax error: ( unexpected
http://www1.imperial.ac.uk/medicine/people/d.soto/
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 07 August 2013 17:22
To: Soto, David
-preproc finished without error at Tue Aug 6 21:27:30 BST 2013
thanks for your help
cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 06 August 2013 19:30
To: Soto, David
Cc
Yes, please attach the dmrirc and trac-all.log. Thanks!
a.y
On Wed, 7 Aug 2013, Alan Francis wrote:
Hi Anastasia:
For one brain I got this error message :
csh::alanf@cerebro
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: trac-all -prep
-c
with ERRORS at Wed Aug 7 13:01:21 EDT 2013
thanks so much,
Alan
On Wed, Aug 7, 2013 at 1:11 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Alan - Try removing the \ character from the end of the dcmlist
definition. That's a change of line
character.
a.y
-preproc exited with ERRORS at Wed Aug 7 13:34:45 EDT 2013
On Wed, Aug 7, 2013 at 1:20 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Please attach the file trac-all.log. I can't tell what's going on just by
looking at the end of it.
On Wed, 7 Aug 2013, Alan Francis wrote
set x = `cat bvecs | awk '{if (NR==1) print}'`
set y = `cat bvecs | awk '{if (NR==2) print}'`
set z = `cat bvecs | awk '{if (NR==3) print}'`
@ k = 1
while ( $k = `head -1 bvecs|wc -w` )
echo $x[$k] $y[$k] $z[$k]
@ k = $k + 1
end
I'd make sure though dcm2nii doesn't L-R flip the gradient
and anonymizing them would be prohibitively difficult.
I could not find the freesurfer archive message you referred to. Any pointers
would be greatly appreciated.
Best wishes,
Sal
On Wed, Aug 7, 2013 at 1:12 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
set x = `cat bvecs
Freeview can do this in principle, but the current version of freeview has
a known bug with displaying eigenvectors as lines (see known issues in
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes), so for now you can
use fslview.
On Wed, 7 Aug 2013, Salil Soman wrote:
Thank you for
6 10:22:18 EDT 2013
Thanks so much,
Alan
On Mon, Aug 5, 2013 at 3:55 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Alan - The file doesn't need to have an extension, .txt or other. But
you do need to set bvecfile to
the full name of the file, including
I see, you're using the old version of tracula (from freesurfer 5.1). In
that version, you had to define the number of low-b images in the
configuration file. I strongly recommend updating to freesurfer 5.3. A lot
of things have improved in tracula since then.
Also, in the future please
/diffusion_recons] : trac-all -prep -c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
TUTORIAL_DATA: Undefined variable.
On Fri, Aug 2, 2013 at 7:16 PM, Alan Francis alandarkene...@gmail.com
wrote:
thanks again.
On Fri, Aug 2, 2013 at 3:51 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu
The error says:
`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt':
No such file or directory
Does this file exist?
On Mon, 5 Aug 2013, Alan Francis wrote:
Hi All:
When I ran trac-preproc I got an error that read s as follows:
trac-preproc exited
suffix. Maybe I will
change the suffix and run this again.
thanks,
Alan
On Mon, Aug 5, 2013 at 1:57 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
The error says:
`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons/bvecs.txt': No such file
Hi David - You need to run each of the steps (-prep, -bedp, -path)
separately. You can't run them all at the same time. See tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula
Hope this helps,
a.y
On Fri, 2 Aug 2013, David Soto wrote:
Hi,
I have
Hi Alan - All the set ... commands for tracula need to be in a
configuration file. You then pass that configuration file as an argument
to the -c option of trac-all. See tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps,
a.y
On Fri, 2 Aug 2013,
Francis alandarkene...@gmail.com
wrote:
Thanks Anastasia.
On Fri, Aug 2, 2013 at 2:26 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Alan - All the set ... commands for tracula need to
be in a configuration file. You then pass that
configuration file
version of the operating system do you have on your computer and how
much memory?
Thanks,
a.y
On Mon, 29 Jul 2013, amirhossein manzouri wrote:
Hi,
Kindly find attched the trac-all.log !
On Thu, Jul 25, 2013 at 6:25 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi
Hi Florian - Do these files exist?
/data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bvecs
/data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bvals
The format of the bvecs and bvals that you sent seems fine, but (and this
has nothing to do with the error
There is a *.thresh.label version of all the BA labels in 5.3, but I don't
think it's used by default. You can try using those labels instead.
On Fri, 26 Jul 2013, Satrajit Ghosh wrote:
hi bruce,
currently 5.3, but the data i was looking at was processed with 5.1 and in
that right ba44/45
that they are biased by the predictability of the
region. less accurate prediction - greater volume.
cheers,
satra
On Fri, Jul 26, 2013 at 10:28 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
There is a *.thresh.label version of all the BA labels in 5.3,
but I don't think it's used
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.ht
ml
Thanks,
On Mon, Jul 22, 2013 at 8:15 PM,
Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu
and
tried and it worked, also bvec should be in three columns as you
have mentioned before.
On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Good to hear! Can you please share with all of us what was
wrong with your original files? It may help
Hi Sal - Are these different scans that you want to merge? If they're all
in one file, then you just define the b-value for each frame as usual in
the bvalfile. There's no rule that all the b-values have to be the same.
Hope this helps,
a.y
On Sun, 21 Jul 2013, Salil Soman wrote:
Hi,
I was
Hi Riccardo - The way this is designed is that you have to have
longitudinal T1 data and run the longitudinal stream of recon-all on it,
before you run the longitudinal version of tracula on your DWI.
You could fake this by simply creating a copy of the recon-all directory
of your first T1
Good to hear! Can you please share with all of us what was wrong with your
original files? It may help others who have the same problem in the
future. Thanks!
On Wed, 17 Jul 2013, amirhossein manzouri wrote:
Thanks Anastasia,
IT HELPED!
On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki
, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Amirhossein - Are your original bvecs/bvals in 3-row format
instead of 3-column format?
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Thanks,
a.y
On Mon, 15 Jul 2013
Hi Gerit - Can you please send the entire trac-all.log for this subject?
There could be some clues in the info that's printed out from the earlier
steps, even if there's no outright error in those steps.
Thanks,
a.y
On Fri, 5 Jul 2013, Gerit Pfuhl wrote:
Dear Freesurfer experts,
for
Hi Matt - For how to tell tracula to use CVS registration, see Specify
the inter-subject registration method here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Does this answer your question?
a.y
On Mon, 8 Jul 2013, Hoptman, Matthew wrote:
Hi all,
I see how to
Hi Andrew - My guess is that it's something about the file
dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send
along that file?
Also, how did you fix your previous configuration file problem? Letting
the list know about the resolution of the issue would help other
Hi Susie - The initial placement of the control points plays a much bigger
role than the end ROIs. The path being initialized in a bad location would
be more of a problem than the end ROIs being too generous. So I'd check
rh.unc_AS_avg32_mni_bbr_cpts_5.nii.gz before editing the end ROIs. Does
Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of
3-column format?
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Thanks,
a.y
On Mon, 15 Jul 2013, amirhossein manzouri wrote:
Dear Experts,
I am running trac-all -prep -c dmrirc on my DWI data. After
summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log
transform.txt
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 12:19 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] application
That is exactly right! Those were added after 5.1.
On Mon, 15 Jul 2013, Susan Kuo wrote:
Hi Anastasia, I believe the issue I had with the pathstats.byvoxel.txt not
displaying the last four values (AD_Avg RD_Avg MD_Avg FA_Avg ) is owing to the
fact
that trac-all was run with FREESURFER
I should add that there several other reasons to be using the newer
version of tracula (from 5.2 or 5.3), including speed and other
improvements listed here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
Also note that using 5.2 or 5.3 won't make a difference in terms of
Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 2:30 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] application of mri_cvs_register question
Hi Matt - The CVS morph under xfms/cvs/ maps the individual
problem :( Maybe something went wrong, but I didn't see
any problem in the log files. Actually, the command I showed below had a typo
(I used --mat rather than --reg to get that error). Is there a way to convert
*.mat to *.dat?
-Original Message-
From: Anastasia Yendiki [mailto:ayend
anatorig2diff.bbr.dat.paramdiff2anatorig.bbr.mat
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 2:56 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] application of mri_cvs_register question
Got
in the
scenario where other processes (e.g., my script, dcm2nii) automatically take
care of generating an fsl compatible file + gradient info.
please let me know if i'm misinterpreting something here.
cheers,
satra
On Tue, Jul 2, 2013 at 8:21 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu
Hi Satra - The orientation of your dwi_orig.nii.gz is LPS. What flip4fsl
will do is convert it to LAS, and perform the same conversion on the
gradient table that you provide. This of course assumes that
dwi_orig.nii.gz and your gradient table are consistent as they come out of
your custom
On Tue, 2 Jul 2013, Satrajit Ghosh wrote:
hi ay,
i'll look into the orientations a little later tonight, but here is V1
overlaid on FA for preflip and postflip execution of dtifit.
cheers,
satra
On Tue, Jul 2, 2013 at 7:48 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi
Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a
deep breath and let it all go.
More to the point, when I view the text file that you sent, I see that
several of the lines are joined together, so both the dcmroot and dcmlist
variables appear commented out. Is this
= (DKI.nii.gz)
On Mon, 1 Jul 2013, Gundran, Andrew wrote:
Yes, the text was saved on a unix system
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 01, 2013 2:34 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re
diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then bvecfile and bvalfile must be specified (see below)
#
set dcmroot = /home/baileype/Desktop/JG005
set dcmlist = (DKI.nii.gz)
-Original Message-
From: Anastasia Yendiki
, Andrew wrote:
Whoops. It doesn't read like that every # is a new line along with each set
I did that and the error was
Line13: syntax error near unexpected token `('
Line 13: `set subjlist = (freesurfer)
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu
Hi Roxana - How tracula works is decribed in detail here:
http://www.frontiersin.org/Journal/DownloadFile.ashx?pdf=1FileId=8155articleId=10815Version=1ContentTypeId=21FileName=fninf-05-00023.pdf
To add a new tract to the tracula atlas that is not currently part of it,
the tract would first have
Sorry, can't open the image.
On Sun, 23 Jun 2013, Rotem Saar wrote:
Hi there,
Long time:). Well I wrote to the list several times regarding high FA values
I got when performing DTI analysis.
Today we know that the problem was an additional direction (we had 17
directions instead of 16 - we
help - so I will really appreciate if u will have
a look but also tell me what is the best way to upload them so that all list
members will be able to see them.
Thank u very much for your help.
Rotem
2013/6/25 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Sorry, can't open the image
Hi Sal - Not sure what you mean by connectivity maps, can you be more
specific? Tracula is not a method for exploratory analyses of the type
what is my seed region connected to? It's a method for reconstructing a
set of 18 major white-matter pathways, which are listed here:
Hi Fred - As with any probabilistic method, volume here is a measure of
the spread of the probability distribution of the pathway (i.e. of
path.pd.nii.gz), so it can be interpreted as the amount of uncertainty in
the data. A more spread out distribution means more uncertainty, a tighter
Sorry, there's no command that will generate that file for anything other
than the output generated by tracula, but if you want to average FA etc
over a volume it's pretty easy to do with fslstats.
On Fri, 14 Jun 2013, Jayachandra Raghava wrote:
Hello All,
Is it possible to generate
You can find the aparc+aseg mapped from T1 space to DWI space in the
dlabel/diff directory. You can overlay it on the paths reconstructed from
tracula to see which aparc+aseg labels the paths overlap with. The
identities of the labels in the aparc+aseg are in
Hi Matt - Thanks for your kind words!
The merged_*.mgz file is just a 4D mgz file where each frame corresponds
to one of the 18 tracts. The only special thing about this mgz file is
that it has some special fields in its header that tell freeview how to
display each tract (color, name, and
This issue has come up on the list a few times recently. Please search for
your error in the email archives before posting to the list. Thanks.
On Thu, 6 Jun 2013, std...@virgilio.it wrote:
Hi Anastasia,
I have resolved the previous problem by writing configuration file with sudo
nano in
Is the setenv SUBJECTS_DIR line really commented out? You must set
SUBJECTS_DIR, see the example configuration file on the wiki and under
$FREESURFER_HOME/bin/dmrirc.example.
On Wed, 5 Jun 2013, std...@virgilio.it wrote:
Hi list and Anastasia,
I'm performing a set of data with tracula
What do you get when you run echo $SUBJECTS_DIR?
On Thu, 6 Jun 2013, std...@virgilio.it wrote:
Hi Anastasia,
yes, I have check the SUBJECTS_DIR. I do not understand why all previous
configuration file start normally and this no.
Do you note some line that might be wrong additionally to
or are there other fixes you suggest?
Thanks again!
Skyler
- Original Message -
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: sholl...@uwm.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, May 21, 2013 10:40:59 AM
Subject: Re: [Freesurfer] tracula error
Hi Skyler
this make sense?
Matt
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 12:31 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula problem
Hi Matt - Can you source try this on the command line
Hi Celine - The way this average is computed for pathstats.byvoxel.txt is
by averaging the values for each one of the sample paths that are drawn by
the MCM algorithm. This essentially weighted sinced voxels that more
sample paths go through will be counted more than voxels that fewer sample
Hi Vincent - Thanks for bringing this to my attention. I can see what
might cause this glitch (only in the longitudinal case) and I'll fix it in
the next version.
In the meantime, if you delete one of the two identical lines from
cpts.map.txt, and then rerun the dmri_pathstats command line
for this tract of this
subject? Thanks!
Vincent
Am 5/20/2013 10:31 AM, schrieb Anastasia Yendiki:
Hi Vincent - Thanks for bringing this to my attention. I can see what might
cause this glitch (only in the longitudinal case) and I'll fix it in the
next version.
In the meantime, if you
To: Anastasia Yendiki
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] TRACULA outputs out of expected range
Hi Anastasia,
Thank you for your response. I think I figured out what was the problem: The
delimiter for the 3 column .bvec file MUST be SPACE/TAB, otherwise
Hi Benjamin - This means that the initial guess for the path based on the
atlas average is way off, due to poor alignment between your subject and
the atlas subejcts. Ways to get around this is to look into the options
for registration, whether diffusion-to-anatomical or anatomical-to-atlas,
Hi Celine - Since 5.2, there are 2 types of measures in the
pathstats.byvoxel.txt file: The value at every point along the trajectory
sampled at roughly the center of the bundle, or the value at every point
along the trajectory averaged over the width of the bundle. Sorry, there
are no other
Hi Skyler - How does the brain mask look like? Any major chunks of brain
missing in the area of the left uncinate? That's the tract where the error
occurs, and based on this info in the log file, I'm guessing it's a
masking issue:
[...]
INFO: Rejected 4221 streamlines for straying off mask
Hi Matt - Can you source try this on the command line:
source dmrirc_53beta
echo $b0mlist
echo $b0plist
Are these filenames correct, do these files exist? This is how you define
them in your configuration file:
set b0mlist = (`ls ${subjlist}/fmag/MR.* | sort -n | head
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