Hi Peggy - If you upload the tracula output directories for me here, I'll
take a look:
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks!
a.y
On Fri, 19 Jun 2015, Peggy Skelly wrote:
It's been a while, but we are still working on computing our tracts in
tracula!
We are still stru
Hi Peggy - Thanks for sending me the data. The tract reconstructions look
much different than what I'm used to seeing, from other users or our own
data. Visually, it seems to me like the 100K one is more converged. The
probability distributions of the pathways look much sharper, so when
thres
n-similar output, but run variability? I'm wondering if
they use the same random number seed for the mcmc algorithm?
Peggy
On Fri, Jun 19, 2015 at 3:04 PM, Anastasia Yendiki
wrote:
Hi Peggy - Thanks for sending me the data. The tract reconstructions look
much different than
just ran 2 scans through the trac-all -path for the 100k run(s)
(results from 2nd run at 100k fa_avg_wgt for rh.cst = 0.532818).
Peggy
On Mon, Jun 22, 2015 at 5:10 PM, Anastasia Yendiki
wrote:
Ok, I didn't realize you were using the longitudinal stream. So
the data sets that you sen
Hi Pedro - The point-wise stats from tracula are a 1D sequence of values,
so they cannot be analyzed with functions that work on 2D data on the
surface or 3D data in the volume. At present, you'd have to do a seperate
analysis for every point along the tract. It's on my list to implement a
mo
Hi Michael - Thanks for finding longitudinal tracula attractive! :) The
paper is under review. There's an ISMRM abstract that I can send you.
About the cluster customization: bedpostx_mgh and fsl_sub_mgh are
supersets of bedpostx and fsl_sub, so they have all the original
functionality of th
Forgot to reply re: merging. You have to merge them yourselves, sorry.
On Mon, 6 Jul 2015, Harms, Michael wrote:
Hi Anastasia,
We are looking at running TRACULA on some data, where we were attracted by the
longitudinal component of TRACULA. Is a paper on the longitudinal
aspect of TRACULA i
the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
>
>
>
> On 7/6/15 12:00 PM, "Anastasi
Hi Celine - You can get this from the protocol print-out from the scanner.
a.y
On Mon, 13 Jul 2015, Celine Louapre wrote:
> Hi Anastasia and Tracula experts,
> We are running a new set of tracula analysis from Bay 6 and are
> wondering how do we define the number of echo spacing in the dmrirc
>
Hi Peggy - It's trying out all the paths from all the atlas subjects for
candidates to use to initialize the path in your subject. If it's having
such a hard time finding a good candidate, I suspect that something went
wrong earlier in the pre-processing, something like a serious registration
Hi Peggy - That's a good question and yet another great feature request. I
can think of one completely inelegant hack for doing this right now in
the absence of an actual feature.
Let's say the path to the lh.cst stats of your subject is:
subj1/blah...lh...blah/pathstats.byvoxel.txt
Hi Leora - I regret to inform you that it's the processing that has
failed, pretty much for all the tracts. I'm guessing it's an earlier
preprocessing (likely registration) step that has failed.
If you upload the tracula output directories (dmri, dlabel, dpath) of your
subject for me here, I
Hi Daniel - You should be able to use CVS with longitudinal tracula,
although it's probably the least tested combination of options in there.
It sounds like this may be a bug. Can you please send me the full log file
and full config file? Thanks!
a.y
On Tue, 4 Aug 2015, Daniel Myall wrote:
Hi Amelia - One day we'll have a proper statistical analysis function with
multiple comparisons correction along the tract, but until then the name
of the -stat option is mostly aspirational. It'll find the point-by-point
correspondence among subjects and produce the table but you'll have to us
Hi Janosch - Are you by any chance using the dev version of freeview?
a.y
On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote:
Hi Anastasia and list,
I'm trying to do analyses along the tract with the path_stats_byvoxel files.
When I am visualizing the points using the waypoint functionality of
15 4:00 AM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Date: Fri, 7 Aug 2015 18:23:41 -0400 (EDT)
From: Anastasia Yendiki
Subject: Re: [Freesurfer] TRACULA longitudinal processing fails when
inter-subject registration to CVS template
To: Freesurfer support list
Cc: Tracy Melzer
Messa
Hi Janosch - That's strange. Can you send me one of those mean path files?
Thanks,
a.y
On Sun, 9 Aug 2015, Janosch Linkersdörfer wrote:
Hi Anastasia,
yes, I am. But it looks similar in the distributed version :(
Thanks,
Janosch
Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki :
if it actually works well, will be happy to release.
>
> Kind regards,
>
> Daniel
>
>
> On 11/08/15 11:32 AM, Anastasia Yendiki wrote:
>>
>> Hi Daniel - That "hack" is not as bad as it may sound. The structural
>> images that TRACULA uses from the
umbia University
NYS Psychiatric Institute
Division of Child and Adolescent Psychiatry
1051 Riverside Drive
New York, NY 10032
amir...@nyspi.columbia.edu
Office: 646-774-5820
On 8/7/15, 6:17 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" wrote:
Hi Leor
Hi Bahram - Can you please send us your entire trac-all.log file? Thanks!
a.y
On Fri, 14 Aug 2015, B M wrote:
Dear experts,
I have the last version of tTrakula. i did the first step with
trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
This worked properly to the end as shown
, I am. But it looks similar in the distributed version :(
Thanks,
Janosch
Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki :
Hi Janosch - Are you by any chance using the dev version of freeview?
a.y
On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote:
Hi Anastasia and list,
I'm trying
:
Hi Anastasia,
Please find attached the trac-all.log file. Thank you very much for your help.
Bahram
2015-08-17 19:31 GMT+02:00 Anastasia Yendiki :
Hi Bahram - Can you please send us your entire trac-all.log file? Thanks!
a.y
On Fri, 14 Aug 2015, B M wrote:
Dear
thanks for looking into this.
Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki :
Hi Janosch - Looking at the stats files of your subjects, just by a quick count
of the number of lines, I see that there are some subjects that have only 1
time point and some that have multiple time points, an
trac-all -stat"
with all subjects together. And then tell us what other problem you find
:)
Best,
a.y
On Thu, 20 Aug 2015, Janosch Linkersdörfer wrote:
Hey Anastasia,
Am 19.08.2015 um 14:03 schrieb Anastasia Yendiki :
Hi Janosch - There is a bug in how the output paths are saved when lon
everything for me here?
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks,
a.y
On Thu, 20 Aug 2015, B M wrote:
Hi Anastasia,
please find the files in attachment.
Best regards
Bahram
2015-08-19 21:55 GMT+02:00 Anastasia Yendiki :
Hi Bahram - There are some errors in there
Hi Michelle - It sounds like there is something wrong with this subject
that affects a part of the brain that the forceps minor of the corpus
callosum goes through. It could be a piece of the brain mask missing, or
poor segmentation of the T1, or poor T1-to-diffusion registration. Can you
loo
Hi Barbara - Yes, just correct with the method of your choice, apply the
rotation to the gradient vectors, pass the corrected images and gradient
vectors to tracula, and turn off the default eddy correction (then it
won't rotate anything, either). I'll probably make it an option in the
upcomin
recommendations. I will try to fix
These Problems. I would like to ask you one more question. Is there any
command which could help me to invert the gradient vectors for my DWI
scan in the z direction?
Best
Bahram
2015-08-24 17:57 GMT+02:00 Anastasia Yendiki :
Hi Bahram - I looked at your
Hi Andrea - Make sure that the b-value table and gradient table are saved
as plain text files. When you run the "more" command on them, you should
see all the numbers and only numbers.
This is what I get when I run more on your files (this may vary depending
on the flavor of unix you have on
iles again? I checked with the command "more bvecs" and
was ok. I really need to solve this problem urgently. I am also sending the dmri
folder.
Thank you very much!
2015-09-04 18:04 GMT-03:00 Anastasia Yendiki :
Hi Andrea - Make sure that the b-value table and gradient table are
Hi Thomas - If you have a .mat transform, try dmri_trk2trk to apply it to
a .trk file. You have to specify reference volumes for the input and
output space.
Best,
a.y
On Wed, 9 Sep 2015, Thomas Potrusil wrote:
Dear FreeSurfers !!
I´m trying to bring a trackvis .trk file to freesurfer space
t file. What
would be the correct format? Unicode-8, Unicode-16, etc.
Thank you very much!
2015-09-08 11:37 GMT-03:00 Anastasia Yendiki :
I need to see the log file. Based on the output files that you
sent me, it ran further along this time, so you must be running
into a dif
ed ROIs. I played
around with mri_segstats but I was not able to open/access the
TrackVis .trk file...
Any suggestions?
Best regards, Thomas
Gesendet: Mittwoch, 09. September 2015 um 15:51 Uhr
Von: "Anastasia Yendiki"
An: "Freesurfer support list"
Betreff: Re: [Freesurfer]
, 2015 at 8:25 PM
Subject: trac-all -prep ERROR: Must specify input table of gradient vectors
To: Anastasia Yendiki
Hello Anastasia,
I have been specifying the subject and the first dicom in the DTI series rather
than creating a configuration file, and it was working well,
but now that I am
ssage --
From: Katherine Damme
Date: Thu, Sep 10, 2015 at 8:25 PM
Subject: trac-all -prep ERROR: Must specify input table of gradient
vectors
To: Anastasia Yendiki
Hello Anastasia,
I have been specifying the subjec
Hi Peggy - Are you by any chance using the development version of
freeview? Or are you using the one that came with the 5.3 release?
a.y
On Tue, 15 Sep 2015, Peggy Skelly wrote:
HI,
I'm looking at the mean path output from the tracula tutorial. I ran 'trac-all
-stat' on the tutorial data a
don't recall replacing the Freeview.app file. But my memory isn't
what it once was ;)). I'm
using freesurfer-Darwin-lion-stable-pub-v5.3.0. Freeview.app is 129 MB and it's
About box says it's Version
1.0 Build Dec 19 2014 16:29:56.
Peggy
On Tue, Sep 15, 2015 at 5:08
Hi Karuna - Which build of freesurfer are you using? It's written in this
file: $FREESURFER_HOME/build-stamp.txt
a.y
On Thu, 24 Sep 2015, Karuna Subra wrote:
Dear Freesurfer experts,
I've been having issues with the trac-prep script opening the bvals file within
the dmri folder that it
c
Hi Karuna - Please read my question again. What's in the build stamp file?
a.y
On Thu, 24 Sep 2015, Karuna Subra wrote:
Hi Anastasia,
We're using version freesurfer 5.3.
On Thu, Sep 24, 2015 at 8:43 AM, Anastasia Yendiki
wrote:
Hi Karuna - Which build of freesurfer are
Anastasia,
We're using version freesurfer 5.3.
On Thu, Sep 24, 2015 at 8:43 AM, Anastasia Yendiki
wrote:
Hi Karuna - Which build of freesurfer are you using? It's written in this
file:
$FREESURFER_HOME/build-stamp.txt
a.y
On Thu, 24 Sep 2015, Karuna Subra wrot
It's trying to find a file called SUBJECTS_DIR/Enzo_recon1/dti.nii. This
is a relative path, i.e., it's trying to find it under the directory where
you are currently cd'd.
This seems like a problem with defining paths properly for unix, rather
than a tracula problem per se.
On Wed, 30 Sep
Hi Laura - It appears that you're using a different configuration file
than the one you attached. To use Laura.txt, you should pass it as the
argument to the "-c" option (instead of
/scratch/lm618/tutorial_data/diffusion_tutorial).
Best,
a.y
On Sun, 8 Nov 2015, L. Moreno-Lopez wrote:
> Dear
Hi Amanda - These are probability distributions, so this has to do with
how you threshold them. When you use the -tv option in freeview to open
the merged file with all tracts, each of them is thresholded at 20% of its
maximum. When you open one of them as a plain volume, freeview doesn't do
Hi Ju - Are you using the same computer and are logged in in as the same
user when you create the directory manually and when you run trac-all?
It's hard to replicate this error. What the program does at that point is
run the system call
mkdir -p
/scratch/TRAC_TEST/First_Exp/First_Exp_
Hi Deniz - It sounds like the reconstruction for this particular tract and
subject may have failed. You can try reinitializing it by using the reinit
variable in your configuration file (search reinit in the freesurfer email
list archives for previous posts on this). If you try that and the er
Hi Ruth - It expects the output format of eddy_correct. It then computes
the transforms between consecutive frames from the transforms between each
frame and the reference frame.
Best,
a.y
On Sun, 29 Nov 2015, Ruth Carper wrote:
Hi,
I'm hoping to use the dmri_motion tool to quantify motio
Hi Noa - If you're still having this issue, please send the complete
trac-all.log file and your configuration file. It's impossible to guess
what goes wrong without seeing the full output.
Best,
a.y
On Fri, 30 Oct 2015, Golan, Noa wrote:
> Hi,
> I am currently analyzing DTI data and I am havi
Hi Doug - This post from the archives addresses the same error message.
Please check if this fixes it for you, too:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37920.html
Best,
a.y
On Mon, 9 Nov 2015, Douglas Merkitch wrote:
Hey D,
I also had the same error in the same
Hi John - The values are weighted (multiplied) by the probability
distribution (path.pd.nii.gz) at the same voxel. So they are the expected
values, from a probabilistic standpoint. The distribution is thresholded
at 20% of its maximum by default (this is a parameter in dmri_pathstats).
Best,
Hi Simon - You are correct, this was a bug specific only to running the
-stat part of trac-all with the CVS template. Your work-around was
correct. I've fixed the bug so that, as of the next version, the
configuration as shown in the sample config file should work with the
-stat part as well.
Hi John - This is a probabilistic tractography method, so it draws samples
from the probability distribution of the particular tract, and then adds
up these sample streamlines to estimate the probability distribution. The
number that you see is the number of sample streamlines. It's a paramete
Hi Doug - Yes, this is possible and indeed it is recommended to use the
latest version of tracula.
Best,
a.y
On Fri, 6 Nov 2015, Douglas Merkitch wrote:
Hello FreeSurfer experts,
We have a large dataset that was processed in FreeSurfer v 5.1 and we would
like to run tracula on the dataset.
Hi Henrik - There's no explicit parameter in the current version, but you
can run bedpostx the multi-exponential model yourself, and then let
tracula use the orientation estimates from that model (as long as the
output dir is called dmri.bedpostX, it'll read the files from there).
We are in
Hi Katherine - I don't see this error in the log file, but the last
command that it ran before it stopped was this:
mri_probedicom --i
/media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm
> /media/Data/Temple/Temple_Tracula/31313422
Here is all of the output to the terminal.
On Thu, Dec 17, 2015 at 5:12 AM, Anastasia Yendiki
wrote:
Hi Katherine - I don't see this error in the log file, but the
last
command that it ran before it stopped was this:
mri_probedicom --i
/media/Data/Temple/Temp
Hi Katherine - Have you looked at any of the intermediate images? Do they
look normal?
a.y
On Mon, 21 Dec 2015, Katherine Damme wrote:
> Hello Everyone!
>
> It looks as though my prep and bedp stages completed properly, but the prep
> stage ends in a segmentation
> errror.
>
> See attached
normal with a normal range and bizarre merged
files.
What do you think could be a cause of these odd merged files?
On Tue, Dec 22, 2015 at 1:54 PM, Anastasia Yendiki
wrote:
Hi Katherine - Have you looked at any of the intermediate images? Do they
look normal?
a.y
On Mon
Hi Emad - I wouldn't do tractography to check the gradient vectors. All
you need is to look at are the principal eigenvectors of the tensors
(dmri/dtifit_V1.nii.gz), displayed as lines (not just RGB map, that's less
informative). If, for example, the z coordinates need to be inverted, then
th
Hi Ruth - Apologies for the omission. It's radians, not degrees. I'll
update the tutorial.
Best,
a.y
On Wed, 27 Jan 2016, Ruth Carper wrote:
What are the units of measure for translation and rotation as output in the
dwi_motion.txt file from
Tracula? It's not stated in the output file or o
That's correct!
On Wed, 27 Jan 2016, Ruth Carper wrote:
Anastasia,
Thanks for the quick reply.
And millimeters for the translation?
Ruth
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo
Hi Karuna - I haven't seen this before. Can you check which version of
freeview you have? Is it the one that came with freesurfer 5.3 or a newer
version of freeview that you downloaded separately from the web site?
a.y
On Thu, 28 Jan 2016, Karuna Subra wrote:
HI Anastasia,
I'm new to trac
Hi Alan - A nifti file with the gradient tables and b-values embedded? All
freesurfer programs can handle nifti volumes, compressed (.nii.gz) or not
(.nii). You can pass those volumes to TRACULA, and pass the gradient table
and b-value table as separate files.
Run "mri_convert --help" to see
Hi Peter - Have you defined "bvecfile" in your configuration file? I
suspect it doesn't know where to find the gradient table.
a.y
On Thu, 4 Feb 2016, Parzer, Peter wrote:
> Hi,
>
> trying to do my first steps with tracula I got stuck early in the
> preprocessing step. The DICOM import and pr
Hi Deniz - It seems that it finds the folders of the 2 time points, but
not the folder of the longitudinal base template. This is the template
that longitudinal recon-all creates in its 2nd processing step. In your
case, it would be
/data_august/Deniz/DTI_long/subjects/med_AhJa94
Doe
s
> in Siemens DICOM format, and my data is in Siemens DICOM format. Do I need
> this additional step to extract bvec and bval from die DICOM images? And what
> is the best way to do it?
>
> Peter
>
> Von: freesurfer-boun...@nmr
Hi again Deniz - This may be confusing but with longitudinal TRACULA there
are separate trac-all.log files in each time point's directory and in the
within-subject template's directory. The former are for things that are
run independently for each time point (mainly pre-processing) and the
la
only 1 set of BVECS/BVALS. Can this set be 'generically'
used for all the images, given that they have been
acquired on the same scanner?
thanks,
Alan
On Wed, Feb 3, 2016 at 4:17 PM, Anastasia Yendiki
wrote:
Hi Alan - A nifti file with the gradient tables and b-v
Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: on behalf of Alan Francis
Reply-To: Freesurfer support list
Date: Friday, February 5, 2016 at 3:57 PM
To: Anastasia Yendiki
Cc: Freesurfer support list
Subject: Re: [Freesurfer] DTI - Tracula question
Hi Anastas
n 29, 2016 at 4:37 PM, Anastasia Yendiki
wrote:
Hi Karuna - I haven't seen this before. Can you check which version of
freeview you have? Is it the one that came with
freesurfer 5.3 or a newer version of freeview that you downloaded
separately from the web site?
a.y
Hi all - I have just posted a tracula software update. This update adds
some new functionality without any changes to any existing functionality,
so you can use it with any analyses you have already done in 5.3.
What's new:
1. Compute measures of head motion, as in our recent paper:
http://www.
jects as is pointed out later by your new feature?
> Best,
> Vincent
>
>
> Am 12/9/2013 9:23 AM, schrieb Anastasia Yendiki:
>> Hi all - I have just posted a tracula software update. This update adds
>> some new functionality without any changes to any existing functi
Hi Emad - The bvecs file that you sent is formatted so that each column is
a gradient vector. The first column is [0, 0, 0] and this corresponds to a
b-value equal to 0 in the bvals file. So that's fine. You'll just have to
download the latest update to tracula to be able to use this column-wis
Hi Ruth - Glad to hear this is useful to you. The rotation and translation
parameters are extracted from the affine registration of each DWI volume
to the first volume, which in trac-all is performed by eddy_correct.
a.y
On Tue, 10 Dec 2013, Ruth Carper wrote:
Hi Anastasia,
We discussed yo
Hi Matthieu - This sample dmrirc file is meant for use with the version of
tracula that's in 5.3, not 5.1. I would strongly recommend switching to
that version of tracula anyway, due to improvements in performance and
speed.
a.y
On Wed, 11 Dec 2013, Matthieu Vanhoutte wrote:
Hello experts
ample" and modify
into "dmrirc.tutorial", so this is meant for use with the version of tracula
that's in 5.1 ?
I will switch to the last version, but before this I'd like to succeed
launching tracula on 5.1...
Best,
Matthieu
2013/12/11 Anastasia Yendiki
Hi Matthieu
2:58 PM, Anastasia Yendiki
wrote:
Of course, you can specify which tracts you want to reconstruct
in the configuration file. Both the sample configuration file in
$FREESURFER_HOME/dmrirc.example and the tracula tutorial have
the info on how to do this.
On Thu, 5 Dec
Hi Matthieu - This error had to do with a change in bedpostx's command
line arguments after an FSL upgrade. The problem is fixed in the newer
version of tracula. Again, I'd strongly recommend upgrading to the newer
tracula.
Hope this helps,
a.y
On Thu, 12 Dec 2013, Matthieu Vanhoutte wrote:
Hi Gari - This is coming from the new code in the update that I posted
recently. Which build of freesurfer 5.3 and which build of the tracula
update do you have? Using our Centos 6 build, I was not able to replicate
your error.
a.y
On Wed, 11 Dec 2013, Garikoitz Lerma-Usabiaga wrote:
> Hi An
A?
--Ruth
____
From: Anastasia Yendiki
To: Ruth Carper
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Tuesday, December 10, 2013 8:28 PM
Subject: Re: [Freesurfer] New features in TRACULA
Hi Ruth - Glad to hear this is useful to y
2013 at 8:11 PM, Anastasia Yendiki
wrote:
Sorry, I can't tell what happened without looking at the log
file. Could you send it along?
On Wed, 11 Dec 2013, David Soto wrote:
hi Anastasia, I tried then to recontruct the
remaining trac
Hi Laura - Please read the information on the wiki page:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
Tracula in 5.2 and 5.3 is identical. The motion measures are not in 5.3
but in a newer update, that you can download from that wiki page.
As an aside, you should not be using reco
tX whereas the TBSS processing steps were all run with a
> mask extracted with BET. Is this different mask a problem for following
> voxelwise TBSS analysis of the data in all_F*_skeletonised?
>
> Best, Vincent
>
>
>
> Am 10/11/2013 2:13 PM, schrieb Anastasia Yendiki:
>
Hi Francesco - Can you please send us your tracula log file, from
scripts/trac-all.log? It's impossible to guess what went wrong without
seeing the log file.
Thanks,
a.y
On Tue, 17 Dec 2013, Francesco Baldacchini wrote:
Hi everybody,
I'm having problems running the trac-all -path command.
moved.
--Ruth
From: Anastasia Yendiki
To: Ruth Carper
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, December 17, 2013 1:28 PM
Subject: Re: [Freesurfer] New features in TRACULA
Hi Ruth - If you download the update and unzip it, you'll see an
executable called dmri
elps,
a.y
On Wed, 18 Dec 2013, Francesco Baldacchini wrote:
Ciao Anastasia,
Here is the log file you requested. Thanks
Francesco Baldacchini
2013/12/17 Anastasia Yendiki
Hi Francesco - Can you please send us your tracula log file,
from scripts/trac-all.log? It's impossible to guess w
dy_correct) and your dropout
measures (3rd and 4th values) were 0 and 1 respectively for every brain.
--Ruth
From: Anastasia Yendiki
To: Ruth Carper
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, December 18, 2013
Are you running this with only one subject? What are you trying to do? The
purpose of this step is to combine measures from multiple subjects.
On Fri, 27 Dec 2013, std...@virgilio.it wrote:
I'm sorry and I'm attaching the files.Thanks,
Stefano
trac-all -stat -c $FREESURFER_HOME/Control0
Hi Sal - It looks like a problem with the spaces at the end of the lines
of the bvecs file. If you remove those spaces, it should work. Thanks for
bringing this to my attention - the row-formatted bvecs files are new in
this version and I'll make sure to allow them to have spaces at the end
o
Hi Sal - The 0's should be included as before. Can you send an example of
these bvals/bvecs file that are causing this problem? If they are also
formatted in rows as with your other example, I'd also check for spaces a
the end of the lines.
Thanks!
a.y
On Fri, 3 Jan 2014, Salil Soman wrote:
Hi Jon - Have you checked the brain mask and aparc+aseg for this subject?
Anything missing there that might affect the left ILF?
a.y
On Wed, 8 Jan 2014, Jon Wieser wrote:
>
> Dear freesurfer experts
> I'm getting the following error when runing trac-all -c dmrirc_single_subject
> -path
>
>
>
Hi Jon - Again I'd look at this subject's aparc+aseg, as well as the DWIs
themselves to see if there's anything going on that might affect the left
ILF.
a.y
On Wed, 8 Jan 2014, Jon Wieser wrote:
>
>
> Hello
> I'm getting the following error when running trac-all -c dmrirc -prep
>
> INFO: Dist
Hi Gari - So if I understand correctly, your inputs to probtrackx are:
mri/hippo_subfield_in_diffusion_space.nii
dmri.bedpostX/merged
dmri.bedpostX/nodif_brain_mask
If these all come from the output of tracula, aren't these all in LAS
orientation?
a.y
On Thu, 9 Jan 20
mostly fsl programs are being used to do the
flips, and then tkregister2 and bbregister for the registrations)
Thanks for the help!
Gari
On Sat, Jan 11, 2014 at 1:31 AM, Anastasia Yendiki
wrote:
Hi Gari - So if I understand correctly, your inputs to
probtrackx are:
Hi Benjamin - The ball-and-stick model doesn't require b-values in the
tens of thousands, that would be for DSI type acquisitions.
a.y
On Sat, 11 Jan 2014, Roschinski, Benjamin wrote:
Dear Anastasia,
in the FS Tutorial/Running Freesurfer you say TRACULA uses bedpostX to fit
the ball-and-st
Hi Christian - Does your data set consist of 1 low-b image and 3
diffusion-weighted images? You'll need at least 6 diffusion-weighted
images to fit tensors to your data, and for tractography you'll need at
least a few tens of them.
Best,
a.y
On Fri, 10 Jan 2014, christian buhl wrote:
> Hi
>
Hi Francesco - The bvecs file that you're attaching has only 3 vectors,
while the bvals file has 65 b-values. Are these your original files, or
the ones saved by trac-all in the dmri/ directory?
a.y
On Mon, 13 Jan 2014, Francesco Baldacchini wrote:
> Hi everybody,
> I'm trying to run the trac
at 3:08 AM, Anastasia Yendiki
wrote:
Has mri/hippo_subfield_in_diffusion_space.nii been actually
transformed to diffusion space by applying the anatorig2diff
transformation? I'm assuming that your diffusion data is not
0.5mm resolution? You can search for the name o
> Linux brain.umd.edu 2.6.32-358.6.2.el6.x86_64 #1 SMP Tue May 14 15:48:21
> EDT 2013 x86_64 x86_64 x86_64 GNU/Linux
>
> trac-preproc exited with ERRORS at Mon Jan 13 15:19:04 EST 2014
>
> Thanks for your help!
>
>
> Laura C. Anderson, B.A.
> Graduate Student
> Cl
the
tract, with the same probability across subjects, and afterwards obtain the FA
values
in order to correlate with behavior.
Thanks again!
Gari
On Mon, Jan 13, 2014 at 7:55 PM, Anastasia Yendiki
wrote:
Hi Gari - Yes, fslmaths should be able to do it, with -thrp 20.
a.y
ctory.
The original files are in attachment in this mail,
Francesco Baldacchini
2014/1/13 Anastasia Yendiki
Hi Francesco - The bvecs file that you're attaching has only 3 vectors,
while the bvals file has 65 b-values. Are these your original files, or
the
ones saved by t
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