Hi Knut - What are the permissions of this file? One thing you could try
is to run bedpostx on /media/Elements/freesurfer/dti/1/dtsave/1/dmri
directly from the command line instead of through trac-all and see if that
works (monitor is a script that bedpostx launches that prints to the
screen t
e
>
> University of Basel
> Birmannsgasse 8
> 4055 Basel - Switzerland
>
> david.coy...@unibas.ch
> tel: +41(0)612.670.240
>
> Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki:
>
>>
>> Hi all - By popular demand we've posted the dmri_*
Hi David - The path.map file is the maximum a posteriori (MAP) estimate of
the path. That is, of all the paths that were generated by the algorithm
and summed to create the posterior distribution path.pd, this is the path
that on average over all its voxels maximizes the posterior probability
appears to contain the first pathway (lh.ccg).
>
> David
>
> Am 23.08.2011 um 17:06 schrieb Anastasia Yendiki:
>
>>
>> Hi David - Glad to hear things are working! I can look into
>> dmri_mergepaths and see if something is wrong with the snow leopard build.
&g
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
On
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
processi
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 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 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 loo
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
ing-Hong Yeh wrote:
> Hi Anastasia,
>
> The both ends were not terribly off of the white matter, though the
> lower end was a bit off at the level of decussation. any suggestion in
> fixing this?
>
> Thanks.
>
> ping
>
> On Thu, Sep 22, 2011 at 12:51 PM, Anastasi
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 runnin
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 wa
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 th
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.m
800.
>
> Ammar
> ____
> 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 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 underl
? Would the
> probabilistic tractography implemented in FSL be good in working
> around this problem by lowering the threshold for tract segmentation?
>
> Thanks.
>
> Ping
>
> On Thu, Sep 22, 2011 at 1:18 PM, Anastasia Yendiki
> wrote:
>>
>> Hi Ping - There are
ocessed
> 45 slices processed
> 46 slices processed
> 46 slices processed
> 46 slices processed
> 46 slices processed
> 47 slices processed
> 47 slices processed
> 47 slices processed
> 48 slices processed
> 48 slices processed
> 49 slices processed
> 49 slices pr
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 /home/joana/FIU/H_
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
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
ssional Research Assistant
> Department of Psychiatry
> University of Colorado Anschutz Medical Campus
> 303-724-5490
> ____
> From: Moiyadi, Ammar
> Sent: Friday, September 23, 2011 12:31 PM
> To: Anastasia Yendiki
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject
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 a
(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
wrote:
I'll have to refer you back to the freesurfe
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
_
weird, but the ones
using 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
wrote:
Hi Ping-Hong,
Yes, you can set usemaskanat = 0 in your dmrirc, and then
hanks.
ping
On Wed, Oct 19, 2011 at 2:52 PM, Anastasia Yendiki
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
On Tue, 18 Oct 2011,
f
forceps major (blue ones are first and the reds are the second
attempt), where the brain masks look fine.
Thanks.
Ping
On Wed, Oct 19, 2011 at 4:58 PM, Anastasia Yendiki
wrote:
Glad things are moving in the right direction. Now it looks like maybe one
of the control points of the path is no
p 28, 2011 at 5:07 PM, Anastasia Yendiki
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 are there
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
run
buckls@paris dmri.bedpostX]$"
+_+_+_+_+_+_+_+_+_+_
Do you have any advice for getting passed 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 y
are using
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:
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
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
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 li
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 wrote:
case I reran trac-all with the 'usemaskanat = 0'
> setting 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
used. However, the end points of the tract were
>>> still within the mask. Just in case I reran trac-all with the
>>> 'usemaskanat = 0' setting and a more generous bet threshold. Even with
>>> these changes I still saw the problem with the bbregister version
Blazey wrote:
>>>>
>>>>> Hi Anastasia,
>>>>>
>>>>> Thanks so much for your quick reply. As far as I can tell the masks
>>>>> seem
>>>>> fine. There was a small amount of erosion around the edge of the brain
>>&g
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 ti
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
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 woul
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 up
header info
Error: failed to open 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
wrote:
Hi Scott - Here are the t
Hi Scott - Which version of FSL are you using? I cannot replicate this
behavior of fslstats on our data.
Thanks,
a.y
On Mon, 12 Dec 2011, Scott Hayes wrote:
> Hi,
> I have received the following error message (copied from trac-all.log file).
>
> fslstats -t /Volumes/RAID_4TB/futhink/nc331_reco
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
wrote:
Hi Scott - Which version of FS
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 loo
logs
> 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
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 Everyo
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
This documentation is still a work in progress. Thank you for
understanding and we appreciate your continuing feedback!
a.y
| Anastasia Yendiki, Ph.D.
| Martinos Center for Biomedical Imaging
| 149 13th St. Suite 2301
| Charlestown, MA 02129
| Tel
Hi Gabriel - We don't develop slicer, so we don't know what the
assumptions are but here's where you can find their tutorials, if that
helps:
http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training
If you scroll down you'll find the one on importing freesurfer files.
a.y
On W
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 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, you
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
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.
Trac
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.
+++
iple the bvecs(extracted from DICOM) by [-1 -1 +1], but
> NOT [+1 -1 +1].
> Why are they different?
>
> Thanks!
>
>
> 2012-02-04
>
>
>
> Xiangzhen Kong
>
>
>
> ·¢¼þÈË£º Anastasia Yendiki
> ·¢ËÍʱ¼ä£º 2012-02-04 00:48:58
> ÊÕ¼þÈË£º Xiangzhen Kong
> ³
an think of that this may be happening?
>
> Thanks in advance,
>
> Kiely
>
>
> On Fri, Dec 23, 2011 at 2:42 PM, Anastasia Yendiki <
> ayend...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Kiely - It'
ed those trailing
>>>> slashes. Could you run this again and let us know if it solves the
>>>> problem?
>>>>
>>>> Hope this is helpful,
>>>> Priti
>>>>
>>>>
>>>>
>>>>
>>>>
>&
l,
>>>> Priti
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>> Thank you Priti and Anastasia,
>>>>>
>>>>> Anastasia, just wanted to clarify, I meant
>>>>> $dtroot/$subjectname/dmri/bvecs
".
> Visually my bval/bvec files seem 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 wrote:
>> I see, thank you :)
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 t
576
> -0. -0. 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
>>
same error.
>> Chris
>>
>> Anastasia Yendiki wrote:
>>
>> > When you run that bet command line outside of trac-all, does it give you
>> > the same error?
>> >
>> > On Wed, 15 Feb 2012, Chris Watson wrote:
>> >
>> &
.3~1/RELEASE_X86_64
> x86_64
>
> trac-preproc exited with ERRORS at Thu Feb 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
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
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 on
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
No
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 wh
Come to think of it, when I ran bedpostx, 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 d
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. Tha
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
ion 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:
>>
&g
anks
> JG
>
> On 03/26/2012 12:41 PM, Anastasia Yendiki wrote:
>>
>> If you want to register your DWI to T1, you should register to
>> mri/brain.mgz. You can do this with bbregister, or with any affine
>> registration tool of your choice.
>>
>> On M
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 F
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 previo
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
disc
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 Siem
Hi Carolina - The bvecs and bvals in the tutorial data should have 3 lines
and 1 line, respectively, with 70 entries in each line. Is that not what
you have?
For different possibilities for inputs, please see the tracula wiki page,
and particularly the link to the example dmrirc file:
I have to
recon-all my structural data and to have the orig DWI
dicoms in order to use trac-all, right?
Thanks for the help!
2012/4/2 Anastasia Yendiki
Hi Carolina - The bvecs and bvals in the tutorial data should have 3
lines and 1 line, respectively, with 70 entries in
each line. I
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 do
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:
http://surfer.nmr.mgh.harvard.edu/fswiki
ORS at Wed Apr 11 18:03:33 CEST 2012
2012/3/27 Anastasia Yendiki :
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
I'm doing 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
wrote:
Hi Viviana - If you upload this data set I'm happy to look at it.
Also,
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 in
Gif sur Yvette – FRANCE
On Wed, Apr 18, 2012 at 1:18 AM, Anastasia Yendiki
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 for i
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 f
t 12:52 AM, Anastasia Yendiki
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/vi
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 s
I changed to fsl_sub because the cluster I am
> using had my modifcation to fsl_sub. Should I change back?
>
> Knut J
>
>
>
>
>
>
>
> On 04/27/2012 05:06 PM, Anastasia Yendiki wrote:
>>
>> Hi Knut - If I understand correctly, your modification was replac
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 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 Ma
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
uired 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
Hi Gabor - The input DWIs can be in any format that can be read
by mri_convert, including the NIfTI format. The gradient
direc
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 - it
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
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