Hi Sean,
You should look at the Exit_status. If it is '0', then your job ran
successfully. If it is '1' or something else, then there is an error. So
it looks like your job ran correctly.
Priti
> Hello,
>
> I'm running bedpostx_seychelles from the seychelles prompt (via trac-all
> -bedp -c $SUBJ
Hi Sean,
Are you sourcing Freesurfer stable 5.1 in seychelles? trac-all -bedp is
supposed to submit multiple jobs (one job for each slice, in addition to
bedpostx_pre and bedpostx_post).. When you ran trac-all -bedp did it
submit all of those jobs?
Priti
> Hi Priti,
>
> Thanks, but would seem th
Can you send us your configuration file (mytracula.conf) and log file (it
should be under scripts/trac-all.log). I can take a look.
Priti
> Hi,
>
> I am trying to run the last step of TRACULA. I used the command line:
>
> % trac-all -path -c mytracula.conf
>
> Here is all the info I got on the sc
d) might be
able to answer that question.
Hope that helps,
Priti
>
> Original Message
> Subject: Re: [Freesurfer] TRACULA dpath problem
> From:"XJ Kang"
>
Hi Torben,
Your trac-preproc exited with errors because of the following error.
Error: bvecs and bvals don't have the same number of entries
You should check to see if your bvals and bvecs have the same no.of lines
and then rerun trac-all -prep.
Priti
> Dear all,
>
> while running trac-all, I
Hi Ping,
The text files get created in the trac-all -prior stage. Maybe something
went wrong in that step. Is this the case for all the tracts or just for
this tract? If you can send us the trac-all.log file under the scripts
directory it'll be easier to troubleshoot as to what went wrong.
-Priti
e configure file in order to run
the "prior", although there are 7 b0 sparked in every 7 volumes. I think
"nb0=7" means the first 7 volumes will be assumed to
> non-diffusion weighted. Correct me if I am wrong.
> Thanks.
>
> Ping
>
>
>
> On Fri, Jul 29, 20
Hi Jürgen,
To chage the no. of anisotropic compartments in a voxel in bedpostx you
might have to run bedpostx_seychelles outside of tracula (instead of
running trac-all -bedp)
bedpostx_seychelles -n 3
You can try this out to see if it works for you.
-Priti
> Dear Tracula experts
>
> Is it po
Hi Carolina,
Tracula is a part of Stable v5.1.0 not Stable v5.0.0, so you need to
update your version.
-Priti
> Hi FS'users,
>
> I'm trying to do the Tracula tutorial but after set the configuration file
> I
> run the command trac-all
> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects
Hi David,
Can you visualize these tracts individually?
type in freeview -v lh.ccg_PP_avg33_mni_flt/path.pd.nii.gz
and to visualize the merged you could try
freeview -tv merged_avg33_mni_flt.nii.gz
If both of these do not work you can try running dmri_mergepaths
seperately using the following c
Hi Ansgar,
If you have your own bvals and bvecs, you should add the following extra
lines to your dmrirc file.
set bvalfile = /path/to/bvals.txt
set bvecfile = /path/to/bvecs.txt
set nb0 = *No. of low-b images* (In your case you can set nb0 to 5 and
tracula will use the first 5 images to get an a
Hi Ping,
Did you try adjusting the threshold for left cst tract? In freeview you
can find the tract labels in the left corner, if you click on the left cst
tract and use the threshold button below to decrease the threshold. Please
let us know if that improves the visualization.
Cheers,
Priti
Hi Paula,
Tracula uses anatomical labels/files from freesurfer cortical
reconstruction to build the posterior distribution of the tracts. It looks
like you may not have run freesurfer recon for your subject.
To run freesurfer recon for your subject please refer to the following page:
http://surf
(Uknown extension)
> Minor opcode: 3 (Unknown request)
> Resource id: 0x24
> Abort
>
>
> On Wed, Dec 7, 2011 at 12:52 PM, Priti Srinivasan <
> rspr...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Paula,
>>
>> Tracula uses anatomical labels/files from fre
t; freeview -tv
> /mindhive/gablab/users/cpdla/Documents/s1001/dmri/dtifit_FA.nii.gz*
> X Error: BadValue (integer parameter out of range for operation) 2
> Extension:146 (Uknown extension)
> Minor opcode: 3 (Unknown request)
> Resource id: 0x24
> Abort
> ba3:/>
&
Hi Shannon,
Thank you for the detailed email, outlining some of the aspects of the
tutorial that we could improve. We really appreciate your effort in
putting these things together and will definitely try to address your
concerns to the best of our ability.
Q2. I updated the wiki to correct the t
Hi Kiely,
I had a similar experience with one of my subjects, but I realized that
the original diffusion image had a lot of signal loss in various regions
and hence the subsequent registration steps failed.
It can happen when either intra-subject or inter-subject registration
fails. I would inspe
Hi Tanja,
It is supposed to be created automatically. Can you send your
configuration file and log file for us to see what's going on?
Thanks,
Priti
> Dear list,
>
> I try to run TRACULA pre-processing step and I get the following
> error: /dmri/bvecs: No such file or directory.
>
> I have a fol
Hi Tanja,
I think the problem may be due to the trailing slash you've included while
specifying $dtroot, $SUBJECTS_DIR etc.
setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1/
should be
setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1
trac-all usually adds the '
file to the one you sent, but unfortunately got
> the same error. I attach the log (although it is basically the same).
> Do you have any ideas what else can cause it?
>
> Thanks again,
> Tanja.
>
> On Fri, Feb 3, 2012 at 4:51 PM, Priti Srinivasan
> wrote:
>> Hi Tanja,
Hi Minjie,
The pathstats.byvoxel.txt gives the statistics of the higest probability
streamline of the posterior distribution of the tract and the
pathstats.overall.txt gives you average diffusion values for the whole
tract.
Please refer to the following:
http://surfer.nmr.mgh.harvard.edu/fswiki/
Hi Antonella,
The eigvals.nii is a 4D file that consists of 3 frames. Each corresponding
to the respective eigenvectors.
You can do the following to split them up:
fslsplit eigvals.nii eigval
This will give you three volumes:
eigval.nii.gz - Axial/Parallel Diffusivity
Mean of the volumes
Hi Martin,
Are you including b0 correction in your preprocessing stream? I can see
b0mag.nii.gz in your log file.
Did you set dob0 = 1 in your configuration file? If so you have to set
also the magnitude and phase maps (using set b0mlist and set b0plist in
the configuration file,Check out $FREESU
Hi Ayaz,
In addition to the platform differences, DTIstudio uses deterministic
tractography algorithm (Fiber Assignment by Continuous Tracking (FACT)
method), whereas the TRACULA uses prior information of anatomy surrounding
the fiber tracts along with a more sensitive probabilistic crossing fiber
Hi Ansgar,
Can you send us an example screenshot of the one of the fiber tracts that
look crippled? If you can send us an overlay of path.pd.nii.gz of that
specific tract on the FA map, it will give us an idea of what is going on.
Best,
Priti
> Hi,
> We are using the ADNI Acc 3D FSPGR for struct
Hi Antonella,
We've not released CVS template /Priors for tracula yet. You can only use
MNI template for tracula now. We're still testing CVS.
Thanks,
Priti
> Hi,
>
> I would like to know if for a probabilistic tractrography using TRACULA I
> can use the CVS space as a common template to registe
Hi Tanja,
Are these healthy controls or do they have any lesions etc on the WM? It
looks like most of the training streamlines from the atlas are rejected
for straying off the subject's brain mask.
Can you please check out a similar posting on the list and overlay your
training histogram over you
Hi Gabriel,
Have you tried mri_label2vol?
If you want the volume in the anatomical space:
mri_label2vol --label labelname.label --temp .nii.gz
--identity --o volumename.nii.gz
If you want it in some other space, you can specify the registration
matrix using --reg and the template using --temp.
Hi Chris,
The diff_slices folder is still there, which means that bedpostX probably
did not finish processing. That folder usually gets deleted after bedpostX
processing completes. It's strange that you have merged_ph2samples.nii.gz
and not merged_ph1samples.nii.gz.
Did you accidentally run bedpo
?
>
> Thanks,
> Chris
>
> PS When running bedpostx I was simply using the defaults, so "bedpostx
> H008B/dmri.bedpostX" was the command line.
>
> On 05/07/2012 02:28 PM, Priti Srinivasan wrote:
>> Hi Chris,
>>
>> The diff_slices folder is still
Hi Kiely,
Have you checked your inter and intra subject registrations? The control
points going off the dwi is not only for one paths but for all the paths.
If the registration goes terribly wrong, this can happen. You can take a
look at
/dmri/lowb_brain_anat.flt.nii.gz (For intra subject registr
>> don't see a brain at all. Is there a way to troubleshoot this?
>> Thanks,
>>
>> Kiely
>>
>> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan
>> wrote:
>> Hi Kiely,
>>
>> Have you checked your inter and intra subject registrat
you have to run flirt commandline separately to check if it solves your
problem.
> Is this something I can change in my dmrirc file or do I need to run flirt
> on it's own?
>
> Thanks,
>
> Kiely
>
> On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan <
>
g corratio and it seems to have fixed
>>>á á á á á áthe registration issue.
>>>á á á á á áI'm very new to this so just want to make sure I
>>> did
>>>á á á á á áit correctly before I
>>>á á á á á ámove
Hi Sarina,
Can you check to see what files are there in the dmri.bedpostX directory?
Do you have the merged_*, mean_*, dyads_* files??
Priti
> Hi, tracula users
>
> I run the trac-all bedp process and resulted this error:
>
> 74 slices processed
> 75 slices processed
> 76 slices processed
>
Hi Gabor,
If you run bedpostX on the data outside of tracula using the default
options, do you get the same error?
Priti
> Dear all,
>
> I've the following error right after starting trac-all -bedp -c
> configuration_file:
>
> Making bedpostx directory structure
> Queuing preprocessing stages
>
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