from:"Anastasia Yendiki"



Were the old .mat files replaced with the new ones?

On Fri, 18 May 2012, Kiely Madhavan wrote:


That seemed to fix the registration issue, but I'm still unable to
reconstruct the tracts using trac-all -path. I'm getting the same error that
the control points are not within the mask. THis happens for all tracts.
Thanks,

Kiely

On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  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 look something
like this if I am
running it in this individuals dmri directory: 

flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz
-out
lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat
-cost corratio


Thanks so much for your help.

Kiely

On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan
rspr...@nmr.mgh.harvard.edu wrote:
     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 
      rspr...@nmr.mgh.harvard.edu wrote:
     
      Kiely, For flirt, try using corratio, cost
function instead
     of
      mutualinfo
      (which is the default in trac-all) to see if
that solves your
      registration
      problem.
     
     
       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 has the option to
initialize with flirt
     or with SPM.
      
       Hope this helps,
       a.y
      
       On Wed, 16 May 2012, Kiely Donnelly wrote:
      
       Hi Priti - Thanks for your help. The
inter-subject
     registration seems
      to
       have run OK, but there must be something
wrong with the
     intra-subject
       registration. When I try to view it using
freeview, it's
     completely
      dark
       - I
       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
       rspr...@nmr.mgh.harvard.edu wrote:
             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
      registration
             diff-anat)
      
             and
      
             /dmri/brain_anat_mni.nii.gz (For
inter-subject
     registration
             anat-mni)
      
             I would start by checking that
first.
      
             Priti
      
              Hello--
             
              I have run Tracula successfully
for ~75 healthy
     subjects.
             However

Re: [Freesurfer] trac-all -path error



The other registration files depend on diff2anat. For example, diff2mni is 
composed of diff2anat and anat2mni. If you're using the old diff2mni, 
it's like you didn't change anything.


The -intra step creates all these. You need to edit the command that 
generates the diff2anat in your version of trac-preproc. Either comment 
that line out so that it runs everything but that, or change that line to 
the options that worked for you.



On Fri, 18 May 2012, Kiely Madhavan wrote:


I only created a diff2anat.flt.mat file which replaced the old one. Do they all 
need to be recreated? If so, is that something I
add to the command line?

On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

  Were the old .mat files replaced with the new ones?

  On Fri, 18 May 2012, Kiely Madhavan wrote:

That seemed to fix the registration issue, but I'm still unable to
reconstruct the tracts using trac-all -path. I'm getting the same 
error that
the control points are not within the mask. THis happens for all 
tracts.
Thanks,

Kiely

On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

     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 look something
           like this if I am
           running it in this individuals dmri directory: 

           flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz
           -out
           lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat
           -cost corratio


           Thanks so much for your help.

           Kiely

           On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan
           rspr...@nmr.mgh.harvard.edu wrote:
                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 
                 rspr...@nmr.mgh.harvard.edu wrote:
                
                 Kiely, For flirt, try using corratio, cost
           function instead
                of
                 mutualinfo
                 (which is the default in trac-all) to see if
           that solves your
                 registration
                 problem.
                
                
                  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 has the option to
           initialize with flirt
                or with SPM.
                 
                  Hope this helps,
                  a.y
                 
                  On Wed, 16 May 2012, Kiely Donnelly wrote:
                 
                  Hi Priti - Thanks for your help. The
           inter-subject
                registration seems
                 to
                  have run OK, but there must be something
           wrong with the
                intra-subject
                  registration. When I try to view it using
           freeview, it's
                completely

Re: [Freesurfer] trac-all -path error



This is a script, it's in the directory where all freesurfer scripts are. 
You can find it by doing which trac-preproc.


On Fri, 18 May 2012, Kiely Madhavan wrote:


OK - Can you point me in the direction of the trac-preproc file that I should 
edit? 

On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

  The other registration files depend on diff2anat. For example, diff2mni 
is composed of diff2anat and anat2mni. If
  you're using the old diff2mni, it's like you didn't change anything.

  The -intra step creates all these. You need to edit the command that 
generates the diff2anat in your version of
  trac-preproc. Either comment that line out so that it runs everything but 
that, or change that line to the options
  that worked for you.


  On Fri, 18 May 2012, Kiely Madhavan wrote:

  I only created a diff2anat.flt.mat file which replaced the old one. Do 
they all need to be recreated? If so,
  is that something I
  add to the command line?

  On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

       Were the old .mat files replaced with the new ones?

       On Fri, 18 May 2012, Kiely Madhavan wrote:

             That seemed to fix the registration issue, but I'm still 
unable to
             reconstruct the tracts using trac-all -path. I'm getting the 
same error that
             the control points are not within the mask. THis happens for 
all tracts.
             Thanks,

             Kiely

             On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
             ayend...@nmr.mgh.harvard.edu wrote:

           á á áThe .mat registration matrix should be saved under dmri/xfms/.


           á á áOn Wed, 16 May 2012, Kiely Donnelly wrote:

           á á á á á áI tried using 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 forward. Should the command line look something
           á á á á á álike this if I am
           á á á á á árunning it in this individuals dmri directory:á

           á á á á á áflirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz
           á á á á á á-out
           á á á á á álowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat
           á á á á á á-cost corratio


           á á á á á áThanks so much for your help.

           á á á á á áKiely

           á á á á á áOn Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan
           á á á á á árspr...@nmr.mgh.harvard.edu wrote:
           á á á á á áá á áyou have to run flirt commandline separately to
           á á á á á ácheck if it
           á á á á á áá á ásolves your
           á á á á á áá á áproblem.


           á á á á á áá á á Is this something I can change in my dmrirc
           á á á á á áfile or do I need
           á á á á á áá á áto run flirt
           á á á á á áá á á on it's own?
           á á á á á áá á á
           á á á á á áá á á Thanks,
           á á á á á áá á á
           á á á á á áá á á Kiely
           á á á á á áá á á
           á á á á á áá á á On Wed, May 16, 2012 at 9:27 AM, Priti
           á á á á á áSrinivasan 
           á á á á á áá á á rspr...@nmr.mgh.harvard.edu wrote:
           á á á á á áá á á
           á á á á á áá á á Kiely, For flirt, try using corratio, cost
           á á á á á áfunction instead
           á á á á á áá á áof
           á á á á á áá á á mutualinfo
           á á á á á áá á á (which is the default in trac-all) to see if
           á á á á á áthat solves your
           á á á á á áá á á registration
           á á á á á áá á á problem.
           á á á á á áá á á
           á á á á á áá á á
           á á á á á áá á á  Hi Kiely - Looks like you used flirt for
           á á á á á áthe intra-subject
           á á á á á áá á á registration,
           á á á á á áá á á  so you can look in trac-all.log for the
           á á á á á áflirt command line
           á á á á á áá á áthat
           á á á á á áá á á registers
           á á á á á áá á á  diffusion to anatomical and play around
           á á á á á áwith the
           á á á á á áá á áparameters.
           á á á á á áá á á 
           á á á á á áá á á  You can also use bbregister instead of
           á á á á á áflirt for the
           á á á á á áá á áintra-subject
           á á á á á áá á á  registration - it has the option to
           á á á á á áinitialize with flirt
           á á á á á áá á áor with SPM.
           á á á á á áá á á 
           á á á á á áá á á  Hope this helps,
           á á á á á áá á á  a.y
           á á á á á áá á á 
           á á á á á áá á á  On Wed, 16 May 2012, Kiely Donnelly wrote:
           á á á á á áá á á 
           á á á á á áá á á  Hi Priti - Thanks for your help. The
           á á á á á áinter-subject
           á á á á á áá á

Re: [Freesurfer] trac-all -path error



This is the help text that you get when you run the script. You need to 
open the script in a text editor.


On Fri, 18 May 2012, Kiely Madhavan wrote:


That's where I looked, but all I see is the following (I don't see the command 
line that creates the diff2anat for me to edit):

Last login: Fri May 18 13:45:47 on ttys000
/Applications/freesurfer/bin/trac-preproc ; exit;
Kielys-MacBook-Air:~ kielydonnelly$ /Applications/freesurfer/bin/trac-preproc ; 
exit;

USAGE: trac-preproc

Required arguments:
  -c file      : dmrirc file (see dmrirc.example)

Other arguments:
  -log file    : default is trac-all.log in the same dir as dmrirc
  -nolog         : do not save a log file
  -cmd file    : default is trac-all.cmd in the same dir as dmrirc
  -nocmd         : do not save a cmd file
  -no-isrunning  : do not check whether this subject is currently being 
processed
  -umask umask   : set unix file permission mask (default 002)
  -grp groupid   : check that current group is alpha groupid 
  -allowcoredump : set coredump limit to unlimited
  -debug         : generate much more output
  -dontrun       : do everything but execute each command
  -version       : print version of this script and exit
  -help          : print full contents of help

logout

[Process completed]

On Fri, May 18, 2012 at 1:59 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

  This is a script, it's in the directory where all freesurfer scripts are. You 
can find it by doing which
  trac-preproc.

  On Fri, 18 May 2012, Kiely Madhavan wrote:

OK - Can you point me in the direction of the trac-preproc file 
that I should edit? 

On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

     The other registration files depend on diff2anat. For example, 
diff2mni is composed of diff2anat
and anat2mni. If
     you're using the old diff2mni, it's like you didn't change 
anything.

     The -intra step creates all these. You need to edit the 
command that generates the diff2anat in
your version of
     trac-preproc. Either comment that line out so that it runs 
everything but that, or change that line
to the options
     that worked for you.


     On Fri, 18 May 2012, Kiely Madhavan wrote:

     I only created a diff2anat.flt.mat file which replaced the old 
one. Do they all need to be
recreated? If so,
     is that something I
     add to the command line?

     On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

          Were the old .mat files replaced with the new ones?

          On Fri, 18 May 2012, Kiely Madhavan wrote:

                That seemed to fix the registration issue, but I'm 
still unable to
                reconstruct the tracts using trac-all -path. I'm 
getting the same error that
                the control points are not within the mask. THis 
happens for all tracts.
                Thanks,

                Kiely

                On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
                ayend...@nmr.mgh.harvard.edu wrote:

           á á áThe .mat registration matrix should be saved under 
dmri/xfms/.


           á á áOn Wed, 16 May 2012, Kiely Donnelly wrote:

           á á á á á áI tried using 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 forward. Should the command line look 
something
           á á á á á álike this if I am
           á á á á á árunning it in this individuals dmri 
directory:á

           á á á á á áflirt -in dwi_orig.nii.gz -ref 
brain_anat.nii.gz
           á á á á á á-out
           á á á á á álowb_brain_anat.flt.nii.gz -omat 
diff2anat.flt.mat
           á á á á á á-cost corratio


           á á á á á áThanks so much for your help.

           á á á á á áKiely

           á á á á á áOn Wed, May 16, 2012 at 10:12 AM, Priti 
Srinivasan
           á á á á á árspr...@nmr.mgh.harvard.edu wrote:
           á á á á á áá á áyou have to run flirt commandline 
separately to
           á á á á á ácheck if it
           á á á á á áá á ásolves your
           á á á á á áá á áproblem.


           á á á á á áá á á Is this something I can change in my 
dmrirc
           á á á á á áfile or do I need
           á á á á á áá á áto run flirt

Re: [Freesurfer] trac-all -path error

2012-05-16 Thread Anastasia Yendiki



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 has the option to initialize with flirt or with SPM.


Hope this helps,
a.y

On Wed, 16 May 2012, Kiely Donnelly wrote:


Hi Priti - Thanks for your help. The inter-subject registration seems to
have run OK, but there must be something wrong with the intra-subject
registration. When I try to view it using freeview, it's completely dark - I
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
rspr...@nmr.mgh.harvard.edu wrote:
  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 registration
  diff-anat)

  and

  /dmri/brain_anat_mni.nii.gz (For inter-subject registration
  anat-mni)

  I would start by checking that first.

  Priti

   Hello--
  
   I have run Tracula successfully for ~75 healthy subjects.
  However, the
   pathway reconstruction seems to fail for a handful of people.
  I've
   attached
   the log file for one of these subjects. It appears that the
  control points
   are not within the dwi. A similar problem occurred in a
  subject with
   substantial signal loss in the dwi, but that doesn't seem to
  be the case
   for this particular person. I have been creating the entire
  set of tracts,
   but at this point, I'm only interested in the SLFt and SLFp.
  
   Thanks,
  
   Kiely
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The information in this e-mail is intended only for the person to whom
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--
Kiely M. Donnelly, M.A.
Doctoral Candidate, Clinical Neuropsychology
University of Cincinnati

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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] trac-all -path error

2012-05-16 Thread Anastasia Yendiki



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 flirt
on it's own?
Thanks,

Kiely

On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan
rspr...@nmr.mgh.harvard.edu wrote:
  Kiely, For flirt, try using corratio, cost function instead of
  mutualinfo
  (which is the default in trac-all) to see if that solves your
  registration
  problem.


   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 has the option to initialize with flirt or
  with SPM.
  
   Hope this helps,
   a.y
  
   On Wed, 16 May 2012, Kiely Donnelly wrote:
  
   Hi Priti - Thanks for your help. The inter-subject
  registration seems to
   have run OK, but there must be something wrong with the
  intra-subject
   registration. When I try to view it using freeview, it's
  completely dark
   - I
   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
   rspr...@nmr.mgh.harvard.edu wrote:
         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
  registration
         diff-anat)
  
         and
  
         /dmri/brain_anat_mni.nii.gz (For inter-subject
  registration
         anat-mni)
  
         I would start by checking that first.
  
         Priti
  
          Hello--
         
          I have run Tracula successfully for ~75 healthy
  subjects.
         However, the
          pathway reconstruction seems to fail for a handful of
  people.
         I've
          attached
          the log file for one of these subjects. It appears
  that the
         control points
          are not within the dwi. A similar problem occurred in
  a
         subject with
          substantial signal loss in the dwi, but that doesn't
  seem to
         be the case
          for this particular person. I have been creating the
  entire
         set of tracts,
          but at this point, I'm only interested in the SLFt
  and SLFp.
         
          Thanks,
         
          Kiely
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Re: [Freesurfer] trac-all -path error

2012-05-16 Thread Anastasia Yendiki



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 look something like this if I am
running it in this individuals dmri directory: 

flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz -out
lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat -cost corratio


Thanks so much for your help.

Kiely

On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan
rspr...@nmr.mgh.harvard.edu wrote:
  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 
   rspr...@nmr.mgh.harvard.edu wrote:
  
   Kiely, For flirt, try using corratio, cost function instead
  of
   mutualinfo
   (which is the default in trac-all) to see if that solves your
   registration
   problem.
  
  
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 has the option to initialize with flirt
  or with SPM.
   
Hope this helps,
a.y
   
On Wed, 16 May 2012, Kiely Donnelly wrote:
   
Hi Priti - Thanks for your help. The inter-subject
  registration seems
   to
have run OK, but there must be something wrong with the
  intra-subject
registration. When I try to view it using freeview, it's
  completely
   dark
- I
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
rspr...@nmr.mgh.harvard.edu wrote:
      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
   registration
      diff-anat)
   
      and
   
      /dmri/brain_anat_mni.nii.gz (For inter-subject
  registration
      anat-mni)
   
      I would start by checking that first.
   
      Priti
   
       Hello--
      
       I have run Tracula successfully for ~75 healthy
  subjects.
      However, the
       pathway reconstruction seems to fail for a handful
  of people.
      I've
       attached
       the log file for one of these subjects. It appears
  that the
      control points
       are not within the dwi. A similar problem occurred
  in a
      subject with
       substantial signal loss in the dwi, but that
  doesn't seem to
      be the case
       for this particular person. I have been creating
  the entire
      set of tracts,
       but at this point, I'm only interested in the SLFt
  and SLFp.
      
       Thanks,
      
       Kiely
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The information in this e-mail is intended only for the
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it is
addressed. If you believe this e-mail was sent to you in
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e-mail
contains patient information, please contact the Partners
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HelpLine at
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--
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University of Cincinnati
   
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Re: [Freesurfer] TRACULA niftii file

2012-05-10 Thread 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 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 input, too.


Hope this helps,
a.y

On Thu, 10 May 2012, Gabor Perlaki wrote:


Dear all,

Is TRACULA able to handle 4D FSL niftii as input for DTI images? Are
bves/bvalues extracted by dcm2nii and MRICro accurate for TRACULA? I think
TRACULA needs the bvecs in the image coordinate system, which is not the
same as scanner coordinate system in case of oblique acquisition. Do I need
to use dcm2nii with correction for slice angulation to 
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Re: [Freesurfer] TRACULA niftii file

2012-05-10 Thread Anastasia Yendiki



You can specify them by setting bvecfile and bvalfile in your 
configuration file.


On Thu, 10 May 2012, Gabor Perlaki wrote:


Dear Anastasia,

I've the original DICOM files, but it is acquired with the standard Siemens
DTI ep2_diff, and not with the MGH-DTI sequence. Is DTI images acquired 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 ayend...@nmr.mgh.harvard.edu

  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 input, too.

  Hope this helps,
  a.y

  On Thu, 10 May 2012, Gabor Perlaki wrote:

Dear all,

Is TRACULA able to handle 4D FSL niftii as input for
DTI images? Are
bves/bvalues extracted by dcm2nii and MRICro
accurate for TRACULA? I think
TRACULA needs the bvecs in the image coordinate
system, which is not the
same as scanner coordinate system in case of oblique
acquisition. Do I need
to use dcm2nii with correction for slice angulation
to 



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Re: [Freesurfer] tracula

2012-05-05 Thread Anastasia Yendiki


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 May 2012, carolina.mr wrote:

 Hello,
 
 Is it possible to track fibers with TRACULA from the cortical parcelation
 masks obtained from recon-all or do we have to use the white matter
 parcelation to do so?
 Another question: if I use QDEC to find the areas with significant
 difference in the cortical tickness between two groups, is it possible to
 use those ROI's to launch the fiber track with TRACULA?
 
 Thank you,
 Carolina Rimkus

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Re: [Freesurfer] mutualinfo in flirt T1-MNI registration

2012-05-01 Thread Anastasia Yendiki



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 as cost function to 
register the anatomical individual
T1 brain (brain_anat.nii.gz) to the MNI152 space T1 template 
(MNI152_T1_1mm_brain.nii.gz), i.e. for an intramodal
registration.

I was wondering why mutualinfo (which is often used for intermodal 
registrations) is also used for a an
intramodal registration in TRACULA'S implementation rather than e.g. least 
squares or correlation ratio, the
latter being the fsl default.

Is mutualinfo preferable not only for intermodal (e.g., b0 - t1) but also for 
intramodal t1-t1 registrations
for your purpose ? - I am just curious to know  :)

kind regards,
andi

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Re: [Freesurfer] Trac-all on a cluster with PBS/torque

2012-04-27 Thread Anastasia Yendiki


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 stage in Trac-all crash without getting finished. This is tested 
 with the tutorial data. I am
 enclosing the modified trac-all script.
 
 Best regard
 
 Knut J Bjuland
 NTNU
 

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Re: [Freesurfer] Trac-all on a cluster with PBS/torque

2012-04-27 Thread Anastasia Yendiki


Hi Knut - I modified fsl_sub to work on our own PBS cluster. This modified 
version is fsl_sub_seychelles. Anything that works with the original 
fsl_sub should also work with fsl_sub_seychelles. You can modify either of 
the two to make it work on your cluster. If you do make it more general to 
work on more clusters, we'll be happy to incorporate the changes but 
there's no way for us to know what would work on every possible local 
setup.

Good luck!
a.y

On Fri, 27 Apr 2012, Knut J Bjuland wrote:

 Hi Anastasia


 I think this hack was also added

 ##  Steinar, steinar, commnet out this to fool the program to run under PBS
 ##  date 20 april 2012
 ##  hack

 #if ($?PBS_JOBID) then
 #   echo ERROR: Do not submit $ProgName as a job with pbsubmit or qsub.
 #   echo ERROR: Run it directly on the command line.
 #   echo ERROR: If run on the cluster, $ProgName will submit the jobs 
 for you.
 #  echo ERROR: Each subject listed in your dmrirc will be submitted as a 
 job.
 #  exit 1
 #endif

 ## end hack

 Should I revert those changes? 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 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 stage in Trac-all crash without getting finished. This is 
   tested with the tutorial data. I am
   enclosing the modified trac-all script.
  
   Best regard
  
   Knut J Bjuland
   NTNU
  
  
 

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  is
  addressed. If you believe this e-mail was sent to you in error and the
  e-mail
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  http://www.partners.org/complianceline . If the e-mail was sent to you in
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  properly
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Re: [Freesurfer] trakula segmentation fault

2012-04-25 Thread Anastasia Yendiki



Hi Viviana - Does it die at that point or does it keep running? If it's 
the latter it doesn't look wrong. For your first problem you should make 
sure that your path includes the bin/ directory under the FSL 
distribution.


a.y

On Wed, 25 Apr 2012, Viviana Siless wrote:


Hi Anastasia,
I ran:

- bedpostx /media/vivi/images/freesurfer/00112288Proc/dmri

and got the following output:

subjectdir is /media/vivi/images/freesurfer/00112288Proc/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage

But before it told me that /bin/fsl_sub was mising,  so i copied from where
i had it to there, and then it arrived at the same place than before

then I ran

- fsl4.1-bedpostx /media/vivi/images/freesurfer/00112288Proc/dmri

I made symbolic link from fsl4.1-whatever to whatever.
Im working in ubuntu 11.04 and I installed fsl from the package manager.

and I got this:

subjectdir is /media/vivi/images/freesurfer/00112288Proc/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
0 slices processed


What should I do?
Thanks!
Viviana



On Wed, Apr 25, 2012 at 12:52 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu 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/vivi/images/freesurfer/00112288Proc/dmri and see if
  that works?

  Thanks for bringing this to our attention,
  a.y

  On Mon, 23 Apr 2012, Viviana Siless wrote:

Hello Anastasia,
It fixed the bug. Thank you so much!

Now Im running  trac-all -bedp -c

But it's been running for already 3 days, and it
just printed that:

 trac-all -bedp -c
/media/vivi/images/freesurfer/dmrirc.example
INFO: SUBJECTS_DIR is /media/vivi/images/freesurfer
INFO: Diffusion root is
/media/vivi/images/freesurfer
Actual FREESURFER_HOME /media/vivi/code/freesurfer
ln 
-sf/media/vivi/images/freesurfer/00112288Proc/dlabel/diff/anat_brain_mask.
flt.nii.gz
/media/vivi/images/freesurfer/00112288Proc/dmri/nodif_brain_mask.nii.gz

ln -sf
/media/vivi/images/freesurfer/00112288Proc/dmri/dwi.nii.gz
/media/vivi/images/freesurfer/00112288Proc/dmri/data.nii.gz
WARN: Running FSL's bedbost locally - this might
take a while
WARN: It is recommended to run this step on a
cluster
bedpostx_seychelles
/media/vivi/images/freesurfer/00112288Proc/dmri
subjectdir is
/media/vivi/images/freesurfer/00112288Proc/dmri
Making bedpostx directory structure
Queuing preprocessing stages
[: 223: NONE: unexpected operator
[: 314: NONE: unexpected operator
[: 327: xbedpostx_pre: unexpected operator
[: 486: x: unexpected operator
[: 486: -le: argument expected
Queuing parallel processing stage


Is it normal?
Thanks for your help!  (let me know if I should
create another thread)

Viviana Siless
--
Parietal Team, INRIA Saclay
Neurospin, Centre CEA de Saclay
91191 Gif sur Yvette – FRANCE


On Wed, Apr 18, 2012 at 1:18 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu 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
inter-subject registration in this version)
     # Default:
$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
     #
     #set mnitemp = /path/to/mni_template.nii.gz
     set mnitemp =
/usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz

     Can you please try changing the above from 2mm
to 1mm and see if it works? If so, I'll make sure
this is handled more elegantly in the next
     version.

     Hope this helps,
     a.y

     On Fri, 6 Apr 2012, Viviana Siless wrote:

           Hi Anastasia,
           Here is the 
data:https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testDa
ta.tar.gz Let me know if you have any
           trouble.
           I changed to the other track-all, and the
error is the same.
           Please let me know if I'm doing anything

Re: [Freesurfer] trakula segmentation fault

2012-04-24 Thread Anastasia Yendiki



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/vivi/images/freesurfer/00112288Proc/dmri and see if that works?


Thanks for bringing this to our attention,
a.y

On Mon, 23 Apr 2012, Viviana Siless wrote:


Hello Anastasia,
It fixed the bug. Thank you so much!

Now Im running  trac-all -bedp -c

But it's been running for already 3 days, and it just printed that:

 trac-all -bedp -c /media/vivi/images/freesurfer/dmrirc.example
INFO: SUBJECTS_DIR is /media/vivi/images/freesurfer
INFO: Diffusion root is /media/vivi/images/freesurfer
Actual FREESURFER_HOME /media/vivi/code/freesurfer
ln -sf 
/media/vivi/images/freesurfer/00112288Proc/dlabel/diff/anat_brain_mask.flt.nii.gz
/media/vivi/images/freesurfer/00112288Proc/dmri/nodif_brain_mask.nii.gz
ln -sf /media/vivi/images/freesurfer/00112288Proc/dmri/dwi.nii.gz 
/media/vivi/images/freesurfer/00112288Proc/dmri/data.nii.gz
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_seychelles /media/vivi/images/freesurfer/00112288Proc/dmri
subjectdir is /media/vivi/images/freesurfer/00112288Proc/dmri
Making bedpostx directory structure
Queuing preprocessing stages
[: 223: NONE: unexpected operator
[: 314: NONE: unexpected operator
[: 327: xbedpostx_pre: unexpected operator
[: 486: x: unexpected operator
[: 486: -le: argument expected
Queuing parallel processing stage


Is it normal?
Thanks for your help!  (let me know if I should create another thread)

Viviana Siless
--
Parietal Team, INRIA Saclay
Neurospin, Centre CEA de Saclay
91191 Gif sur Yvette – FRANCE


On Wed, Apr 18, 2012 at 1:18 AM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu 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 inter-subject registration in this 
version)
  # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
  #
  #set mnitemp = /path/to/mni_template.nii.gz
  set mnitemp = /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz

  Can you please try changing the above from 2mm to 1mm and see if it 
works? If so, I'll make sure this is handled more elegantly in the next
  version.

  Hope this helps,
  a.y

  On Fri, 6 Apr 2012, Viviana Siless wrote:

Hi Anastasia,
Here is the data: 
https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gz
 Let me know if you have any
trouble.
I changed to the other track-all, and the error is the same.
Please let me know if 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 
ayend...@nmr.mgh.harvard.edu wrote:

     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/Tracula

     Thanks,
     a.y


On Wed, 4 Apr 2012, Viviana Siless wrote:

     Hello,
     I'm trying to run trac-all prec and I'm getting a segmentation 
fault error.

     Loading streamlines from 
/media/vivi/code/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS.flt.trk
     Loading streamline start ROI from 
/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
     Loading streamline end ROI from 
/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
     Loading streamlines from 
/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS.flt.trk
     INFO: Rejected 0 streamlines for straying off mask
     INFO: Rejected 0 streamlines for reversing direction
     Segmentation fault
     Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP 
Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64
     GNU/Linux

     trac-preproc exited with ERRORS at Wed Apr  4 18:24:21 CEST 
2012


     - When I look at the trak-all.error I see this error:

     --
     SUBJECT 00112288Proc
     DATE Wed Apr  4 18:24:21 CEST 2012
     USER vivi
     HOST vivi-ThinkStation

Re: [Freesurfer] Running Tracula -bedpostx and -path

2012-04-24 Thread Anastasia Yendiki



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 from the -path part you can definitely ignore.

Hope this helps,
a.y

On Tue, 24 Apr 2012, Richard Binney wrote:


Hi Anastasia,

I ran bedpost directly: bedpostx dmri

It seemed to run fine, not exiting with any errors. the only thing that 
concerned me was that the last output in the terminal was

50 slices processed  [when I have 54]
queing post-processing stage

then it exited. It seemed to run rather quicker than I expected and I expected it to at 
least output  all slices processed and/or something after queing post

Is there any reason to be concerned?

Furthermore, in running the -path, the terminal window constantly outputting...

ERROR: Degenerate spline segment
58 81 24
56 69 24
..
ERROR: Degenerate spline segment
..

but it seems to continue on without exiting. Is there any reason to be 
concerned about this? what doe sit mean?

Thanks for your help

R

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Re: [Freesurfer] TRacula and Philips

2012-04-19 Thread Anastasia Yendiki



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 tracula?

Thanks.
Fabrício.

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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] trac-all -prep error

2012-04-17 Thread Anastasia Yendiki



Hi Sarina - You'll have to specify the list of gradient directions 
(bvecfile) and b-values (bvalfile), see here for more info:

http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

Please send email to the freesurfer list and not to me directly. Emails 
sent to the freesurfer list are saved in a searchable archive so that 
other users can benefit from these pearls of wisdom.

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/

a.y

On Wed, 11 Apr 2012, Sarina Sacco wrote:


Ciao Anastasia ho risolto il problema di FSL,ora l'installazione è
corretta,però mi si presenta sempre un errore inerente al bvecs non li
trova,potrebbe forse dipendere dai files DICOM che utilizzo?
Questo è l'errore:
sarina@thunder:/opt/freesurfer/subjects$ trac-all -prep -c
$SUBJECTS_DIR/subjects_trac_all/scripts/dmrircFiles/dmrirc_Diff001_F.B.
INFO: SUBJECTS_DIR is /opt/freesurfer/subjects/subjects_recon_all
INFO: Diffusion root is /opt/freesurfer/subjects/subjects_trac_all
Actual FREESURFER_HOME /opt/freesurfer
trac-preproc -c
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./scripts/dmrirc.local
-log 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./scripts/trac-all.log
-cmd 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./scripts/trac-all.cmd
#-
/opt/freesurfer/bin/trac-preproc
#-
#@# Image corrections Wed Apr 11 18:01:15 CEST 2012
mri_convert 
/opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz
mri_convert 
/opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from 
/opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm...
Starting DICOMRead2()
dcmfile = 
/opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm
dcmdir = /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig
Ref Series No = 7
Found 2242 files, checking for dicoms
Found 2240 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0.029 0.321 1.9739
Vs: 0.0144997 0.160497 0.98693
Second Sorting
Counting frames
nframes = 28
nslices = 80
ndcmfiles = 2240
PE Dir = COL (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2--
jpegUID:   --1.2.840.10008.1.2.4--
Loading pixel data
TR=10050.00, TE=87.10, TI=0.00, flip angle=90.00
i_ras = (-0.999859, -0.0058291, -0.0157782)
j_ras = (0.00830111, -0.987041, -0.160255)
k_ras = (-0.0144997, -0.160497, 0.98693)
writing to 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz...
mri_probedicom --i
/opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm

/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dcminfo.dat

flip4fsl 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 2
fslswapdim 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz
x -y z 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz
mv -f 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/bvecs
mv: cannot stat
`/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs':
No such file or directory
Linux thunder 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC
2011 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Apr 11 18:03:33 CEST 2012


2012/3/27 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu:


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 FS5.1) mi crea questo errore:

/opt/freesurfer/bin/trac-preproc
#-
#@# Image corrections Tue Mar 27 11:17:27 CEST 2012
mri_convert
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm

/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz
mri_convert
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B

Re: [Freesurfer] trakula segmentation fault

2012-04-17 Thread Anastasia Yendiki



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 inter-subject registration in this 
version)

# Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
#
#set mnitemp = /path/to/mni_template.nii.gz
set mnitemp = /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz

Can you please try changing the above from 2mm to 1mm and see if it works? 
If so, I'll make sure this is handled more elegantly in the next version.


Hope this helps,
a.y

On Fri, 6 Apr 2012, Viviana Siless wrote:


Hi Anastasia,
Here is the data: 
https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gz
 Let me know if you have any
trouble.
I changed to the other track-all, and the error is the same.
Please let me know if 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 
ayend...@nmr.mgh.harvard.edu wrote:

  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/Tracula

  Thanks,
  a.y


On Wed, 4 Apr 2012, Viviana Siless wrote:

  Hello,
  I'm trying to run trac-all prec and I'm getting a segmentation fault 
error.

  Loading streamlines from 
/media/vivi/code/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS.flt.trk
  Loading streamline start ROI from 
/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
  Loading streamline end ROI from 
/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
  Loading streamlines from 
/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS.flt.trk
  INFO: Rejected 0 streamlines for straying off mask
  INFO: Rejected 0 streamlines for reversing direction
  Segmentation fault
  Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 
03:31:24 UTC 2011 x86_64 x86_64 x86_64
  GNU/Linux

  trac-preproc exited with ERRORS at Wed Apr  4 18:24:21 CEST 2012


  - When I look at the trak-all.error I see this error:

  --
  SUBJECT 00112288Proc
  DATE Wed Apr  4 18:24:21 CEST 2012
  USER vivi
  HOST vivi-ThinkStation-C20X
  PROCESSOR x86_64
  OS Linux
  Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 
03:31:24 UTC 2011 x86_64 x86_64 x86_64
  GNU/Linux
  $Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki Exp $
  /media/vivi/code/freesurfer/bin/trac-preproc
  PWD /media/vivi/code/freesurfer
  CMD /media/vivi/code/freesurfer/bin/dmri_train --outdir 
/media/vivi/images/freesurfer/00112288Proc/dlabel/mni
  --out
  lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt 
rh.unc_AS_avg33_mni_flt
  lh.ilf_AS_avg33_mni_flt
  rh.ilf_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt 
lh.atr_PP_avg33_mni_flt
  rh.atr_PP_avg33_mni_flt
  lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt 
rh.cab_PP_avg33_mni_flt
  lh.slfp_PP_avg33_mni_flt
  rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt 
rh.slft_PP_avg33_mni_flt --slist
  /tmp/subj33.00112288Proc.16360.txt --trk
  dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk 
dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk
  dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk 
dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk
  dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk 
dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk
  dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk 
dlabel/mni/lh.slfp_PP.flt.trk
  dlabel/mni/rh.slfp_PP.flt.trk
  dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg 
dlabel/mni/aparc+aseg.nii.gz --cmask
  dlabel/mni/cortex+2mm.nii.gz
  --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois 
dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
  dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
  dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz 
dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
  dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz 
dlabel/mni/rh.unc_AS_roi2.flt.nii.gz
  dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz 
dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
  dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz 
dlabel/mni/fmajor_PP_roi2.flt.nii.gz
  dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz 
dlabel/mni

Re: [Freesurfer] TRACULA trac-all -path does not generate all the paths

2012-04-05 Thread Anastasia Yendiki


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 done without error as last, but actually it didn't
 generate any reconstructed paths.
 
 When I looking through the 'trac-all.log' file, I found only one error on 
 dmri_mergepaths saying ERROR: must specify input
 volume(s). But it looks like the function dmri_paths, which is before the 
 'mergepaths', was not successfully done as it didn't
 generate any output. (but the log file didn't say anything about this.)
 
 This occurred in only 3 subjects out of ~70 total. I've rerun the trac-all 
 code on different machines to no avail. Can anyone help on
 this matter?
 
 
 Best,
 Juke
 
 

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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] trakula segmentation fault

2012-04-05 Thread Anastasia Yendiki



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/Tracula

Thanks,
a.y

On Wed, 4 Apr 2012, Viviana Siless wrote:


Hello,
I'm trying to run trac-all prec and I'm getting a segmentation fault error.

Loading streamlines from 
/media/vivi/code/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS.flt.trk
Loading streamline start ROI from 
/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
Loading streamline end ROI from 
/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
Loading streamlines from 
/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS.flt.trk
INFO: Rejected 0 streamlines for straying off mask
INFO: Rejected 0 streamlines for reversing direction
Segmentation fault
Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 
03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Apr  4 18:24:21 CEST 2012


- When I look at the trak-all.error I see this error:

--
SUBJECT 00112288Proc
DATE Wed Apr  4 18:24:21 CEST 2012
USER vivi
HOST vivi-ThinkStation-C20X
PROCESSOR x86_64
OS Linux
Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 
03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux
$Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki Exp $
/media/vivi/code/freesurfer/bin/trac-preproc
PWD /media/vivi/code/freesurfer
CMD /media/vivi/code/freesurfer/bin/dmri_train --outdir 
/media/vivi/images/freesurfer/00112288Proc/dlabel/mni --out
lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt 
rh.unc_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt
rh.ilf_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt 
lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt
lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt 
rh.cab_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt
rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt 
--slist /tmp/subj33.00112288Proc.16360.txt --trk
dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk 
dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk
dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk 
dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk
dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk 
dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk
dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk 
dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk
dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg 
dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz
--lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois 
dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz 
dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz 
dlabel/mni/rh.unc_AS_roi2.flt.nii.gz
dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz 
dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz 
dlabel/mni/fmajor_PP_roi2.flt.nii.gz
dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz 
dlabel/mni/lh.atr_PP_roi1.flt.nii.gz
dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz 
dlabel/mni/rh.atr_PP_roi2.flt.nii.gz
dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz 
dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz
dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz 
dlabel/mni/lh.cab_PP_roi2.flt.nii.gz
dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz 
dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz
dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz 
dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz
dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz 
dlabel/mni/rh.slft_PP_roi1.flt.nii.gz
dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask 
/media/vivi/images/freesurfer/00112288Proc/dlabel/mni/aparc+aseg_mask.nii.gz
 --fa
/media/vivi/images/freesurfer/00112288Proc/dmri/mni/dtifit_FA.flt.nii.gz 
--ncpts 5 --debug


- If I run that command, I get the same (of course):

INFO: Rejected 0 streamlines for straying off mask
INFO: Rejected 0 streamlines for reversing direction
Segmentation fault


Can anybody give me an idea of the problem? I run recon-all and finished 
without errors.
I attach the log file, the error file, and my dmrirc file. Please let me know 
if you need anything else.

Thanks in advance!

Viviana Siless
--
Parietal Team, INRIA Saclay
Neurospin, Centre CEA de Saclay
91191 Gif sur Yvette – FRANCE

Re: [Freesurfer] Tracula Siemens DTI

2012-04-01 Thread Anastasia Yendiki



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 Siemens diffusion 
protocol that we use at MGH. If you're using anything different than that
(including if you concatenate two DWI series into one), then you should 
set bvecfile, bvalfile, nb0. For more info see:

http://www.freesurfer.net/fswiki/dmrirc

If you have doubts about your bvecs is you can check the primary 
eigenvectors from dtifit (dmri/dtifit_V1.nii.gz) to make sure they're 
pointing the way you'd expect.


Hope this helps,
a.y

On Sat, 31 Mar 2012, Gabor Perlaki wrote:


Dear Freesurfers,

I have DTI images acquired on a Siemens 3T TIM Trio (software version
VB17A).

1, Is TRACULA able to extract the correct b-values and b-vectors from the
DICOM headers of Siemens IMA files or do I need to specify them?

2, I'm not sure whether the gradient directions are stored in the image- or
in the scanner coordinate system in the headers of Siemens IMA files. Does
anybody have any experience with this version of Syngo software (VB17A)?
Does TRACULA need the b-vecs in the image or in the scanner coordinate
system? Is it able to reorient the bvecs if they are stored in the wrong
coordinate system in the header?

3, My DTI protocol (30 diffusion weighted directions and 1 b0) was repeated
twice (in separate series, the second right after the first one, same
orientation). Because I'd like to correct for eddy current and movement I
don't want to average them on the scanner. Is it possible to put the 62
volume (30+30 diffusion weighted directions and 2 b0) into the same TRACULA
evaluation in dicom format or do I need to convert them into a single niftii
file?
 
Thanks a lot,
Gabor

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Re: [Freesurfer] TRACULA and CVS space

2012-03-29 Thread Anastasia Yendiki



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 
discusses all this:

http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00023/abstract

On Thu, 29 Mar 2012, Antonella Kis wrote:


Hi,

I would like to know if for a probabilistic tractrography using TRACULA I
can use the CVS space as a common template to register the diffusion data
instead of  MNI template.

How I should change for the CVS space the following:

set doregmni = 1 which is the default for the MNI space. If I want to use bo
th MNI template and CVS template for comparison purposes how this can be don
e?
THANKS.
Antonella


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Re: [Freesurfer] dt_recon and tractography

2012-03-28 Thread Anastasia Yendiki


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 previous results from FSTutorial/Diffusion more
 exactly my results after running dt_recon and registrations on the CVS space.
 If not can you please advise me if for a DTI probabilistic tractography using
 my previous results as mentioned above I can use TracVis.
 
 
 Thank you.
 Antonella
 
 
 

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Re: [Freesurfer] trac-all -prep error

2012-03-27 Thread 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 Tue, 27 Mar 2012, Sarina Sacco wrote:


quando avvio il trac-all (relase FS5.1) mi crea questo errore:

/opt/freesurfer/bin/trac-preproc
#-
#@# Image corrections Tue Mar 27 11:17:27 CEST 2012
mri_convert 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz
mri_convert 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm...
Starting DICOMRead2()
dcmfile = 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm
dcmdir = /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig
Ref Series No = 7
Found 2242 files, checking for dicoms
Found 2240 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0.029 0.321 1.9739
Vs: 0.0144997 0.160497 0.98693
Second Sorting
Counting frames
nframes = 28
nslices = 80
ndcmfiles = 2240
PE Dir = COL (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2--
jpegUID:   --1.2.840.10008.1.2.4--
Loading pixel data
TR=10050.00, TE=87.10, TI=0.00, flip angle=90.00
i_ras = (-0.999859, -0.0058291, -0.0157782)
j_ras = (0.00830111, -0.987041, -0.160255)
k_ras = (-0.0144997, -0.160497, 0.98693)
writing to 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz...
mri_probedicom --i
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm

/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dcminfo.dat

flip4fsl 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 2
fslswapdim 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz
x -y z 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz
fslorient -forceradiological
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz
fslorient: Command not found.
mv -f 
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/bvecs
mv: cannot stat
`/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs':
No such file or directory
Linux thunder 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC
2011 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Tue Mar 27 11:18:21 CEST 2012

Non riesco a capire perchè,da cosa può dipendere?

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Re: [Freesurfer] volume mapping

2012-03-26 Thread Anastasia Yendiki


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 coordinates to T1 using AIR 
 5.0 from LONI lab.
 They provide a transformation matrix.
 Now I want to transform the coordinates from T1 to Freesurfer space, so
 my question is: what is the transformation matrix that relates the T1
 which FS have used for parcellation and segmentation with the aparc+aseg.mgz 
 file?
 I searched the logs but couldn't find such matrix.
 I don't want to do a registration step since it will be less accurate than 
 the one that was generated during the segmentation process.
 Also is it just one transformation or a combination of transformations?

 thanks


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Re: [Freesurfer] volume mapping

2012-03-26 Thread Anastasia Yendiki


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 Mon, 26 Mar 2012, Johnson wrote:

 Hi
 I found it in a 256x256x256 space while the T1 we use is in different space, 
 I found this page on the registration step:
 http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
 I wish to know how this script work?

 mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz 
 --regheader aseg.mgz

 what is the transformation 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:
 
   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 coordinates to T1 using 
   AIR 5.0 from LONI lab.
   They provide a transformation matrix.
   Now I want to transform the coordinates from T1 to Freesurfer space, so
   my question is: what is the transformation matrix that relates the T1
   which FS have used for parcellation and segmentation with the 
   aparc+aseg.mgz file?
   I searched the logs but couldn't find such matrix.
   I don't want to do a registration step since it will be less accurate 
   than the one that was generated during the segmentation process.
   Also is it just one transformation or a combination of transformations?
  
   thanks
  
  
 

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  is
  addressed. If you believe this e-mail was sent to you in error and the
  e-mail
  contains patient information, please contact the Partners Compliance
  HelpLine at
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  error
  but does not contain patient information, please contact the sender and
  properly
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Re: [Freesurfer] volume mapping

2012-03-26 Thread Anastasia Yendiki


Actually, (1) should be more accurate, because bbregister uses the surface 
reconstruction obtained from the T1 to optimize the contrast across the 
gray/white boundary in the registered DWI.

However if you want to convert to the 1mm, 256^3 voxel size that was used 
as input to freesurfer, see mri_convert --conform.

On Mon, 26 Mar 2012, Johnson wrote:

 Hi
 Let me re-phrase my question:
 I already did registration from DWI to T1, this step is OK.
 Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz file not the 
 aparc+aseg-in-rawavg file). I know I have two choices:
 1) do registration using bbregister
 2) since Freesurfer during processing have already done this step, the 
 transformation matrix is there somewhere, the question is where to find it? 
 which log or which file? this choice is better since it is more accurate.

 Thanks
 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 Mon, 26 Mar 2012, Johnson wrote:
 
   Hi
   I found it in a 256x256x256 space while the T1 we use is in different 
   space, I found this page on the registration step:
   http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
   I wish to know how this script work?
  
   mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz 
   --regheader aseg.mgz
  
   what is the transformation 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:
   
  Hi FS expert
  I need to know the transformation matrix itself since I will do 
   thetransformation in matlab.
  I successfully transformed white matter fibers coordinates to T1 
   usingAIR 5.0 from LONI lab.
  They provide a transformation matrix.
  Now I want to transform the coordinates from T1 to Freesurfer 
space, so
  my question is: what is the transformation matrix that relates 
the T1
  which FS have used for parcellation and segmentation with the  
aparc+aseg.mgz file?
  I searched the logs but couldn't find such matrix.
  I don't want to do a registration step since it will be less 
accurate   than the one that was generated during the segmentation 
process.
  Also is it just one transformation or a combination of 
transformations?
   thanks
 
   
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it
 is
 addressed. If you believe this e-mail was sent to you in error and 
 the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to 
you in
 error
 but does not contain patient information, please contact the sender 
and
 properly
 dispose of the e-mail.
   
  
  
  
 



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Re: [Freesurfer] trac-all -path error

2012-03-23 Thread Anastasia Yendiki


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 when I run the next step I
 get the following error:

 Loading BEDPOST parameter samples from
 /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX
 niiRead(): error opening file
 /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz
 ERROR: Could not read
 /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz
 Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7
 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux

 trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012

 Word too long.
 

 Indeed, the merged file doesn't exist. I am running Freesurfer 5.1.0
 and FSL 4.1.9.
 Here's what's in the dmri.bedpostX directory:

 [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/
 bvals  bvecs  commands.txt  diff_slices  logs  monitor
 nodif_brain_mask.nii.gz  xfms

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Re: [Freesurfer] trac-all -path error

2012-03-23 Thread Anastasia Yendiki

Oh, ok. That's a known issue, it has to do with changes in the command
line of the latest version of bedpostx. We've updated trac-all and it'll
be working in our next release but for now you'll have to run bedpostx by
itself and not through trac-all. Sorry for the inconvenience!

On Fri, 23 Mar 2012, Chris Watson wrote:

[freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/
dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz
mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz
th1samples.nii.gz

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 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 when I run the next step I
get the following error:

Loading BEDPOST parameter samples from
/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX
niiRead(): error opening file

/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

ERROR: Could not read

/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7
04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012

Word too long.

Indeed, the merged file doesn't exist. I am running Freesurfer 5.1.0
and FSL 4.1.9.
Here's what's in the dmri.bedpostX directory:

[freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/
bvals bvecs commands.txt diff_slices logs monitor
nodif_brain_mask.nii.gz xfms

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Re: [Freesurfer] trac-all -path error

2012-03-23 Thread Anastasia Yendiki

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:

On Fri, 23 Mar 2012, Chris Watson wrote:

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 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 when I run the next
step I
get the following error:
Loading BEDPOST parameter samples from

/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX
niiRead(): error opening file

/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

ERROR: Could not read

/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed
Mar 7
04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012
Word too long.

Indeed, the merged file doesn't exist. I am running
Freesurfer 5.1.0
and FSL 4.1.9.
Here's what's in the dmri.bedpostX directory:
[freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/
bvals bvecs commands.txt diff_slices logs monitor
nodif_brain_mask.nii.gz xfms
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Re: [Freesurfer] Tracula preproc failure

2012-03-01 Thread Anastasia Yendiki



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

Note that any ILF streamlines from the atlas that go off the brain mask of 
your subject have been removed before creating the *histo.nii.gz file, so 
you can compare with a healthy subject and see if there's much less left 
in the pathological subject, and if what's there goes through the same 
parts of the aparc+aseg in both cases.


Hope this helps,
a.y

On Thu, 1 Mar 2012, Martijn Steenwijk wrote:


Thanks for your reply, sorry for the delay. The problems appear in the left
hemisphere ILF_AS. The subject has atrophy and a number of periventricular
lesions. 
Does the error indicate that set of the endpoints could not be mached? In
that case it could be that the points in the temporal pole give problems
since the original FS segmentation is a bit too tight there. Is there a way
to visualize the suspected points onto the subjects data? 

Best,
Martijn

On Mon, Feb 27, 2012 at 10:16 PM, ayend...@nmr.mgh.harvard.edu wrote:
  Hi Martijn,

  Which pathway does it fail on? Is the pathology of your subject
  affecting
  the structures in the aparc+aseg that surround that pathway?

  a.y

 Dear all,

 I'm running Tracula on a brain with some pathology. During the
preproc
 phase it fails with the following error:

 INFO: Rejected 843 streamlines for straying off mask
 INFO: Rejected 0 streamlines for reversing direction
 INFO: Rejected 10 streamlines as length outliers
 INFO: Have 2748 total streamlines (min/mean/max length: 38/70/105)
 Processing pathway 3 of 18...
 Matching streamline ends
 INFO: Have 0 non-truncated streamlines (min/mean/max length: 0/0/0)
 INFO: Center of mass of start points: (nan+/-nan, nan+/-nan,
nan+/-nan)
 INFO: Center of mass of midpoints: (nan+/-nan, nan+/-nan, nan+/-nan)
 INFO: Center of mass of end points: (nan+/-nan, nan+/-nan,
nan+/-nan)
 Segmentation fault (core dumped)
 Linux lnx-rad-03 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST
2008
 x86_64 x86_64 x86_64 GNU/Linux

 trac-preproc exited with ERRORS at Mon Feb 27 19:41:00 CET 2012

 I understand that no streamlines are available for initialization.
Is that
 correct?

 Best,
 Martijn
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Re: [Freesurfer] tracula - submit via fsl_sub / qsub ?

2012-02-29 Thread Anastasia Yendiki



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 our local 
compute clusters (that run PBS). So trac-all recognizes when it's run on 
one of our clusters and submits each subject as a job. If it's run on any 
other machine, it won't do that, so this doesn't affect you. You're free 
to make your own modifications to fsl_sub or otherwise make use of your 
own cluster.


Let me know if you have any other questions,
a.y

On Wed, 29 Feb 2012, Andi Heckel wrote:


Dear Tracula Team,

recently i ran trac-all (-prep / -bedp / -path), but I happened to submit the 
commands to our SGE
computer cluster using fsl_sub (which is fsl's  wrapper for qsub)

According to the header comments of the trac-all script, however, trac-all 
should not be submitted to
a cluster. (it is self-submitting as i understand)

Do I need to worry about the results being invalid when submitting the command 
with  qsub/fsl_sub  or
would you suggest re-running trac-all without fsl_sub / qsub, although all 
processes finished without
errors according to the logs ?

Actually, i would really like to submit the trac-all command line using fsl_sub 
/ qsub to
a) make use of fsl_sub / qsub features
and b) make full use of our cluster, so I can process multiple subjects in 
parallel, as it seems that
not all time-consuming processing steps in the trac-all scripts are 
self-submitting (i guess only
trac-all -bedp self-submits)

Are there general concerns, why one should not use fsl_sub/qsub on the trac-all 
(-prep / - path)
command ? (I used fsl_sub on other self-submitting scripts, which seemed to 
work so far.)

Tracula is quite useful !

Thank you very much for your time !
Kind Regards,
andi





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Re: [Freesurfer] TRACULA question: pathstats.byvoxel.txt

2012-02-20 Thread Anastasia Yendiki


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 low anisotropy area? Can you rerun the dmri_paths command for just one 
of these fmajor paths with --debug and send us the log.txt file?

Thanks!
a.y

On Mon, 20 Feb 2012, Minjie Wu wrote:

 Hi Priti,

 Thank you very much for the detailed instructions. The tracts with
 empty pathstat.byvoxel.txt files are slfp, slft, and unc tracts.
 After your email, I have checked all 10+ subjects with such problems.
 They all share similar motion problems (the parietal or temporal part
 of brain is cut due to motion), which may be why TRACULA is not
 working.

 The other issue is with fmajor. For many subjects (almost 1/3 of
 overall subjects), the fiber tracking for fmajor (path.pd.nii.gz)
 looks like a single fiber (or 2,3 fibers) instead of a bundle of
 fibers.  The volume from pathstats.overall.txt (195 voxels) is
 significantly lower than the mean fmajor volume (1000 voxels) from the
 population (see attached file). These brain images are complete (no
 cutting issue at fmajor). Also I have checked the FA-MNI
 co-registration, and the registration seems to be accurate.  Any idea
 of how to avoid this problem will be really appreciated.

 Thanks,
 Minjie




 [minjiewu@ccmfsl1 fmajor_PP_avg33_mni_bbr]$ more pathstats.overall.txt
 # Title Pathway Statistics
 #
 # generating_program /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats
 # cvs_version
 # cmdline /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats --intrc
 /ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr
 --dtbase /ccm/pavuluri/rest/DTI/data/20191/dmri/dtifit --path
 fmajor --subj 20191 --out
 /ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt
 --outvox 
 /ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr/pathstats
 .byvoxel.txt
 # sysname Linux
 # hostname ccmfsl2.psych.uic.edu
 # machine x86_64
 # user minjiewu
 # anatomy_type pathway
 #
 # subjectname 20191
 # pathwayname fmajor
 #
 Count 1000
 Volume 195
 Len_Min 136
 Len_Max 179
 Len_Avg 149.767
 Len_Center 164
 AD_Avg 0.00145274
 AD_Avg_Weight 0.00149492
 AD_Avg_Center 0.00165127
 RD_Avg 0.000615351
 RD_Avg_Weight 0.00058665
 RD_Avg_Center 0.000529699
 MD_Avg 0.00089448
 MD_Avg_Weight 0.000889406
 MD_Avg_Center 0.000903556
 FA_Avg 0.475963
 FA_Avg_Weight 0.507926
 FA_Avg_Center 0.610243






 On Wed, Feb 15, 2012 at 9:25 AM, Priti Srinivasan
 rspr...@nmr.mgh.harvard.edu wrote:
 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/FsTutorial/TraculaStatistics

 Your pathstats.overall.txt does not look right. For instance the center
 streamline's length (Len_Center = 0). Did you open the posterior
 probability distribution of this tract?

 You can use the following command to do the same:

 freeview path/to/your/data/dpath/path.pd.nii.gz

 If it does not look right then something probably went wrong during the
 path reconstruction. If you can send us your trac-all.log, we can check
 for anything that went wrong.

 Hope this is helpful.,

 Priti


 Hello Tracula Developer  User,

 I found a few subjects have pathstat.overall.txt information but with
 blank voxel information in pathstats.byvoxel.txt. For such tracts,
 they usually len_min = len_max = len_avg. Anyone know what happened
 for the fiber tracking? Is it possible to extract the byvoxel
 information along the tract?

 Thanks,
 Minjie

 For example:

 [minjiewu@ccmfsl1 data]$ more
 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt
 # Title Pathway Statistics
 #
 # generating_program /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats
 # cvs_version
 # cmdline /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats --intrc
 /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr
 --dtbase /ccm/pavuluri/rest/DTI/data/223
 31/dmri/dtifit --path rh.slfp --subj 22331 --out
 /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt
 --outvox /ccm/pavuluri/rest/DTI/data/
 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.byvoxel.txt
 # sysname Linux
 # hostname ccmfsl2.psych.uic.edu
 # machine x86_64
 # user minjiewu
 # anatomy_type pathway
 #
 # subjectname 22331
 # pathwayname rh.slfp
 #
 Count 1000
 Volume 86
 Len_Min 86
 Len_Max 86
 Len_Avg 86
 Len_Center 0
 AD_Avg 0.00112029
 AD_Avg_Weight 0.00112029
 AD_Avg_Center nan
 RD_Avg 0.000783836
 RD_Avg_Weight 0.000783836
 RD_Avg_Center nan
 MD_Avg 0.000895987
 MD_Avg_Weight 0.000895987
 MD_Avg_Center nan
 FA_Avg 0.264347
 FA_Avg_Weight 0.264347
 FA_Avg_Center nan

Re: [Freesurfer] TRACULA bvecs question

2012-02-16 Thread Anastasia Yendiki


This is because the mac executables in freesurfer where compiled on the 
leopard verion of OSX. There's an update here compiled on snow leopard 
that should solve this error:

https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula

On Thu, 16 Feb 2012, Tetiana Dadakova wrote:

 Thanks for the note. I used tr '\r' '\n\ bvec_dos_file
 bvec_unix_file to convert dos end-of-line character into unix ones.
 But something is wrong again (I attach log file):

 dmri_train(82757) malloc: *** mmap(size=159744) failed (error code=12)
 *** error: can't allocate region
 *** set a breakpoint in malloc_error_break to debug
 MRIalloc(218, 182, 182): could not allocate 158704 bytes for 14th slice

 Cannot allocate memory
 Darwin 130-229-40-185.cns.ki.se 10.8.0 Darwin Kernel Version 10.8.0:
 Tue Jun  7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/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 8:02 PM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

 When I look at them with the more command on a linux machine, I see 2 lines
 in bval and 6 lines in bvec. Most likely this is a problem with the text
 files being created with a windows program like excel and not having
 unix-compatible end-of-line characters. It's been discussed a few times in
 the archives. You'll have to make sure you have text files that can be read
 properly on unix.


 On Wed, 15 Feb 2012, Tetiana Dadakova wrote:

 Sorry for bothering you again,

 I have another error now: Error: bvecs and bvals don't have the same
 number of entries.
 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 tetian...@gmail.com
 wrote:

 I see, thank you :)


 On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:


 PS: The info on what you need to set it here:

 https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

 # Number of low-b images
 # Must be specified if inputs are not DICOM
 # Default: Read from DICOM header
 #
 set nb0 = 10



 On Tue, 14 Feb 2012, Tetiana Dadakova wrote:

 Dear Priti, Anastasia,

 Thank you for your help, I created bvec and bval files and it went
 fine.
 But now I have another error in preprocessing step.
 I attach a log file. Could you please take a look at that?

 Thank you,
 Tanja.



 trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012




 On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan
 rspr...@nmr.mgh.harvard.edu wrote:


 Hi Tanja,

 Can you check if the
 $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs
 was created at all? It looks like that may not have been created and
 that's why it can't find dwi_orig_flip.mghdti.bvecs. If your bvals
 and
 bvecs information is not encoded in the dicom header, then you can
 specify
 it explicitly in the dmrirc file.

 Please refer to the following page for instructions on how to specify
 your
 bvals and bvecs for tracula:

 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

 Hope this helps,
 Priti


 Hi Priti,

 I changed the dmrirc 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
 rspr...@nmr.mgh.harvard.edu wrote:


 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 '/' and since you're adding an extra '/',
 it's
 giving an error. I've edited your dmrirc file and removed those
 trailing
 slashes. Could you run this again and let us know if it solves the
 problem?

 Hope this is helpful,
 Priti





 Thank you Priti and Anastasia,

 Anastasia, just wanted to clarify, I meant
 $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry
 for
 this misunderstanding.

 I attach my configuration file and the command I use is  trac-all
 -prep -c
 /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc


 .


 I also attach a picture of my file tree and a track-all.log file.

 Thank you for your time and help,
 Tanja.

 On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:



 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


 On Thu, 2 Feb 2012, Tetiana Dadakova wrote

Re: [Freesurfer] TRACULA bvecs question


When I look at them with the more command on a linux machine, I see 2 
lines in bval and 6 lines in bvec. Most likely this is a problem with the 
text files being created with a windows program like excel and not having 
unix-compatible end-of-line characters. It's been discussed a few times in 
the archives. You'll have to make sure you have text files that can be 
read properly on unix.

On Wed, 15 Feb 2012, Tetiana Dadakova wrote:

 Sorry for bothering you again,

 I have another error now: Error: bvecs and bvals don't have the same
 number of entries.
 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 tetian...@gmail.com wrote:
 I see, thank you :)


 On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

 PS: The info on what you need to set it here:

 https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

 # Number of low-b images
 # Must be specified if inputs are not DICOM
 # Default: Read from DICOM header
 #
 set nb0 = 10



 On Tue, 14 Feb 2012, Tetiana Dadakova wrote:

 Dear Priti, Anastasia,

 Thank you for your help, I created bvec and bval files and it went fine.
 But now I have another error in preprocessing step.
 I attach a log file. Could you please take a look at that?

 Thank you,
 Tanja.



 trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012




 On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan
 rspr...@nmr.mgh.harvard.edu wrote:

 Hi Tanja,

 Can you check if the $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs
 was created at all? It looks like that may not have been created and
 that's why it can't find dwi_orig_flip.mghdti.bvecs. If your bvals and
 bvecs information is not encoded in the dicom header, then you can
 specify
 it explicitly in the dmrirc file.

 Please refer to the following page for instructions on how to specify
 your
 bvals and bvecs for tracula:

 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

 Hope this helps,
 Priti


 Hi Priti,

 I changed the dmrirc 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
 rspr...@nmr.mgh.harvard.edu wrote:

 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 '/' and since you're adding an extra '/',
 it's
 giving an error. I've edited your dmrirc file and removed those
 trailing
 slashes. Could you run this again and let us know if it solves the
 problem?

 Hope this is helpful,
 Priti





 Thank you Priti and Anastasia,

 Anastasia, just wanted to clarify, I meant
 $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for
 this misunderstanding.

 I attach my configuration file and the command I use is  trac-all
 -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc

 .

 I also attach a picture of my file tree and a track-all.log file.

 Thank you for your time and help,
 Tanja.

 On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:


 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


 On Thu, 2 Feb 2012, Tetiana Dadakova wrote:

 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 folder with reconstructed T1 data and a folder with raw
 dicom
 DTI data. When I start trac-all -prep, it creates directory /dmri/,
 but it doesn't create the bvecs file.
 Should I create it myself using dcm2nii or is it supposed to be
 created automatically?

 Thank you,
 Tanja.
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Re: [Freesurfer] trac-all -prep error


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 that it can't
 open lowb.nii.gz.hdr:

 fslroi
 /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz
 /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
 0 1
 fslmaths
 /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
 -Tmean
 /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
 bet
 /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
 /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz
 -m -f 0.3
 Can't open
 /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr
 Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10
 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux

 trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012

 The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't encounter this
 problem with other subjects that I am processing. Any thoughts?

 Thanks,
 Chris

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Re: [Freesurfer] trac-all -prep error


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:

 Here's output from mri_info:
 [freesurfer@occipital dmri]$ mri_info lowb.nii.gz
 Volume information for lowb.nii.gz
  type: nii
   dimensions: 96 x 96 x 56
  voxel sizes: 2.5000, 2.5000, 2.5000
 type: FLOAT (3)
   fov: 240.000
   dof: 0
xstart: -120.0, xend: 120.0
ystart: -120.0, yend: 120.0
zstart: -70.0, zend: 70.0
   TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
 degrees
   nframes: 1
   PhEncDir: UNKNOWN
 ras xform present
   xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 
 0.9450
 :  x_a =   0., y_a =   1., z_a =   0., c_a = 
 31.8560
 :  x_s =   0., y_s =   0., z_s =   1., c_s = 
 25.3936
 Orientation   : LAS
 Primary Slice Direction: axial

 voxel to ras transform:
   -2.5000   0.   0.   120.9450
0.   2.5000   0.   -88.1440
0.   0.   2.5000   -44.6064
0.   0.   0. 1.

 voxel-to-ras determinant -15.625

 ras to voxel transform:
   -0.4000   0.   0.48.3780
   -0.   0.4000  -0.35.2576
   -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
  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 that it can't
   open lowb.nii.gz.hdr:
  
   fslroi
   
  /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz
   
  /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
   0 1
   fslmaths
   
  /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
   -Tmean
   
  /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
   bet
   
  /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
   
  /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz
   -m -f 0.3
   Can't open
   
  /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr
   Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10
   17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
  
   trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012
  
   The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't encounter this
   problem with other subjects that I am processing. Any thoughts?
  
   Thanks,
   Chris
  
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Re: [Freesurfer] trac-all -prep error


Weird. Glad it got fixed, let us know if you have any more trouble.

On Wed, 15 Feb 2012, Chris Watson wrote:

 Actually, it now works when I re-source my .bash_profile and .bashrc files. 
 Not sure why that would be.
 Chris

 Chris Watson wrote:
  Yes, the 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:
  
  
Here's output from mri_info:
[freesurfer@occipital dmri]$ mri_info lowb.nii.gz
Volume information for lowb.nii.gz
 type: nii
 dimensions: 96 x 96 x 56
 voxel sizes: 2.5000, 2.5000, 2.5000
type: FLOAT (3)
  fov: 240.000
  dof: 0
   xstart: -120.0, xend: 120.0
   ystart: -120.0, yend: 120.0
   zstart: -70.0, zend: 70.0
  TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 
0.00 degrees
  nframes: 1
  PhEncDir: UNKNOWN
ras xform present
  xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 
0.9450
   :   x_a =   0., y_a =   1., z_a =   0., c_a = 
31.8560
   :   x_s =   0., y_s =   0., z_s =   1., c_s = 
25.3936
Orientation   : LAS
Primary Slice Direction: axial
   
voxel to ras transform:
  -2.5000   0.   0.   120.9450
   0.   2.5000   0.   -88.1440
   0.   0.   2.5000   -44.6064
   0.   0.   0. 1.
   
voxel-to-ras determinant -15.625
   
ras to voxel transform:
  -0.4000   0.   0.48.3780
  -0.   0.4000  -0.35.2576
  -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
  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 that it 
 
 can't

   open lowb.nii.gz.hdr:
 
fslroi
  
 
 
 
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz
 


 
 
 
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
 


   0 1
   fslmaths
 
 
 
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
 


   -Tmean
 
 
 
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
 


   bet
 
 
 
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
 


 
 
 
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz
 


   -m -f 0.3
   Can't open
 
 
 
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr
 


   Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue 
 
 Jan 10

   17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
 
trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012
The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't 
  
 encounter this

   problem with other subjects that I am processing. Any thoughts?
 
Thanks,
  
   Chris
 
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Re: [Freesurfer] TRACULA bvecs question

2012-02-14 Thread Anastasia Yendiki


You need to set the nb0 parameter (number of low-b volumes in the 
beginning of your DWI series).

On Tue, 14 Feb 2012, Tetiana Dadakova wrote:

 Dear Priti, Anastasia,

 Thank you for your help, I created bvec and bval files and it went fine.
 But now I have another error in preprocessing step.
 I attach a log file. Could you please take a look at that?

 Thank you,
 Tanja.



 trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012




 On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan
 rspr...@nmr.mgh.harvard.edu wrote:
 Hi Tanja,

 Can you check if the $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs
 was created at all? It looks like that may not have been created and
 that's why it can't find dwi_orig_flip.mghdti.bvecs. If your bvals and
 bvecs information is not encoded in the dicom header, then you can specify
 it explicitly in the dmrirc file.

 Please refer to the following page for instructions on how to specify your
 bvals and bvecs for tracula:

 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

 Hope this helps,
 Priti


 Hi Priti,

 I changed the dmrirc 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
 rspr...@nmr.mgh.harvard.edu wrote:
 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 '/' and since you're adding an extra '/', it's
 giving an error. I've edited your dmrirc file and removed those trailing
 slashes. Could you run this again and let us know if it solves the
 problem?

 Hope this is helpful,
 Priti





 Thank you Priti and Anastasia,

 Anastasia, just wanted to clarify, I meant
 $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for
 this misunderstanding.

 I attach my configuration file and the command I use is  trac-all
 -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc
 .
 I also attach a picture of my file tree and a track-all.log file.

 Thank you for your time and help,
 Tanja.

 On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

 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


 On Thu, 2 Feb 2012, Tetiana Dadakova wrote:

 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 folder with reconstructed T1 data and a folder with raw
 dicom
 DTI data. When I start trac-all -prep, it creates directory /dmri/,
 but it doesn't create the bvecs file.
 Should I create it myself using dcm2nii or is it supposed to be
 created automatically?

 Thank you,
 Tanja.
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 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
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Re: [Freesurfer] TRACULA bvecs question

2012-02-14 Thread Anastasia Yendiki


PS: The info on what you need to set it here:

https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

# Number of low-b images
# Must be specified if inputs are not DICOM
# Default: Read from DICOM header
#
set nb0 = 10


On Tue, 14 Feb 2012, Tetiana Dadakova wrote:

 Dear Priti, Anastasia,

 Thank you for your help, I created bvec and bval files and it went fine.
 But now I have another error in preprocessing step.
 I attach a log file. Could you please take a look at that?

 Thank you,
 Tanja.



 trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012




 On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan
 rspr...@nmr.mgh.harvard.edu wrote:
 Hi Tanja,

 Can you check if the $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs
 was created at all? It looks like that may not have been created and
 that's why it can't find dwi_orig_flip.mghdti.bvecs. If your bvals and
 bvecs information is not encoded in the dicom header, then you can specify
 it explicitly in the dmrirc file.

 Please refer to the following page for instructions on how to specify your
 bvals and bvecs for tracula:

 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

 Hope this helps,
 Priti


 Hi Priti,

 I changed the dmrirc 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
 rspr...@nmr.mgh.harvard.edu wrote:
 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 '/' and since you're adding an extra '/', it's
 giving an error. I've edited your dmrirc file and removed those trailing
 slashes. Could you run this again and let us know if it solves the
 problem?

 Hope this is helpful,
 Priti





 Thank you Priti and Anastasia,

 Anastasia, just wanted to clarify, I meant
 $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for
 this misunderstanding.

 I attach my configuration file and the command I use is  trac-all
 -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc
 .
 I also attach a picture of my file tree and a track-all.log file.

 Thank you for your time and help,
 Tanja.

 On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

 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


 On Thu, 2 Feb 2012, Tetiana Dadakova wrote:

 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 folder with reconstructed T1 data and a folder with raw
 dicom
 DTI data. When I start trac-all -prep, it creates directory /dmri/,
 but it doesn't create the bvecs file.
 Should I create it myself using dcm2nii or is it supposed to be
 created automatically?

 Thank you,
 Tanja.
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 The information in this e-mail is intended only for the person to whom
 it is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you
 in
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Re: [Freesurfer] Tracula - bedpost failure

2012-02-10 Thread Anastasia Yendiki



Hi Kiely - If part of the brain is cut off in dwi_orig.nii.gz, it means it 
was cut off in your original dicom. If there's actualy part of the brain 
missing in all the volumes in your diffusion series, you may not be able 
to reconstruct tracts that go through that part.


a.y

On Fri, 10 Feb 2012, Kiely Donnelly wrote:


Hi Priti,
Thanks for your help. I took another look at the original diffusion and
anatomical images. The anatomical looks OK, but in the diffusion image a
posterior region of the brain appears cutoff and when I view the image in
freeview there is a green box in the lower left hand corner that I've never
seen before (I've attached a shot). I'm new to Freesurfer so I would
appreciate any help you may have.

Thanks again,

Kiely

On Tue, Jan 24, 2012 at 1:21 PM, Priti Srinivasan
rspr...@nmr.mgh.harvard.edu wrote:
  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 inspect the original diffusion image
  (dmri/dwi_orig.nii.gz)
  and the original anatomical (dlabel/anat_brain_mask.nii.gz) to
  see if they
  have any problems (signal loss etc) which could lead to failures
  in
  registration as a first step.

  If both your diffusion and anatomical are both good, then I'd
  try to do
  flirt seperately to see if you get the same results as the one
  produced by
  tracula.

  Hope this is helpful,

  Priti





   Hi Anastasia,
  
   Sorry for my slow reply. I am working with data that I only
  have access
  to
   intermittently. We were able to fix the problem by deleting
  the original
  files from the folder and re-running the bedpost step. The old
  files
  must
   have been interfering in some way.
  
   I am hoping you can help me with a different problem I ran
  into. For
  several of our subjects, each pathway reconstruction fails and I
  get an
  error like the following for all 18 tracts:
  
   Processing pathway 16 of 18...
   Initializing MCMC
   INFO: Path from initial control points is not entirely in mask
   INFO: or is self-intersecting
   INFO: Attemping to perturb control points
   ERROR: Path from initial control points is not entirely in
  mask
   ERROR: or is self-intersecting
   ERROR: Initialization failed
   ERROR: Pathway reconstruction failed
   Done in 0.216 sec.
  
   I am able to view the FA image in native space, but when I
  attempt to
  view
   the FLIRT-registered FA image it's completely dark. Is there
  any reason you
   can 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'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 Everyone --
   I've been having difficulty getting Tracula to run smoothly
  on our
  cluster. Similar to others on the listserv, the bedpost step
   was not creating the necessary files causing an error during
  the -path
  step. Based on previous posts, I ran bedpostx on the dmri
   directory. This initially seemed to work (I no longer
  received the
  message 1 slice processed over and over), but for some reason
  the
  merged_ph1samples.nii.gz file is still not being created and I
  continue to run into an error when I run -path. It does create a
  merged_ph2samples.nii.gz output file.
   Any help would be greatly appreciated.
   Thanks,
   Kiely
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Re: [Freesurfer] What does trac-all do on the file 'bvecs'?

2012-02-07 Thread Anastasia Yendiki



Hi - It's hard to tell without access to the actual data, but it sounds 
like you've found the right way to reconcile your nifti volume and 
gradient directions, so you should pass those to trac-all directly instead 
of the dicom.


Anastasia.

On Tue, 7 Feb 2012, Xiangzhen Kong wrote:



Hi Yendiki：

Sorry to bother you again. The DWI volume and bvec orientation issues
confused me very much, so I resort to you. In my case, DWI data were scanned
from siemens 3T Trio system. The data were then unpacked using unpacksdcmdir
command from FS, and the bvecs is directly read from dicom tag
'Private_0019_100e' with Matlab dicominfo function. After unpacked, DWI
volume is in LPS orientation, so bvec is also LPS, am I right?

If so, when we use fslswapdim to covert the volume to LAS using x, -y, z
option, we should also reverse the bvecs with the same option (i.e. only
swap the second dimension). But I found that trac-all uses –x –y z to bvecs,
rather than x –y z as in converting volume data. The related code of
trac-all is line 59 to line 100 in flip4fsl.

Results from our data show that x –y z option to bvecs can give us the right
tensor (attachment Fig1), but –x –y z gives us the tensor with left-right of
reversed (attachment Fig2). These two figs both show the first eigenvector
V1, with FA map as background.

Can you give me some clues to understand the difference? Thanks you very
much.

 

Thanks.

 

Xiangzhen

 
 


发件人： ayendiki
发送时间： 2012-02-04  15:22:09
收件人： Xiangzhen Kong
抄送： freesurfer
主题： Re: [Freesurfer] What does trac-all do on the file 'bvecs'?
You don't have to multiply the bvecs with anything yourself, it will do it
for you. Of course you should check that it does it correctly, check the
help of the flip4fsl script for how to do that.
 Could you give me something about the transpsition here?
 I checked the code flip4fsl and found there are two kinds of sign.
 line 59.   set sign = `echo $inorient | sed s/[LAS]/+\ /g; s/[RPI]/-\
 /g`
 line 99.   set sign = `echo $inorient | sed s/[RAS]/+\ /g; s/[LPI]/-\
 /g`
 e.g.
 When the orientation of DWI is LPS, we have to transform data to RAS.
 ($fslplipx=1)
 The first sign = +-+ and the second sign = --+.
 So I have to multiple 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
 ·¢ËÍÊ±¼ä£º 2012-02-04  00:48:58
 ÊÕ¼þÈË£º Xiangzhen Kong
 ³ËÍ£º freesurfer
 Ö÷Ìâ£º Re: [Freesurfer] What does trac-all do on the file 'bvecs'?
 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-all requires a bvecs file in 3 columes, but FSL need that in 3
 raws.
 I wonder what does trac-all do on the bvecs file that I specify.
 And I have check the code 'trac-preproc' and the log, but found
 nothing,
 except copy and Eddy-current correction.
 ?
 ps: The orientation of my dicom and .nii fils are both LPS, and the
 bvecs is
 read from the DICOM header via nibabel.
 But FSL requires LAS. I thinks trac-all have done the transposition on
 the
 bvecs somewhere.
 What orientation of bvecs does trac-all need when run with .nii files?
 ?
 Thanks!
 ?
 Xiangzhen
 ?
 2012-02-03
 ?


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Re: [Freesurfer] What does trac-all do on the file 'bvecs'?

2012-02-03 Thread Anastasia Yendiki



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-all requires a bvecs file in 3 columes, but FSL need that in 3 raws.
I wonder what does trac-all do on the bvecs file that I specify.
And I have check the code 'trac-preproc' and the log, but found nothing,
except copy and Eddy-current correction.
 
ps: The orientation of my dicom and .nii fils are both LPS, and the bvecs is
read from the DICOM header via nibabel.
But FSL requires LAS. I thinks trac-all have done the transposition on the
bvecs somewhere.
What orientation of bvecs does trac-all need when run with .nii files?
 
Thanks!
 
Xiangzhen
 
2012-02-03
 

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Re: [Freesurfer] /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory

2012-02-03 Thread Anastasia Yendiki



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.
+++
mv -f /xxx/dmri/dwi_orig_flip.mghdti.bvecs //dmri/bvecs
mv: cannot stat `/xxx/dmri/dwi_orig_flip.mghdti.bvecs': No such file or dir
ectory
+++
I check the dir /xxx/dmri/ and there are only two files
'dwi_orig_flip.nii.gz' , 'dwi_orig.nii.gz'  and a dir 'xfms'.
Does trac-all extract bvals/bvecs automatically when start with DICOM data?
My data is from a siemens scanner.
 
Thanks!
 
Xiangzhen
 
2012-02-03


Xiangzhen Kong

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Re: [Freesurfer] Two questions when using the new trac-all

2012-02-02 Thread Anastasia Yendiki



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'll just have to specify the runlist explicitly in your
   config file instead of relying on the default, i.e., set runlist = (1 2
   3 ...), however many subjects you have.

2. There's no increase in compute time by having a separate config file
   for each subject. Being able to specify multiple subjects in the same
   file with all other options being the same was just done for
   convenience.

Hope this helps,
a.y

On Wed, 1 Feb 2012, Xiangzhen Kong wrote:


Hi, all
I am using trac-all these days.
But I came across two quetions:
1. If I don't Specify Subjects To Be Analyzed, which means running the analysis on all 
subjects, there is an error saying jot: Command not found..
The OS I am using is CentOS and I think jot is not installed by default. And 
some one says jot is part of freeBSD.
Do we need to replace 'jot' in trac-all with other commands, such as seq?
 
2. If I run trac-all for just one subject each time,(that is to say, one 
config-file each subject), I wonder whether the time loss will be increase
too much, compared with that one config-file for all subjects.
 
Thanks!
 
 
conxz
 
 
2012-02-01

_
Xiangzhen Kong

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Re: [Freesurfer] TRACULA bvecs question

2012-02-02 Thread Anastasia Yendiki


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

On Thu, 2 Feb 2012, Tetiana Dadakova wrote:

 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 folder with reconstructed T1 data and a folder with raw dicom
 DTI data. When I start trac-all -prep, it creates directory /dmri/,
 but it doesn't create the bvecs file.
 Should I create it myself using dcm2nii or is it supposed to be
 created automatically?

 Thank you,
 Tanja.
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Re: [Freesurfer] dividing a label into equal parts

2012-01-18 Thread Anastasia Yendiki


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 accurate.

 Please let me know.

 Thanks

 Ri
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Re: [Freesurfer] Tracula - bedpost failure

2011-12-23 Thread Anastasia Yendiki


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 Everyone --
 
 I've been having difficulty getting Tracula to run smoothly on our cluster. 
 Similar to others on the listserv, the bedpost step
 was not creating the necessary files causing an error during the -path step. 
 Based on previous posts, I ran bedpostx on the dmri
 directory. This initially seemed to work (I no longer received the message 1 
 slice processed over and over), but for some reason
 the merged_ph1samples.nii.gz file is still not being created and I continue 
 to run into an error when I run -path. It does create
 a merged_ph2samples.nii.gz output file.
 
 Any help would be greatly appreciated.
 
 Thanks,
 
 Kiely
 
 
 

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Re: [Freesurfer] bedpost failure using tracula

2011-12-16 Thread Anastasia Yendiki


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 looks like data from only one slice was
 written (dmri.bedpostX/diff_slices/data_slice_0002).  This issue has
 replicated across multiple subjects.  I'm processing data locally on
 mac os 10.6.8 (16 GB RAM; two 3.2 quadcore processors, which should be
 able to handle bedpost), using FSL 4.1.9.  I don't see any errors in
 the tracula log files (until I run -path), and no complaints in the
 terminal window (which writes:  Queuing parallel processing stage
 0 slices processed
 1 slices processed
 1 slices processed
 etc...

 Any insight as to what might be causing the issue?

 Thanks,
 Scott
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Re: [Freesurfer] bedpost failure using tracula

2011-12-16 Thread Anastasia Yendiki


Hi Scott - Could you try running bedpostx on the dmri/ directory directly 
and see what if any error you get?

a.y

On Fri, 16 Dec 2011, Scott Hayes wrote:

 Hi,
 The following files  directories are listed directly under dmri.bedpostX:

 bvals commands.txtlogs
 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 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 looks like data from only one slice was
 written (dmri.bedpostX/diff_slices/data_slice_0002).  This issue has
 replicated across multiple subjects.  I'm processing data locally on
 mac os 10.6.8 (16 GB RAM; two 3.2 quadcore processors, which should be
 able to handle bedpost), using FSL 4.1.9.  I don't see any errors in
 the tracula log files (until I run -path), and no complaints in the
 terminal window (which writes:  Queuing parallel processing stage
 0 slices processed
 1 slices processed
 1 slices processed
 etc...

 Any insight as to what might be causing the issue?

 Thanks,
 Scott
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Re: [Freesurfer] tracula and snow leopard: can't allocate region / memory error

2011-12-12 Thread Anastasia Yendiki



Hi Scott - Sending to the list is always good so that others can find it 
in the archives when they have similar problems.


Do you specify the .dcm or .mgz file in your dmrirc? Does dwi.nii.gz have 
the right dimensions/frames?


a.y

On Mon, 12 Dec 2011, Scott Hayes wrote:


Thanks for the prompt response Anastasia--I ran it over the weekend
and it worked.

I've subsequently encountered a new issue (copied below from the
trac-all.log). The file (dwi.nii.gz) exists in the correct location
(it was written there by tracula).  I use unpacksdcmdir for unpacking
the dicoms, and then point the config file to the appropriate .mgz
file, so I'm not doing anything particularly unusual in terms of
unpacking or messing w/ the headers (We scan on a Siemens 3T tim
trio.)  I can send this to the listserv if you prefer.
Best,
Scott

fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k
/Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz
-m -s | awk '{print $1/$2}' 
/Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt
** ERROR (nifti_image_read): failed to find header file for '-t'
** ERROR: nifti_image_open(-t): bad 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
ayend...@nmr.mgh.harvard.edu wrote:


Hi Scott - Here are the tracula executables for snow leopard that we posted
in response to that thread:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz

Let me know if this solves the memory errors.

a.y


On Fri, 9 Dec 2011, Scott Hayes wrote:


Hi Anastasia,
I've encountered an error using tracula w/ snow leopard OS that was
previously reported on the FS listserv:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18829.html

I'm wondering if there is a documented solution available?
Recompiling from source code would be beyond my expertise.

David:  I'm cc'ing you just as a heads up--all of the workstations in
the imaging center run snow leopard OS.

Best,
Scott




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Re: [Freesurfer] tracula failed to find header file for -t

2011-12-12 Thread Anastasia Yendiki



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
ayend...@nmr.mgh.harvard.edu wrote:


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_recon/dmri/dwi.nii.gz -k

/Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz
-m -s | awk '{print $1/$2}' 
/Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt
** ERROR (nifti_image_read): failed to find header file for '-t'
** ERROR: nifti_image_open(-t): bad 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'


The file (dwi.nii.gz) exists in the correct location, and appears to
have the correct number of frames (60 directions + 10 b0).
We scan on a Siemens 3T tim trio.  I unpack the data using
unpacksdcmdir and I specify the resulting .mgz file in the tracula
config file.  Running locally on mac os 10.6.8.

Any suggestions would be appreciated.
Thanks,
Scott
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Re: [Freesurfer] tracula and corona radiata

2011-12-08 Thread Anastasia Yendiki


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 would like to be able to get measurements of the anterior portion of the
 corona radiata using tracula. Is this a possibility? I did not see it as an
 option in paths to reconstruct.
 thank you very much for your help,
 catherine
 

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Re: [Freesurfer] trac-all flag for doing all 3 processing steps?

2011-12-08 Thread Anastasia Yendiki


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 
everything at once but it'd get crazy and probably cause more confusion 
than it solves. Not the most elegant solution, I know...

On Thu, 8 Dec 2011, Scott Hayes wrote:

 Hi,
 I'm new to tracula, but I'm wondering if I'm overlooking or
 misunderstanding the flags.  It appears that one types in the trac-all
 command 3 times to process a subject (or group of subjects)
 trac-all -prep -c ConfigFile
 trac-all -bedp -c ConfigFile
 trac-all -path -c ConfigFile

 Is there a way to specify all three steps w/ one command?  That is,
 could I specify:
 trac-all -all -C ConfigFile
 (I don't see it stated in the help, but maybe it's implicitly
 understood to work this way?)

 Thanks for your guidance.
 Best,
 Scott
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Re: [Freesurfer] trctrain/trainlist

2011-12-06 Thread Anastasia Yendiki



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 time, and I am having trouble locating 
$FREESURFER/HOME/trctrain/trainlist.txt..of 33
normal subjects to enter in for set trainfile command. This is what my 
Freesurfer home directory looks like:
cpdla@ba3:/software/Freesurfer/5.0.0$ ls
ASegStatsLUT.txt  FreeSurferColorLUT.txt  SegmentNoLUT.txt
AUTHORS   FreeSurferEnv.csh   sessions
average   FreeSurferEnv.sh    SetUpFreeSurfer.csh
bin   fsafd   SetUpFreeSurfer.sh
build-stamp.txt   fsfast  Simple_surface_labels2009.txt
DefectLUT.txt lib subjects
diffusion matlab  tkmeditParcColorsCMA
docs  mni WMParcStatsLUT.txt.

Is there a way I can get this file?

Thanks for the help in advance. Sorry for the confusion.

-C. Paula
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Re: [Freesurfer] trctrain/trainlist

2011-12-06 Thread Anastasia Yendiki


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 am having trouble
 locating $FREESURFER/HOME/trctrain/trainlist.txt..of 33 normal
 subjects to enter in for set trainfile command. This is what my
 Freesurfer home directory looks like:
 cpdla@ba3:/software/Freesurfer/5.0.0$ ls
 ASegStatsLUT.txt  FreeSurferColorLUT.txt  SegmentNoLUT.txt
 AUTHORS   FreeSurferEnv.csh   sessions
 average   FreeSurferEnv.shSetUpFreeSurfer.csh
 bin   fsafd   SetUpFreeSurfer.sh
 build-stamp.txt   fsfast
 Simple_surface_labels2009.txt
 DefectLUT.txt lib subjects
 diffusion matlab  tkmeditParcColorsCMA
 docs  mni WMParcStatsLUT.txt.

 Is there a way I can get this file?

 Thanks for the help in advance. Sorry for the confusion.

 -C. Paula
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Re: [Freesurfer] Tracula: Small Tracts

2011-12-01 Thread Anastasia Yendiki


Hi Tyler - In general this means that for some reason the pathway doesn't 
move at all from the location where it's initialized when the algorithm is 
run. There are a few different reasons why that'd happen, the mask being 
only one of them.

If you could find the dmri_paths command line in trac-all.log, add 
--debug to it and run it again and send the log file, I can try to track 
down what's going on. The command line will probably contain all the 
tracts, but you can run it only for one that fails.

Thanks,
a.y

On Wed, 30 Nov 2011, Tyler 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 when 
 the recon mask was 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 of a tract. Is there anything 
 else I should check/change?

 Thanks again,

 -Tyler

 On Nov 30, 2011, at 4:00 PM, Anastasia Yendiki wrote:


 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:

 Hi List,

 I recently ran a group of around 70 subjects through trac-all. I have 
 started to check the results, and have noticed that Tracula will often 
 produce a tract with a really small volume and a posterior distribution 
 that consists of just 0s and 1000s. When this occurs, the end point images 
 usually contain only one voxel greater than 0. I am not sure what, if 
 anything, is going wrong. The original recons are all of good quality, and 
 the registrations to MNI space look good (the end point images look fine in 
 MNI space as well). I also noticed this same issue in the right SLFP 
 (bbregister version) of the Tracula tutorial subject.

 Is this a fixable error, or is it actually expected behavior? Thanks for 
 any help.

 - Tyler



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Re: [Freesurfer] Tracula: Small Tracts

2011-12-01 Thread Anastasia Yendiki


Thanks, Tyler. It looks like the initial pathway is problematic in that it 
goes off the white matter (look at the Reject due to lines in the log 
for exact voxel coords where this happens).

This could mean that the subject is not well aligned to the atlas in that 
area, or that you just got unlucky. If it's the latter, you can try set 
reinit = 1 in your dmrirc and rerun that pathway and see if you get a 
better result with the new initialiation.

Let me know if this makes sense.

a.y

On Thu, 1 Dec 2011, bla...@artsci.wustl.edu wrote:

 Hi Anastasia,

 Attached is the log.txt produced by dmri_paths for the failed tract. I
 also have included the output of the terminal command in case that helps.
 Thanks again for all of your help.

 - Tyler



 Hi Tyler - In general this means that for some reason the pathway doesn't
 move at all from the location where it's initialized when the algorithm is
 run. There are a few different reasons why that'd happen, the mask being
 only one of them.

 If you could find the dmri_paths command line in trac-all.log, add
 --debug to it and run it again and send the log file, I can try to track
 down what's going on. The command line will probably contain all the
 tracts, but you can run it only for one that fails.

 Thanks,
 a.y

 On Wed, 30 Nov 2011, Tyler 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
 when the recon mask was 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 of a
 tract. Is there anything else I should check/change?

 Thanks again,

 -Tyler

 On Nov 30, 2011, at 4:00 PM, Anastasia Yendiki wrote:


 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:

 Hi List,

 I recently ran a group of around 70 subjects through trac-all. I have
 started to check the results, and have noticed that Tracula will often
 produce a tract with a really small volume and a posterior
 distribution that consists of just 0s and 1000s. When this occurs, the
 end point images usually contain only one voxel greater than 0. I am
 not sure what, if anything, is going wrong. The original recons are
 all of good quality, and the registrations to MNI space look good (the
 end point images look fine in MNI space as well). I also noticed this
 same issue in the right SLFP (bbregister version) of the Tracula
 tutorial subject.

 Is this a fixable error, or is it actually expected behavior? Thanks
 for any help.

 - Tyler



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 e-mail
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Re: [Freesurfer] Tracula: Small Tracts

2011-12-01 Thread Anastasia Yendiki


Great! You just need to rerun cases where the original initialization was 
bad.

On Thu, 1 Dec 2011, bla...@artsci.wustl.edu wrote:

 Anastasia,

 Rerunning with the reinit = 1 option worked great. One last question. If I
 want to compare tracts across subjects, should I rerun every subject with
 the reinitialization, or is it ok to only rerun the subjects/tracts that
 need it? Thanks for all you help.

 -Tyler



 Thanks, Tyler. It looks like the initial pathway is problematic in that it
 goes off the white matter (look at the Reject due to lines in the log
 for exact voxel coords where this happens).

 This could mean that the subject is not well aligned to the atlas in that
 area, or that you just got unlucky. If it's the latter, you can try set
 reinit = 1 in your dmrirc and rerun that pathway and see if you get a
 better result with the new initialiation.

 Let me know if this makes sense.

 a.y

 On Thu, 1 Dec 2011, bla...@artsci.wustl.edu wrote:

 Hi Anastasia,

 Attached is the log.txt produced by dmri_paths for the failed tract. I
 also have included the output of the terminal command in case that
 helps.
 Thanks again for all of your help.

 - Tyler



 Hi Tyler - In general this means that for some reason the pathway
 doesn't
 move at all from the location where it's initialized when the algorithm
 is
 run. There are a few different reasons why that'd happen, the mask
 being
 only one of them.

 If you could find the dmri_paths command line in trac-all.log, add
 --debug to it and run it again and send the log file, I can try to
 track
 down what's going on. The command line will probably contain all the
 tracts, but you can run it only for one that fails.

 Thanks,
 a.y

 On Wed, 30 Nov 2011, Tyler 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
 when the recon mask was 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 of a
 tract. Is there anything else I should check/change?

 Thanks again,

 -Tyler

 On Nov 30, 2011, at 4:00 PM, Anastasia Yendiki wrote:


 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:

 Hi List,

 I recently ran a group of around 70 subjects through trac-all. I
 have
 started to check the results, and have noticed that Tracula will
 often
 produce a tract with a really small volume and a posterior
 distribution that consists of just 0s and 1000s. When this occurs,
 the
 end point images usually contain only one voxel greater than 0. I am
 not sure what, if anything, is going wrong. The original recons are
 all of good quality, and the registrations to MNI space look good
 (the
 end point images look fine in MNI space as well). I also noticed
 this
 same issue in the right SLFP (bbregister version) of the Tracula
 tutorial subject.

 Is this a fixable error, or is it actually expected behavior? Thanks
 for any help.

 - Tyler



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 whom
 it is
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 the
 e-mail
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 you
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Re: [Freesurfer] persistent bvecs error

2011-11-30 Thread Anastasia Yendiki


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. You can look at the tracula tutorial and see what files each step 
of trac-all outputs and try to copy them over from your other analysis 
with the names that trac-all expects, but that may be more trouble than 
rerunning everything from scratch.

Hope this helps,
a.y

On Wed, 30 Nov 2011, Alexander Lebedev wrote:

 Dear Freesurfer users and developers,

 I decided to run Tracula with our DTI data and eventually got bvecs
 error. I tried different solutions without any results: added decimals
 after zeros, shortened all decimal points to 3, modified my locale -
 nothing helped.
 I'm providing you my trac-all log, original (with shortened and long decimal 
 points: MMADI_C* ) and output bvecs- and bvals-, parameter file and my locale 
 as well.
 [Workstation: CentOS 5.6 x86_64]

 Any advises and suggestions are very welcome...
 Thank you beforehand.
 ---
 Best Regards,
 Alex Lebedev
 Stavanger University Hospital, Norway

 P.S.: And one short question... I was just thinking that it might make sense 
 to perform some of the preprocessing steps in FSL (considering that FS and 
 FSL share these algorithms and the preprocessing for TBSS ran perfectly), but 
 I didn't find any solution on this. Is there such an opportunity?

 ***
 LOCALE:

 LANG=en_US.UTF-8
 LC_CTYPE=en_US
 LC_NUMERIC=en_US
 LC_TIME=en_US
 LC_COLLATE=en_US
 LC_MONETARY=en_US
 LC_MESSAGES=en_US
 LC_PAPER=en_US
 LC_NAME=en_US
 LC_ADDRESS=en_US
 LC_TELEPHONE=en_US
 LC_MEASUREMENT=en_US
 LC_IDENTIFICATION=en_US
 LC_ALL=en_US

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Re: [Freesurfer] Tracula: Small Tracts

2011-11-30 Thread Anastasia Yendiki


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:

 Hi List,

 I recently ran a group of around 70 subjects through trac-all. I have started 
 to check the results, and have noticed that Tracula will often produce a 
 tract with a really small volume and a posterior distribution that consists 
 of just 0s and 1000s. When this occurs, the end point images usually contain 
 only one voxel greater than 0. I am not sure what, if anything, is going 
 wrong. The original recons are all of good quality, and the registrations to 
 MNI space look good (the end point images look fine in MNI space as well). I 
 also noticed this same issue in the right SLFP (bbregister version) of the 
 Tracula tutorial subject.

 Is this a fixable error, or is it actually expected behavior? Thanks for any 
 help.

 - Tyler



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Re: [Freesurfer] trac-all Error: bvecs and bvals don't have the same number of entries

2011-11-28 Thread Anastasia Yendiki


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 line
- your dmrirc file
- your trac-all.log
- the actual bvecs and bvals files that you specify in your dmrirc

Thanks,
a.y

On Mon, 28 Nov 2011, Peter J. Molfese wrote:

 Sorry for the delay in responding, I wanted to try every permutation that I 
 could think of.  I updated the tracula binaries for snow leopard 
 (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019946.html)
  and that gives me some of the same, and some different issues that may help. 
  First, if the bvec file is in the correct format (3 columns), then it copies 
 the file correctly and trac-all continues smoothly.  If the file is in the 3 
 row format (needing to be transposed), then tracula will only copy the first 
 9 numbers out of it giving the error of not having the correct number of 
 bvecs to bvals.  So that seems fixable, I just need to reorient all of our 
 bval and bvec files into the correct format.

 I'm still a bit unsure why tracula won't create the bvec and bval files 
 during the mri_convert stage.  I have been using dcm2nii to create these two 
 files but then continue to give tracula the path to the dicom files.  So the 
 orientation of this file could be related to how dcm2nii writes the files.  
 Any suggestions would be very welcome.  As it stands, my current workflow is:

 1. use dcm2nii to create bvec and bval files
 2. reorient bvec and bval files to be 3 column and 1 column format 
 respectively.
 3. run trac-all -prep with a config file showing where the dicom images are 
 and hand specifying the bvec and bval files

 Peter


 Peter J. Molfese, Ph.D.
 Postdoctoral Associate
 Haskins Laboratories
 300 George Street, Suite 900
 New Haven, CT 06511
 peter.molf...@yale.edu


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Re: [Freesurfer] trac-all Error: bvecs and bvals don't have the same number of entries

2011-11-18 Thread Anastasia Yendiki



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 numbers in bvecs (could be zero in a few cases).


If you suspect that the bvals and bvecs files are not correct, you should 
consult your MR physicist. If you think they're correct but trac-all isn't 
reading them properly, you can attach those 2 files and I can take a look.


a.y

On Fri, 18 Nov 2011, Peter J. Molfese wrote:


Hello,

I'm running trac-all (trac-preproc) on some DTI data and receive the following 
error: 

dtifit -k /Users/pete/Documents/dti/pete/run7/peter/dmri/dwi.nii.gz -m
/Users/pete/Documents/dti/pete/run7/peter/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
 -r
/Users/pete/Documents/dti/pete/run7/peter/dmri/bvecs -b 
/Users/pete/Documents/dti/pete/run7/peter/dmri/bvals -o
/Users/pete/Documents/dti/pete/run7/peter/dmri/dtifit

Error: bvecs and bvals don't have the same number of entries

I found the following 
thread http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19747.html but
 when I attempted to add
export LC_ALL=en_US, the problem persists.  I have looked in the files and 
found that they do indeed have different numbers of
entries.  The scans were performed on a Siemens TimTrio 3T scanner.  

Is there something else I should set?  

Peter J. Molfese, Ph.D.
Postdoctoral Associate
Haskins Laboratories
300 George Street, Suite 900
New Haven, CT 06511
peter.molf...@yale.edu


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Re: [Freesurfer] DTI Group Analysis Study

2011-11-11 Thread Anastasia Yendiki



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 you using tracula? Go through the tracula
   tutorial and read the tracula paper below to understand what tracula
   does:
  http://frontiersin.org/neuroinformatics/10.3389/fninf.2011.00023/abstract

On Fri, 11 Nov 2011, Antonella Kis wrote:


Hi,


I am trying to do a DTI Group Analysis study using a MNI152 standard space
for registration.



1). I wonder in case I want to use MNI 152 and not CVS space using TRACULA
if I have to follow all the steps 

   starting Setting Up a Configuration File to run Tracula and then to 
continue with the following three steps in the TRACULA processing stream
(which is called by the command trac-all):
 *  Pre-processing
 *  FSL's bedpostX
 *  Reconstructing white-matter (WM) pathways
2). Can I check the registration for individual subjects to see if it worked
well or not on the MNI 152 template?


3) How can I  see if there are clusters that survives to multiple comparison
in group 1 (controls) versus group 2 (patients) without and covariant (not
gender, not age).
Can I get a txt file as output for this clusters?



Thank you.
Antonella

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Re: [Freesurfer] Tracula Question, step 2

2011-11-10 Thread Anastasia Yendiki



That should be the latest version, so I'm not sure why the file was not 
saved. I'll have ro refer you to the FSL list for further support with 
running bedpost.


On Thu, 10 Nov 2011, Shannon Buckley wrote:


Hi Anastasia,

I checked the brain mask and it looks good. We 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: Wednesday, November 09, 2011 4:57 PM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: RE: [Freesurfer] Tracula Question, step 2


Hi Shannon - Which version of FSL do you have? Older versions didn't use
to save the mean_dsamples.nii.gz, but that was a while ago.

How quickly it runs depends on the size of the brain mask, so I'd check
that that's ok too.

a.y

On Wed, 9 Nov 2011, Shannon Buckley wrote:


Hi Anastasia,

It turns out that I was NOT able to run the original bedpostx on our 
cluster, so thank you for pointing me in the right direction! In case other 
users experience a similar problem, this is what we did to get the ball rolling 
on our grid:

We found the fsl_sub_seychelles and fsl_sub scripts where the 
default q-names were identified. We modified the files (changing long and short.q to reflect the 
naming convention used here) and ran the original bedpostx. The preproc and datacheck functions 
worked perfectly. The bedpostx function SEEMED to have launched fine, but we hit another snag...

The program finished far too quickly for it to have worked properly (an hour, 
tops), and when I try to run the next -prep step I get the following error, 
which confirms that suspicion:

_+_+_+_+_+_+_+_+_+_+_
Loading BEDPOST parameter samples from 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX
niiRead(): error opening file 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
ERROR: Could not read 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
Linux paris 2.6.18-194.11.1.el5 #1 SMP Tue Aug 10 19:05:06 EDT 2010 x86_64 
x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Wed Nov  9 16:18:53 PST 2011

Word too long.
+_+_+_+_+_+_+_+_+_+_+_


I have to confess I'm not familiar with the word too long error. In any case, 
bedpostx seems to fail to produce the requisite files for -prep (mean_dsamples.nii.gz). Since I'm 
not sure what the inputs would be for creating such a file, I'm including my ls output 
for our dmri.bedpostX path.

_+_+_+_+_+_+_+_+_+_+_+

[vhasfcbuckls@paris dmri.bedpostX]$ ls
bvals dyads2.nii.gz   mean_ph2samples.nii.gz
merged_ph2samples.nii.gz
bvecs error.log   mean_th1samples.nii.gz
merged_th1samples.nii.gz
cancellogsmean_th2samples.nii.gz
merged_th2samples.nii.gz
commands.txt  mean_f1samples.nii.gz   merged_f1samples.nii.gz   monitor
dmri.bedpostX.nii.gz  mean_f2samples.nii.gz   merged_f2samples.nii.gz   
nodif_brain_mask.nii.gz
dyads1.nii.gz mean_ph1samples.nii.gz  merged_ph1samples.nii.gz  xfms
[vhasfcbuckls@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 your help and patience,

~Shannon B.
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Thursday, November 03, 2011 7:39 AM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: Re: [Freesurfer] Tracula Question, step 2


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
runs on our clusters.

In either case, trac-all is meant to always be run from the command line,
whether you're on a personal computer (where is runs jobs serially) or a
cluster (where it submits them as jobs using qsub). But probably some
editing will be needed as I said.

Hope this helps,
a.y

On Wed, 2 Nov 2011, Shannon Buckley wrote:



Hi Anastasia,



I am trying to run Tracula for the first time in our lab and
I’m getting errors during step 2 that seem to involve how the program wants
to be launched via grid. I’ve attached the configuration file I’m using and
the error message is below...





$trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI

Re: [Freesurfer] Tracula Question, step 2

2011-11-09 Thread Anastasia Yendiki



Hi Shannon - Which version of FSL do you have? Older versions didn't use 
to save the mean_dsamples.nii.gz, but that was a while ago.


How quickly it runs depends on the size of the brain mask, so I'd check 
that that's ok too.


a.y

On Wed, 9 Nov 2011, Shannon Buckley wrote:


Hi Anastasia,

It turns out that I was NOT able to run the original bedpostx on our 
cluster, so thank you for pointing me in the right direction! In case other 
users experience a similar problem, this is what we did to get the ball rolling 
on our grid:

We found the fsl_sub_seychelles and fsl_sub scripts where the 
default q-names were identified. We modified the files (changing long and short.q to reflect the 
naming convention used here) and ran the original bedpostx. The preproc and datacheck functions 
worked perfectly. The bedpostx function SEEMED to have launched fine, but we hit another snag...

The program finished far too quickly for it to have worked properly (an hour, 
tops), and when I try to run the next -prep step I get the following error, 
which confirms that suspicion:

_+_+_+_+_+_+_+_+_+_+_
Loading BEDPOST parameter samples from 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX
niiRead(): error opening file 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
ERROR: Could not read 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
Linux paris 2.6.18-194.11.1.el5 #1 SMP Tue Aug 10 19:05:06 EDT 2010 x86_64 
x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Wed Nov  9 16:18:53 PST 2011

Word too long.
+_+_+_+_+_+_+_+_+_+_+_


I have to confess I'm not familiar with the word too long error. In any case, 
bedpostx seems to fail to produce the requisite files for -prep (mean_dsamples.nii.gz). Since I'm 
not sure what the inputs would be for creating such a file, I'm including my ls output 
for our dmri.bedpostX path.

_+_+_+_+_+_+_+_+_+_+_+

[vhasfcbuckls@paris dmri.bedpostX]$ ls
bvals dyads2.nii.gz   mean_ph2samples.nii.gz
merged_ph2samples.nii.gz
bvecs error.log   mean_th1samples.nii.gz
merged_th1samples.nii.gz
cancellogsmean_th2samples.nii.gz
merged_th2samples.nii.gz
commands.txt  mean_f1samples.nii.gz   merged_f1samples.nii.gz   monitor
dmri.bedpostX.nii.gz  mean_f2samples.nii.gz   merged_f2samples.nii.gz   
nodif_brain_mask.nii.gz
dyads1.nii.gz mean_ph1samples.nii.gz  merged_ph1samples.nii.gz  xfms
[vhasfcbuckls@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 your help and patience,

~Shannon B.
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Thursday, November 03, 2011 7:39 AM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: Re: [Freesurfer] Tracula Question, step 2


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
runs on our clusters.

In either case, trac-all is meant to always be run from the command line,
whether you're on a personal computer (where is runs jobs serially) or a
cluster (where it submits them as jobs using qsub). But probably some
editing will be needed as I said.

Hope this helps,
a.y

On Wed, 2 Nov 2011, Shannon Buckley wrote:



Hi Anastasia,



I am trying to run Tracula for the first time in our lab and
I’m getting errors during step 2 that seem to involve how the program wants
to be launched via grid. I’ve attached the configuration file I’m using and
the error message is below...





$trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI/Tracula.sh

Using Freesurfer version 5.1.



  Subjects Directory is /cind/00/PPMI/Freesurfer/Tracula/

  Sessions Directory is /home/vhasfcbuckls/sessions



INFO: SUBJECTS_DIR is /cind/07/PPMI/Freesurfer/subjects

INFO: Diffusion root is /cind/00/PPMI/Freesurfer/Tracula

Actual FREESURFER_HOME /cind/01/apps/freesurfer/64bit/freesurfer5.1

ln 
-sf/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dlabel/diff/anat_brain_
mask.bbr.nii.gz/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/nodif_brain_mask.n
ii.gz

ln -sf /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/dwi.nii.gz
/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/data.nii.gz

WARN: Running FSL's bedbost locally - this might take a while

WARN: It is recommended to run

Re: [Freesurfer] Tracula Question, step 2

2011-11-03 Thread Anastasia Yendiki

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
runs on our clusters.

In either case, trac-all is meant to always be run from the command line,
whether you're on a personal computer (where is runs jobs serially) or a
cluster (where it submits them as jobs using qsub). But probably some
editing will be needed as I said.

Hope this helps,
a.y

On Wed, 2 Nov 2011, Shannon Buckley wrote:

Hi Anastasia,

I am trying to run Tracula for the first time in our lab and
I’m getting errors during step 2 that seem to involve how the program wants
to be launched via grid. I’ve attached the configuration file I’m using and
the error message is below...

$trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI/Tracula.sh

Using Freesurfer version 5.1.

Subjects Directory is /cind/00/PPMI/Freesurfer/Tracula/

Sessions Directory is /home/vhasfcbuckls/sessions

INFO: SUBJECTS_DIR is /cind/07/PPMI/Freesurfer/subjects

INFO: Diffusion root is /cind/00/PPMI/Freesurfer/Tracula

Actual FREESURFER_HOME /cind/01/apps/freesurfer/64bit/freesurfer5.1

ln
-sf/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dlabel/diff/anat_brain_
mask.bbr.nii.gz/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/nodif_brain_mask.n
ii.gz

ln -sf /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/dwi.nii.gz
/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/data.nii.gz

WARN: Running FSL's bedbost locally - this might take a while

WARN: It is recommended to run this step on a cluster

bedpostx_seychelles /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri

subjectdir is /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri

Making bedpostx directory structure

Queuing preprocessing stages

Unable to run job: Job was rejected because job requests unknown queue
short.q.

Exiting.

Queuing parallel processing stage

Unable to run job: Job was rejected because job requests unknown queue
long.q.

Exiting.

Queuing post processing stage

Unable to run job: denied: 60 is not a valid object name (cannot start
with a digit)

Job was rejected because job requests unknown queue long.q.

Exiting.

Although we DO have a grid, I am trying to test the program for feasibility
purposes, just on my own system’s terminal, since we aren’t sure how results
will look with our specific data set (3.0 Tesla Siemens, 64 directional DWI
@ b=1000, with 1 b0 image). We are very interested in performing
tractography in T1-space… I am open to running this over the grid, if that’s
really the best way to do it, but the problem is that I don’t see anywhere
to specify the name of the queue that should be used for launching the
program.

Can you please tell me how to launch this without using the so-called long.q
and short.q? We typically launch jobs to our grid using our “bash.linux.q”,
but I haven’t been able to locate a place in the configuration file, or any
switches to use in the cmd line, to specify that this queue should be used.
I tried specifically launching Tracula’s step 2 onto our bash.linux.q via
the cmd line using “qsub”, but received the same old error I had been
getting. I checked the data independently using “bedpostx_preproc.sh”, and
it appears that all the required data are set up properly. As far as I can
tell, the only issue we have is this inability to use the long.q and
short.q…

What do you think?

I’ve cc’d our IT specialist, Henry Mensch, who oversees our grid system in
case you need someone to chime-in with any specific information about how
our Linux systems are set-up.

Thanks very much for your time,

Shannon T. Buckley
SRA III - Supervisor
CIND, UCSF
4150 Clement St. (114M)
San Francisco, CA 94121
Phone: (415) 221-4810 x4251
Fax: (415) 386-3954

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] TRACULA: how to implement DTI repeat sequence?

2011-10-28 Thread Anastasia Yendiki



Hi Ansgar - If the 2 series are in register with each other, you can just 
concatenate them with mri_concat. You'd also have to concatenate the 
respective bvals and bvecs in the same order.


For average FA, look in the pathstats.overall.txt file of each 
reconstructed pathway. For more on this see the tutorial:


https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics

Hope this helps,
a.y

On Fri, 28 Oct 2011, Ansgar Furst wrote:


Dear Anastasia,
Re-running bedpostX just did it and I didn't encounter the problem on any 
subjects after that.
Everything is running great now. I just had 2 more follow-up questions:
what's the best way to concatenate the 2 repeat DICOM DWI series into 1 NIFTI 
file (you mentioned that
below)?
How do I extract average FA values constrained by the extracted fiber tracts?
Thanks so much for all your help,
Ansgar

On Wed, Sep 28, 2011 at 5:07 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu 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 in the dmri.bedpostX directory. See 
for list of
  bedpost output files:
         http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html

  a.y


On Wed, 28 Sep 2011, Ansgar Furst wrote:

  Hi Anastasia,
  Thanks so much for your message. You were right about the recon 
directory, the
  contents had been accidentally moved elsewhere (sorry!) and once I moved 
them
  back and reran the script everything worked like a charm without any 
errors.
  However, it looks like I'm now stuck at the next processing stage (fsl's
  bedpostX). I pasted the output with the error message below. FYI: I'm
  unfortunately forced to run the bedpostX on a single Linux box (64-bit 
dual core
  with 8GB of RAM) which I hope is OK?
  Thanks so much for all your help,

  Ansgar

  ==
  trac-all -bedp -c scripts/dmrirc_single_subject_1only
  INFO: SUBJECTS_DIR is /home/ajfurst/Data/WRIISC
  INFO: Diffusion root is /home/ajfurst/Data/WRIISC/TRACULA
  Actual FREESURFER_HOME /usr/local/freesurfer
  ln -sf
  
/home/ajfurst/Data/WRIISC/TRACULA/015/dlabel/diff/anat_brain_mask.bbr.nii.gz
  /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/nodif_brain_mask.nii.gz
  ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/dwi.nii.gz
  /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/data.nii.gz
  WARN: Running FSL's bedbost locally - this might take a while
  WARN: It is recommended to run this step on a cluster
  bedpostx_seychelles /home/ajfurst/Data/WRIISC/TRACULA/015/dmri
  subjectdir is /home/ajfurst/Data/WRIISC/TRACULA/015/dmri
  Making bedpostx directory structure
  Queuing preprocessing stages
  Queuing parallel processing stage
  0 slices processed
  5 slices processed
  6 slices processed
  7 slices processed
  8 slices processed
  9 slices processed
  9 slices processed
  10 slices processed
  11 slices processed
  11 slices processed
  12 slices processed
  12 slices processed
  13 slices processed
  14 slices processed
  14 slices processed
  14 slices processed
  15 slices processed
  15 slices processed
  16 slices processed
  16 slices processed
  16 slices processed
  17 slices processed
  17 slices processed
  17 slices processed
  18 slices processed
  18 slices processed
  18 slices processed
  18 slices processed
  19 slices processed
  19 slices processed
  19 slices processed
  19 slices processed
  20 slices processed
  20 slices processed
  20 slices processed
  20 slices processed
  21 slices processed
  21 slices processed
  21 slices processed
  21 slices processed
  21 slices processed
  22 slices processed
  22 slices processed
  22 slices processed
  22 slices processed
  23 slices processed
  23 slices processed
  23 slices processed
  23 slices processed
  23 slices processed
  24 slices processed
  24 slices processed
  24 slices processed
  24 slices processed
  24 slices processed
  24 slices processed
  25 slices processed
  25 slices processed
  25 slices processed
  25 slices processed
  25 slices processed
  26 slices processed
  26 slices processed
  26 slices processed
  26 slices processed
  26 slices processed
  26 slices processed
  27 slices processed
  27 slices processed
  27 slices processed
  27 slices processed
  27 slices processed
  28 slices processed
  28 slices processed
  28 slices processed
  28 slices processed
  28 slices processed
  28 slices processed

Re: [Freesurfer] trac-all results

2011-10-19 Thread Anastasia Yendiki



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, Ping-Hong Yeh wrote:


Hi Anastasia,

I got fixed of the aparc+aseg (see aparc+aseg.png) in one of
problematic data and re-ran the trac-all following your suggestions.
However, the segmented forceps major using FLIRT still not getting
good result (see flt.png) though BBR one is OK (see bbr.png).
Similarly the segmented L CST using BBR looks 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
ayend...@nmr.mgh.harvard.edu wrote:


Hi Ping-Hong,

Yes, you can set usemaskanat = 0 in your dmrirc, and then the brain mask
will be extracted from the DWI data by the bet tool, instead of using the
aparc+aseg.

But, and this is a big but, TRACULA uses the aparc+aseg to constrain the
tractography solutions, i.e. the aparc+aseg is where the UnderLying Anatomy
in TRACULA comes from. So the quality of the trac-all results depend on the
quality of the aparc+aseg regardless of where your mask came from.

a.y

On Fri, 14 Oct 2011, Ping-Hong Yeh wrote:


Hi Anastasia,

Can trac-all just use the mask in diffusion native space (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
ayend...@nmr.mgh.harvard.edu wrote:


I'll have to refer you back to the freesurfer list for that one. There
are
people with much more expertise than me on troubleshooting the recon-all
stream.

Once you get your recons fixed, you'll have to rerun all trac-all steps
except 1.1 (image corrections).

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


The original aparc+aseg are not good, at least for these two cases. So
which parameters in recon-all should be tweaked?

On Tue, Oct 11, 2011 at 5:38 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:


Is the original aparc+aseg from the freesurfer recon not good either
(from
mri/aparc+aseg.mgz)? Or is it messed up only after registration into
diffusion space (dlabel/diff/aparc+aseg.flt.nii.gz,
dlabel/diff/aparc+aseg.bbr.nii.gz)? This will determine if the
freesurfer
recon needs to be fixed or if the registration needs to fixed.

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


yeap, the aparc+aseg_masks are not good.
Any way to fix this? Thanks.

On Tue, Oct 11, 2011 at 5:00 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:


I see, the mask may be the answer to the initialization failures! It
seems
like the fmajor you sent me also has its endings masked out? That'd
cause
it
to fail. I wish I'd thought of this earlier!

With usemaskanat = 1, the mask that's used is a slightly dilated
version
of
the aparc+aseg from the FS recon, mapped to diffusion space. So if
the
aparc+aseg has those parts missing, or if the diffusion-anatomical
registration is not good, parts will be masked out that shouldn't.
The
anatomical mask can be found in dlabel/diff/aparc+aseg_mask* (if
you've
run
both flirt and bbregister registrations, there'll be 2 of them). Does
this
mask look like something went wrong?

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


I used the default, i.e. set usemaskanat =1, but it looks that
tracts
were not reconstructed at the place where it was masked out (see the
cross-bar at L_unc.png).

I still have no luck in fixing the initialization issue (see
fmajor.png for example).

Thanks.


On Tue, Oct 11, 2011 at 3:19 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:


Hi Ping - If you're using the anatomical brain as a mask (set
usemaskanat
=
1, which is the default), then the diffusion-based mask won't have
an
effect
on your outputs.

BTW, have you had any luck with your initialization issues? Sorry I
haven't
had another chance to look at your data since we last emailed, I
got
bogged
down with some other stuff.

a.y

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


Hi Anastasia,

I'd like to lower the bet threshold value by set thrbet = 0.01
for
skull-stripping because some of the brains have been cut, but it
does
not seem to  make any changes (see attached).

Any suggestion? Thank you,

Ping

On Fri, Sep 30, 2011 at 12:09 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:


Yes! Please add the set reinit = 1 to the file that you pass
with
-c.

On Fri, 30 Sep 2011, Ping-Hong Yeh wrote:


so I should pass with the -c argument instead?

On Fri, Sep 30, 2011 at 12:04 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:


That file gets overwritten by whatever is in the file that you
pass
with
the
-c argument to trac-all. Sorry for the confusion.

On Fri, 30 Sep 2011, Ping-Hong Yeh wrote:


I edited the file under scripts/dmrirc.local

Re: [Freesurfer] trac-all results

2011-10-19 Thread Anastasia Yendiki



Glad things are moving in the right direction. Now it looks like maybe one 
of the control points of the path is not moving around, which is why you 
get that very bright thin spot in the distribution. I can't tell by 
looking at that one slice of the mask only, but could it be that there 
voxels missing from the mask around there? If so you could fill them in 
and try again. You can also overlay the path.pd on the FA map and check if 
that part is off the white matter or on its edge.


On Wed, 19 Oct 2011, Ping-Hong Yeh wrote:


The mask sort of covers the whole brain (see attached). It may be due
to the display thresholding, when I viewed the path.pd.nii.gz using
fslview, the tract actually has been recovered as compared to the
previous one (old_path.png).

However, the path.pd still does seem normal, i.e. with quite a few
extraordinary high intensity (probability, yellow)?

Thanks.

ping

On Wed, Oct 19, 2011 at 2:52 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu 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, Ping-Hong Yeh wrote:


Hi Anastasia,

I got fixed of the aparc+aseg (see aparc+aseg.png) in one of
problematic data and re-ran the trac-all following your suggestions.
However, the segmented forceps major using FLIRT still not getting
good result (see flt.png) though BBR one is OK (see bbr.png).
Similarly the segmented L CST using BBR looks 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
ayend...@nmr.mgh.harvard.edu wrote:


Hi Ping-Hong,

Yes, you can set usemaskanat = 0 in your dmrirc, and then the brain mask
will be extracted from the DWI data by the bet tool, instead of using the
aparc+aseg.

But, and this is a big but, TRACULA uses the aparc+aseg to constrain the
tractography solutions, i.e. the aparc+aseg is where the UnderLying
Anatomy
in TRACULA comes from. So the quality of the trac-all results depend on
the
quality of the aparc+aseg regardless of where your mask came from.

a.y

On Fri, 14 Oct 2011, Ping-Hong Yeh wrote:


Hi Anastasia,

Can trac-all just use the mask in diffusion native space (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
ayend...@nmr.mgh.harvard.edu wrote:


I'll have to refer you back to the freesurfer list for that one. There
are
people with much more expertise than me on troubleshooting the
recon-all
stream.

Once you get your recons fixed, you'll have to rerun all trac-all steps
except 1.1 (image corrections).

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


The original aparc+aseg are not good, at least for these two cases. So
which parameters in recon-all should be tweaked?

On Tue, Oct 11, 2011 at 5:38 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:


Is the original aparc+aseg from the freesurfer recon not good either
(from
mri/aparc+aseg.mgz)? Or is it messed up only after registration into
diffusion space (dlabel/diff/aparc+aseg.flt.nii.gz,
dlabel/diff/aparc+aseg.bbr.nii.gz)? This will determine if the
freesurfer
recon needs to be fixed or if the registration needs to fixed.

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


yeap, the aparc+aseg_masks are not good.
Any way to fix this? Thanks.

On Tue, Oct 11, 2011 at 5:00 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:


I see, the mask may be the answer to the initialization failures!
It
seems
like the fmajor you sent me also has its endings masked out? That'd
cause
it
to fail. I wish I'd thought of this earlier!

With usemaskanat = 1, the mask that's used is a slightly dilated
version
of
the aparc+aseg from the FS recon, mapped to diffusion space. So if
the
aparc+aseg has those parts missing, or if the diffusion-anatomical
registration is not good, parts will be masked out that shouldn't.
The
anatomical mask can be found in dlabel/diff/aparc+aseg_mask* (if
you've
run
both flirt and bbregister registrations, there'll be 2 of them).
Does
this
mask look like something went wrong?

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


I used the default, i.e. set usemaskanat =1, but it looks that
tracts
were not reconstructed at the place where it was masked out (see
the
cross-bar at L_unc.png).

I still have no luck in fixing the initialization issue (see
fmajor.png for example).

Thanks.


On Tue, Oct 11, 2011 at 3:19 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:


Hi Ping - If you're using the anatomical brain as a mask (set
usemaskanat
=
1, which is the default), then the diffusion-based mask won't
have
an
effect
on your outputs.

BTW, have you had any luck

[Freesurfer] open-access article on TRACULA now available

2011-10-17 Thread Anastasia Yendiki


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
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] trac-all results

2011-10-14 Thread Anastasia Yendiki



Hi Ping-Hong,

Yes, you can set usemaskanat = 0 in your dmrirc, and then the brain mask 
will be extracted from the DWI data by the bet tool, instead of using the 
aparc+aseg.


But, and this is a big but, TRACULA uses the aparc+aseg to constrain the 
tractography solutions, i.e. the aparc+aseg is where the UnderLying 
Anatomy in TRACULA comes from. So the quality of the trac-all results 
depend on the quality of the aparc+aseg regardless of where your mask 
came from.


a.y

On Fri, 14 Oct 2011, Ping-Hong Yeh wrote:


Hi Anastasia,

Can trac-all just use the mask in diffusion native space (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
ayend...@nmr.mgh.harvard.edu wrote:


I'll have to refer you back to the freesurfer list for that one. There are
people with much more expertise than me on troubleshooting the recon-all
stream.

Once you get your recons fixed, you'll have to rerun all trac-all steps
except 1.1 (image corrections).

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


The original aparc+aseg are not good, at least for these two cases. So
which parameters in recon-all should be tweaked?

On Tue, Oct 11, 2011 at 5:38 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:


Is the original aparc+aseg from the freesurfer recon not good either
(from
mri/aparc+aseg.mgz)? Or is it messed up only after registration into
diffusion space (dlabel/diff/aparc+aseg.flt.nii.gz,
dlabel/diff/aparc+aseg.bbr.nii.gz)? This will determine if the freesurfer
recon needs to be fixed or if the registration needs to fixed.

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


yeap, the aparc+aseg_masks are not good.
Any way to fix this? Thanks.

On Tue, Oct 11, 2011 at 5:00 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:


I see, the mask may be the answer to the initialization failures! It
seems
like the fmajor you sent me also has its endings masked out? That'd
cause
it
to fail. I wish I'd thought of this earlier!

With usemaskanat = 1, the mask that's used is a slightly dilated
version
of
the aparc+aseg from the FS recon, mapped to diffusion space. So if the
aparc+aseg has those parts missing, or if the diffusion-anatomical
registration is not good, parts will be masked out that shouldn't. The
anatomical mask can be found in dlabel/diff/aparc+aseg_mask* (if you've
run
both flirt and bbregister registrations, there'll be 2 of them). Does
this
mask look like something went wrong?

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


I used the default, i.e. set usemaskanat =1, but it looks that tracts
were not reconstructed at the place where it was masked out (see the
cross-bar at L_unc.png).

I still have no luck in fixing the initialization issue (see
fmajor.png for example).

Thanks.


On Tue, Oct 11, 2011 at 3:19 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:


Hi Ping - If you're using the anatomical brain as a mask (set
usemaskanat
=
1, which is the default), then the diffusion-based mask won't have an
effect
on your outputs.

BTW, have you had any luck with your initialization issues? Sorry I
haven't
had another chance to look at your data since we last emailed, I got
bogged
down with some other stuff.

a.y

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


Hi Anastasia,

I'd like to lower the bet threshold value by set thrbet = 0.01 for
skull-stripping because some of the brains have been cut, but it
does
not seem to  make any changes (see attached).

Any suggestion? Thank you,

Ping

On Fri, Sep 30, 2011 at 12:09 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:


Yes! Please add the set reinit = 1 to the file that you pass with
-c.

On Fri, 30 Sep 2011, Ping-Hong Yeh wrote:


so I should pass with the -c argument instead?

On Fri, Sep 30, 2011 at 12:04 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:


That file gets overwritten by whatever is in the file that you
pass
with
the
-c argument to trac-all. Sorry for the confusion.

On Fri, 30 Sep 2011, Ping-Hong Yeh wrote:


I edited the file under scripts/dmrirc.local

On Fri, Sep 30, 2011 at 12:00 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:


Hi Ping - Thanks for trying that. When you say in the
dmrirc.local,
do
you
mean that you edit the file under scripts/dmrirc.local, or the
file
that
you
pass to trac-all as -c dmrirc?

a.y

On Fri, 30 Sep 2011, Ping-Hong Yeh wrote:


Hi Anastasia,

I've rerun NCNC0047, the one I sent you, and another one,  but
it
does
not help fixing the tracts.

I redone trac-all -prior with set reinit =1 in the
dmrirc.local
file
and then trac-all -path

Any further suggestions? Thanks.

ping

On Thu, Sep 29, 2011 at 5:58 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:


I wonder if the problem is with the replacement executables
for
snow
leopard. They should not have a time stamp of April 14th, I
don't
know
how
that could've

Re: [Freesurfer] coregistration - FA to Freesurfer

2011-10-13 Thread Anastasia Yendiki


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 and
 was wondering if someone could help me out.
 
 These are the steps that i carried out:
 
 mri_convert subj_01/mri/brain.mgz brain.nii.gz
 
 fslswapdim brain.nii.gz x z -y brain_swap.nii.gz
 
 flirt -ref brain_swap.nii.gz -in nodif_brain.nii.gz -out XXX.nii.gz -omat 
 XXX.mat -cost corratio -dof 6
 -interp trilinear
 
 flirt -in myFA.nii.gz -ref XXX.nii.gz -out myFA_coregistered.nii.gz -applyxfm 
 -init XXX.mat
 
 
 Unfortunately myFA_coregistered.nii.gz was not as good as i expected since I 
 want to extract the mean FA
 values of a subcortical ROI from freesurfer and to do that you need quite 
 good coregistration.
 
 Does anyone know a better way to do this?
 
 Many thanks,
 
 Joana
 

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula Memory Requirements

2011-10-11 Thread Anastasia Yendiki


Hi Ammar - You mentioned that you were able to run things fine on another 
computer with 16 Gb of RAM. How much memory was being utilized on that 
computer by these processes (dmri_train and dmri_paths)?

a.y

On Tue, 11 Oct 2011, Moiyadi, Ammar wrote:

 Hi - After upgrading my total RAM to 12 gb (from 6) I am continuing to run 
 into memory allocation problems running  tracula preproc and paths with the 
 error messages as follows:

 
 1. preproc error

 Loading cortex mask from 
 /usr/local/freesurfer5.1/trctrain/trc010/dlabel/mni/cortex+2mm.nii.gz
 MRIalloc(218, 182, 182): could not allocate 872 bytes for 112th slice

 Cannot allocate memory
 Linux coolguy 2.6.38-10-generic-pae #46~lucid1-Ubuntu SMP Wed Jul 6 20:34:59 
 UTC 2011 i686 GNU/Linux

 trac-preproc exited with ERRORS at Fri Oct  7 12:33:56 MDT 2011

 2. paths error

 Loading BEDPOST parameter samples from 
 /usr/local/freesurfer5.1/subjects/1052/dmri.bedpostX
 MRIalloc(256, 256, 50): could not allocate 262144 bytes for 431th slice

 Cannot allocate memory
 Linux coolguy 2.6.38-10-generic-pae #46~lucid1-Ubuntu SMP Wed Jul 6 20:34:59 
 UTC 2011 i686 GNU/Linux

 trac-paths exited with ERRORS at Tue Oct 11 12:54:59 MDT 2011

 ***

 Has anyone else had these memory errors with their machines? I am running on 
 a linux box ubuntu 10.04. When the code exits, the script is only utilizing 
 about 20 percent of the memory so I am certain that the problem lies within 
 my machine reading the code or within the code itself. Thank you in advance 
 for any suggestions in solving this problem.

 Ammar Moiyadi, BS
 Professional 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: RE: [Freesurfer] Tracula Memory Requirements

 Hi - The voxel dimensions are 1.0156 x 1.0156 x 2.6 mm in the merged_f1 
 bedpost output and the total number of voxels in the nodif_brain_mask is 
 3,276,800.

 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 Ammar - Can you check the voxel dimensions of one of the merged_* files
 in the bedpost directory, and also how many voxels are included in the
 mask that was used for bedpost? It seems to be failing when loading the
 bedpost outputs, which is before it reads any tracula-specific inputs.

 a.y

 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.mgh.harvard.edu]
 Sent: Friday, September 23, 2011 10:30 AM
 To: Moiyadi, Ammar
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Tracula Memory Requirements

 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 was able to
 run these steps on a computer with 16 gb, I want to know, what is the
 minimum memory requirement for running tracula?  Is the memory
 allocation error resulting from a lack of memory or is there something
 else going on that I am not aware of?

 Error:

 Loading BEDPOST parameter samples from
 /usr/local/freesurfer5.1/subjects/1052/dmri.bedpostX MRIalloc(256, 256,
 50): could not allocate 262144 bytes for 431th slice

 Thanks always,

 Ammar Moiyadi, BS
 Professional Research Assistant
 Department of Psychiatry
 University of Colorado Anschutz Medical Campus
 303-724-5490
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 The information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.







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Re: [Freesurfer] tracula -bedp - path

2011-10-07 Thread Anastasia Yendiki



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 any case you don't need to run 
bedpostx_single_slice.sh.


2. The error seems to occur either when it's reading the bvecs file, or 
right after that when it's accessing the bedpostx outputs. So I'd try to 
look those for that subject and see if everything is ok.


Hope this helps,
a.y

On Fri, 7 Oct 2011, Judit Haasz wrote:



Hi,

I ran into 2 problems related to tracula.

1. trac-all -bedp command exits with following message.

 WARN: Running FSL's bedbost locally - this might take a while
  WARN: It is recommended to run this step on a cluster
  bedpostx_seychelles /usr/local/freesurfer/subjects/C001/dmri
  subjectdir is /usr/local/freesurfer/subjects/C001/dmri
  Making bedpostx directory structure
  Queuing preprocessing stages
  [: 223: NONE: unexpected operator
  [: 314: NONE: unexpected operator
  [: 327: xbedpostx_pre: unexpected operator
  [: 486: x: unexpected operator
  [: 486: -le: argument expected
  Queuing parallel processing stage
  [: 223: NONE: unexpected operator
  [: 327: xbedpostx: unexpected operator
  [: 486: x53: unexpected operator
  0 slices processed
  Queuing post processing stage
  [: 223: NONE: unexpected operator
  [: 314: NONE: unexpected operator
  [: 327: xbedpostx_post: unexpected operator
  [: 486: x: unexpected operator
  [: 486: -le: argument expected
 

This problem has been posted in May and June. bedpostx from command line
runs perfectly and that is how I have been running it so far. One of u
suggested to try the following:

/usr/local/fsl/bin/bedpostx_single_slice.sh/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri
2 1 1000 1250 25 1 0

then I got:

** ERROR (nifti_image_read): failed to find header file 
for'/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmr
i/data_slice_'
** 
ERROR:nifti_image_open(/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2
005/subj_523/dmri/data_slice_): bad header info
ERROR: failed to open 
file/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri
/data_slice_
ERROR: Could not open 
image/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri
/data_slice_
Image Exception : #22 :: Failed to read 
volume/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri
/data_slice_

An exception has been thrown
Failed to read 
volume/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri
/data_slice_Trace: read_volume4DROI.

Done

Can u suggest a reason behind all this? This happens on Linux machine
(2.6.35-28-generic #50-Ubuntu 10.10, x86_64, Java VM Version: Java
1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM
mixed mode).
On Mac OS X (version 10.7.1 - Lion, 2 x 2.66 GHz 6-core Intel Xeon
processors, 32 GB 1333 MHz DDR3 RAM) trac-all -bedp runs well.

My other question is:
trac-all -path exists with error (in case of a single subject):

Loading DWIs 
from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri
/dwi.nii.gz
Loading mask 
from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dlab
el/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter samples 
from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri
.bedpostX
Loading segmentation map 
from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dlab
el/mni/aparc+aseg.nii.gz
Loading b-values 
from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri
/bvals
Loading gradients 
from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri
/bvecs
Segmentation fault 
Linux Odd 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011
x86_64 GNU/Linux

trac-paths exited with ERRORS at Fri Oct  7 10:21:20 CEST 2011

thanks for help.
Judit




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Re: [Freesurfer] Table for aparc+aseg

2011-10-07 Thread Anastasia Yendiki


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 thalamus...) when I see it on FSL viewer.

 Where can I find the table that shows the relationship between the intensity
 and the name of brain region? I want to extract the specific brain regions
 (e.g. parahippocampal gyrus, fusiform gyrus...) from the result of
 aparc+aseg, and use them for the seed mask or the termination mask in
 structural connectivity analysis (tractography).

 I appreciate your help.

 Thank you,
 Shige



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Re: [Freesurfer] Trac-all dyld load error mac os 10.5 darwin

2011-10-02 Thread Anastasia Yendiki


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
 I am getting the following error when @ Priors
 
 Trace/BPT trap
 dyld: unknown required load command 0x8022
 
 
 This error is shown right at the start of the trac-all too, but the script 
 exits when priors are being
 drawn.
 
 Can you help please? I downloaded the most stable version last week. (could 
 it still be the library
 dependency eror?)
 
 Cheers
 Lena
 
 ___
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 Clinical Lecturer  Wellcome Training Fellow | Division of Psychiatry ( 
 University of Nottingham)
 South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
 Ph: 0115 82 30407
 
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Re: [Freesurfer] tracula bvecs bvals error

2011-09-30 Thread Anastasia Yendiki


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_P01/dmri/dwi.nii.gz -m
 /home/joana/FIU/H_P01/dlabel/diff/aparc+aseg_mask.flt.nii.gz -r
 /home/joana/FIU/H_P01/dmri/bvecs -b /home/joana/FIU/H_P01/dmri/bvals -o
 /home/joana/FIU/H_P01/dmri/dtifit
 Error: bvecs and bvals don't have the same number of entries
 Linux ub029113 2.6.18-164.11.1.el5 #1 SMP Wed Jan 6 13:26:04 EST 2010 x86_64
 x86_64 x86_64 GNU/Linux
 
 trac-preproc exited with ERRORS
 
 Although i saw a previous email reporting the same problem i wasn't able to
 solve it following that email's instructions...
 
 I think there is something wrong with my bvec file since dmri/bvecs.txt only
 contains zeros.
 
 I've tried changing bvec.txt columns to three decimals and then to 1, -1 and 0
 but nothing seems to work.
 
 I've attached my bvals and bvecs files.
 
 Does anyone have any idea why this is happening?
 
 Many thanks to you all!
 
 Joana
 

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Re: [Freesurfer] trac-all results

2011-09-28 Thread Anastasia Yendiki


Hi Ping - You can upload your data if you want me to take a look at it.

1. The initial points ideally should be along the midline of the pathway, 
starting from one end region of the pathway and going all the way to the 
other end region. (The default number is 5 control points but you can set 
ncpts = ... in your dmrirc to change that.)

2. You can look in $FREESURFER_HOME/bin/dmrirc.example for how to specify 
the field map inputs. They don't need to have the same matrix size and 
resolution as the DWIs.

3a. If it's the initialization that's failed, the output will just be the 
initial path and nothing else (which is I think what you mean by fewer 
voxels).

3b. The diffusion model used here is the same as the ball-and-stick model 
that FSL uses. If the threshold you're referring to is the minimum volume 
fraction for the anisotropic compartments of that model, you can set fmin 
= ... in your dmrirc to choose one.

I hope this helps a bit!
a.y

On Wed, 28 Sep 2011, Ping-Hong Yeh wrote:

 Hi Anastasia,

 I've tried both options, the choice 1 fixed some of the cases, but
 not all; and the choice 2 did not work at all. Maybe I've missed
 something here.

 Few more questions:

 1. Will the initial points have to include the points around start,
 way, and end points of the tracts need to be segmented? Can I just
 enter the points in the main stem of tracts?

 2. Will EPI distortion correction, like using field map, in the
 preprocessing steps help co-registration and thus improving the
 labeling? So far more than 80% (4 out of 5 data sets) of the data
 have at least one suboptimal tract, either in flt or bbr. (BTW, which
 flag will call B0 fieldmaps (or phase and magnitude images) for
 distortion correction? Do the fieldmap images need to be in the same
 matrix size and resolution as DWI? )

 3.  I wonder why these suboptimal segmented tracts are not terribly
 off the white matter paths but just fewer voxels? 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
 ayend...@nmr.mgh.harvard.edu wrote:

 Hi Ping - There are 2 possibilities:

 1. You can try to fiddle with the initialization points yourself to make
 sure they're well in the CST. The point coordinates are saved in a text file
 - look at the --init argument of the dmri_paths command line, which you can
 find in trac-all.log.

 2. You can let trac-all select a different initialization by adding set
 reinit = 1 to your dmrirc file, then running trac-all -prior again.

 Once you change the initialization by doing either 1. or 2. above, you need
 to run trac-all -path to reconstruct this path again.

 You can change the pathlist in dmrirc to do only the path that failed.

 We jump through various hoops to make sure this sort of thing doesn't happen
 but in a few cases it can't be prevented, unfortunately.

 Let me know if this has helped or if you have any other questions!
 a.y

 On Thu, 22 Sep 2011, Ping-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, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

 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
 going off the white matter for example. Does the blue line in your
 snapshot
 look like it may not coincide well with you subject's CST, going off the
 white matter close to the end, etc?

 a.y

 On Thu, 22 Sep 2011, Ping-Hong Yeh wrote:

 Hello,

 The segmented left CST tracts of one of our 3T data was not
 satisfactory, which has only few voxels with 1000 gray values (see
 attached snapshot pictures for trac-all and cst_prob). The
 manually tracking using deterministic tractography seems OK (see
 cst_stremline). Any suggestions on which step may go wrong in
 trac-all?

 Thank you,

 Ping



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Re: [Freesurfer] TRACULA: how to implement DTI repeat sequence?

2011-09-28 Thread Anastasia Yendiki

 processed
 43 slices processed
 43 slices processed
 43 slices processed
 43 slices processed
 44 slices processed
 44 slices processed
 44 slices processed
 44 slices processed
 45 slices processed
 45 slices processed
 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 processed
 49 slices processed
 50 slices processed
 50 slices processed
 51 slices processed
 51 slices processed
 52 slices processed
 53 slices processed
 Queuing post processing stage
 58 slices processed
 For some reason the bedpostX process DOES NOT appear
 to have successfully completed. Please examine your
 results carefully.
 /usr/local/freesurfer/bin/bedpostx_seychelles: line 281: kill: (12792) - No 
 such
 process
 ===
 
 On Thu, Sep 22, 2011 at 5:17 AM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

   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 looks like maybe the freesurfer recon wasn't
   found, so it skipped some steps (diffusion-to-anatomical
   registration and mask creation). Does the freesurfer recon dir
   /home/ajfurst/Data/WRIISC/014/ exist?

   a.y
 
 
 

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Re: [Freesurfer] Tracula references

2011-09-26 Thread Anastasia Yendiki



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 underlying anatomy, Frontiers in 
Neuroinformatics, In press, 2011.


We'll send a note to the list as soon as it becomes available, which 
should be very soon.


a.y

On Sat, 24 Sep 2011, Shanqing Cai wrote:


Hi,

I am using Tracula in my diffusion data analysis and am interested in finding
out what would be the best citations or references for this tool. A quick
Internet search brings me to two conference papers, one in ISMRM and one in an
IEEE conference. Are there any journal articles that have been published on
Tracula? I need the information for better understanding of the tool and
possible citations in future publications.

Thank you.

Best regards,
Shanqing Cai
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Re: [Freesurfer] tracula - if expression syntax


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 running tracula on a Linux machine, without a problem. Now I am
 trying to run tracula on a Mac-Pro machine (running Mac OS X version 10.7.1
 - Lion). I followed the tutorial and set up the requested structure and
 configuration file.
 When I try running the preprocessing step (trac-all -prep -c
 ./scripts/dmrirc, both in bash and tcsh) I get the following message:
 If: expression syntax.
 
 Do u have some suggestions that i could try to overcome the problem?
 thanks,
 Judit
 
 
 

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Re: [Freesurfer] Tracula Memory Requirements


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 was able to 
 run these steps on a computer with 16 gb, I want to know, what is the 
 minimum memory requirement for running tracula?  Is the memory 
 allocation error resulting from a lack of memory or is there something 
 else going on that I am not aware of?

 Error:

 Loading BEDPOST parameter samples from 
 /usr/local/freesurfer5.1/subjects/1052/dmri.bedpostX MRIalloc(256, 256, 
 50): could not allocate 262144 bytes for 431th slice

 Thanks always,

 Ammar Moiyadi, BS
 Professional Research Assistant
 Department of Psychiatry
 University of Colorado Anschutz Medical Campus
 303-724-5490
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Re: [Freesurfer] defining our own regions for tractography


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 this list.

Hope this helps,
a.y

On Fri, 23 Sep 2011, Ritobrato Datta wrote:

 Hello All,

 I am a total newbee in dt-recon and tracula. So sorry if this is a very basic 
 question.

 From what I gathered so far-

 TRACULA uses the aparc+aseg.mgz from the FreeSurfer recon (T1-weighted 
 volume) as ROIs to construct the tracts and also constructs a few tracts by 
 default.

 Is there a way of defining our own ROIs and get tracts ?

 Thanks

 Ri


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Re: [Freesurfer] Tracula Memory Requirements


Hi Ammar - Can you check the voxel dimensions of one of the merged_* files 
in the bedpost directory, and also how many voxels are included in the 
mask that was used for bedpost? It seems to be failing when loading the 
bedpost outputs, which is before it reads any tracula-specific inputs.

a.y

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.mgh.harvard.edu]
 Sent: Friday, September 23, 2011 10:30 AM
 To: Moiyadi, Ammar
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Tracula Memory Requirements

 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 was able to
 run these steps on a computer with 16 gb, I want to know, what is the
 minimum memory requirement for running tracula?  Is the memory
 allocation error resulting from a lack of memory or is there something
 else going on that I am not aware of?

 Error:

 Loading BEDPOST parameter samples from
 /usr/local/freesurfer5.1/subjects/1052/dmri.bedpostX MRIalloc(256, 256,
 50): could not allocate 262144 bytes for 431th slice

 Thanks always,

 Ammar Moiyadi, BS
 Professional Research Assistant
 Department of Psychiatry
 University of Colorado Anschutz Medical Campus
 303-724-5490
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 at
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 properly
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Re: [Freesurfer] Tracula Memory Requirements