Re: [Freesurfer] Trakula

2015-08-26 Thread Anastasia Yendiki


Hi Bahram - The gradient table is a text file with 3 columns. You need to 
multiply the 3rd column by -1. You can do this in matlab, awk, perl, or 
any scripting language that handles text files.


Best,
a.y

On Wed, 26 Aug 2015, B M wrote:


Hi Anastasia,
Thank you very much for your help and recommendations. I will try to fix
These Problems. I would like to ask you one more question. Is there any
command which could help me to invert the gradient vectors for my DWI
scan in the z direction?
Best
Bahram 

2015-08-24 17:57 GMT+02:00 Anastasia Yendiki :

  Hi Bahram - I looked at your subject's files. First, the
  freesurfer recon failed in the right hemisphere, probably
  because of a visible artifact on your T1 (see aseg screenshot).
  This affects the aparc+aseg, so you can't run tracula before you
  fix it.

  Second, the gradient vectors for your DWI scan probably need to
  be inverted in the z direction (see other screenshot with the
  principal eigenvectors of the tensors shown over the FA map).
  The vectors are oriented correctly in the axial view, but not in
  the sagittal or coronal view (see for example their orientation
  in the cingulum bundle in saggital view, where the cross-hair is
  centered, or in the corticospinal tract in coronal view). This
  is not causing your error, but you have to fix it for the
  tractography to work properly.

  Third, your DWI data has very anisotropic resolution (1.8 x 1.8
  x 6.5 mm). Your voxels are almost 4 times as big in z than in
  x/y. This is not causing your error, but it is not optimal for
  diffusion analysis. Anisotropic voxels can bias estimates of
  diffusion anisotropy. Also, you only have 12 directions with
  b=1000 and the other directions were acquired with a much lower
  b-value (b=200). It's unlikely that you'll get reliable fits of
  crossing-fiber models like the one used by tracula on this data.
  Again, this is not causing the error you're seeing but it will
  make it difficult to get usable results from this DWI data.

  Best,
  a.y

  On Thu, 20 Aug 2015, B M wrote:

Hi Anastasia,
please find the files in attachment.
Best regards

Bahram

2015-08-19 21:55 GMT+02:00 Anastasia Yendiki
:

      Hi Bahram - There are some errors in there
related to registration files. Can you please send
these files?

     

bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat
     
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat

      Thanks,
      a.y

      On Tue, 18 Aug 2015, B M wrote:

            Hi Anastasia,
            Please find attached the trac-all.log
file. Thank you very much for your help.
            Bahram

            2015-08-17 19:31 GMT+02:00 Anastasia
Yendiki :

                  Hi Bahram - Can you please send us
your entire trac-all.log file? Thanks!

                  a.y

                  On Fri, 14 Aug 2015, B M wrote:

                        Dear experts,
                        I have the last version of
tTrakula. i did the first step with
                          trac-all -prep -c
bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
                        This worked properly to the
end as shown below:
                        trac-preproc finished
without error at Fri Aug 14 17:31:29 CEST 2015

                        However looking at logfile i
found following errors:
                        flirt 
-inbmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.ni
i.gz
            -ref
                       
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz
-out
                       
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bb
r.nii.gz
            -applyxfm -init
                       

bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat
-interp
            nearestneighbour
                        terminate called after
throwing an instance of 'NEWMAT::SingularException'
                        Abort (core dumped)

                        OR

                        Loading brain mask of output
subject from
                       
/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_
mask.bbr.nii

Re: [Freesurfer] Trakula

2015-08-26 Thread B M
Hi Anastasia,
Thank you very much for your help and recommendations. I will try to fix
These Problems. I would like to ask you one more question. Is there any
command which could help me to invert the gradient vectors for my DWI
scan in the z direction?
Best
Bahram

2015-08-24 17:57 GMT+02:00 Anastasia Yendiki :

>
> Hi Bahram - I looked at your subject's files. First, the freesurfer recon
> failed in the right hemisphere, probably because of a visible artifact on
> your T1 (see aseg screenshot). This affects the aparc+aseg, so you can't
> run tracula before you fix it.
>
> Second, the gradient vectors for your DWI scan probably need to be
> inverted in the z direction (see other screenshot with the principal
> eigenvectors of the tensors shown over the FA map). The vectors are
> oriented correctly in the axial view, but not in the sagittal or coronal
> view (see for example their orientation in the cingulum bundle in saggital
> view, where the cross-hair is centered, or in the corticospinal tract in
> coronal view). This is not causing your error, but you have to fix it for
> the tractography to work properly.
>
> Third, your DWI data has very anisotropic resolution (1.8 x 1.8 x 6.5 mm).
> Your voxels are almost 4 times as big in z than in x/y. This is not causing
> your error, but it is not optimal for diffusion analysis. Anisotropic
> voxels can bias estimates of diffusion anisotropy. Also, you only have 12
> directions with b=1000 and the other directions were acquired with a much
> lower b-value (b=200). It's unlikely that you'll get reliable fits of
> crossing-fiber models like the one used by tracula on this data. Again,
> this is not causing the error you're seeing but it will make it difficult
> to get usable results from this DWI data.
>
> Best,
> a.y
>
>
> On Thu, 20 Aug 2015, B M wrote:
>
> Hi Anastasia,
>> please find the files in attachment.
>> Best regards
>>
>> Bahram
>>
>> 2015-08-19 21:55 GMT+02:00 Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>:
>>
>>   Hi Bahram - There are some errors in there related to registration
>> files. Can you please send these files?
>>
>>
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat
>>   bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat
>>
>>   Thanks,
>>   a.y
>>
>>   On Tue, 18 Aug 2015, B M wrote:
>>
>> Hi Anastasia,
>> Please find attached the trac-all.log file. Thank you very
>> much for your help.
>> Bahram
>>
>> 2015-08-17 19:31 GMT+02:00 Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>:
>>
>>   Hi Bahram - Can you please send us your entire
>> trac-all.log file? Thanks!
>>
>>   a.y
>>
>>   On Fri, 14 Aug 2015, B M wrote:
>>
>> Dear experts,
>> I have the last version of tTrakula. i did the
>> first step with
>>   trac-all -prep -c
>> bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
>> This worked properly to the end as shown below:
>> trac-preproc finished without error at Fri Aug 14
>> 17:31:29 CEST 2015
>>
>> However looking at logfile i found following
>> errors:
>> flirt -in
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz
>> -ref
>>
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out
>>
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
>> -applyxfm -init
>>
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat
>> -interp
>> nearestneighbour
>> terminate called after throwing an instance of
>> 'NEWMAT::SingularException'
>> Abort (core dumped)
>>
>> OR
>>
>> Loading brain mask of output subject from
>>
>> /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
>> niiRead(): error opening file
>>
>> /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
>> ERROR: Could not read
>>
>> /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
>>
>>
>> AND as i tried the next step i got the following
>> error:
>>
>> bm@bm-linux:~$ trac-all -bedp -c
>> bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
>> INFO: SUBJECTS_DIR is
>> bmdaten/Auswertung/ALS-Review/Trakula/
>> INFO: Diffusion root is
>> bmdaten/Auswertung/ALS-Review/Trakula/
>> Actual FREESURFER_HOME /usr/local/freesurfer
>> WARN: Running FSL's bedbost locally - this might
>> take a while
>> WARN: It is recommende

Re: [Freesurfer] Trakula

2015-08-20 Thread Anastasia Yendiki


Hi Bahram - The anatomical-to-diffusion registration matrix is all zeros, 
so something went wrong there. I'll need to see all the output files to 
investigate. Can you please zip up this subject's tracula output 
directories (dmri, dmri.bedpostX, dpath, dlabel, scripts) and upload 
everything for me here?

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks,
a.y

On Thu, 20 Aug 2015, B M wrote:


Hi Anastasia,
please find the files in attachment.
Best regards

Bahram

2015-08-19 21:55 GMT+02:00 Anastasia Yendiki :

  Hi Bahram - There are some errors in there related to registration files. 
Can you please send these files?

  bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat
  bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat

  Thanks,
  a.y

  On Tue, 18 Aug 2015, B M wrote:

Hi Anastasia,
Please find attached the trac-all.log file. Thank you very much for 
your help.
Bahram

2015-08-17 19:31 GMT+02:00 Anastasia Yendiki 
:

      Hi Bahram - Can you please send us your entire trac-all.log 
file? Thanks!

      a.y

      On Fri, 14 Aug 2015, B M wrote:

            Dear experts,
            I have the last version of tTrakula. i did the first 
step with
              trac-all -prep -c 
bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
            This worked properly to the end as shown below:
            trac-preproc finished without error at Fri Aug 14 
17:31:29 CEST 2015

            However looking at logfile i found following errors:
            flirt -in 
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz
-ref
            
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out
            
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
-applyxfm -init
            
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp
nearestneighbour
            terminate called after throwing an instance of 
'NEWMAT::SingularException'
            Abort (core dumped)

            OR

            Loading brain mask of output subject from
            
/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
            niiRead(): error opening file
            
/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
            ERROR: Could not read
            
/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz


            AND as i tried the next step i got the following error:

            bm@bm-linux:~$ trac-all -bedp -c 
bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
            INFO: SUBJECTS_DIR is 
bmdaten/Auswertung/ALS-Review/Trakula/
            INFO: Diffusion root is 
bmdaten/Auswertung/ALS-Review/Trakula/
            Actual FREESURFER_HOME /usr/local/freesurfer
            WARN: Running FSL's bedbost locally - this might take a 
while
            WARN: It is recommended to run this step on a cluster
            bedpostx_mgh -n 2 
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri
            /usr/local/freesurfer/bin/bedpostx_mgh: 131: 
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax
error: "("
            unexpected

            Could you please advise me what to do?
            Best

            Bahram


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Re: [Freesurfer] Trakula

2015-08-20 Thread B M
Hi Anastasia,
please find the files in attachment.
Best regards

Bahram

2015-08-19 21:55 GMT+02:00 Anastasia Yendiki :

>
> Hi Bahram - There are some errors in there related to registration files.
> Can you please send these files?
>
> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat
> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat
>
> Thanks,
> a.y
>
>
> On Tue, 18 Aug 2015, B M wrote:
>
> Hi Anastasia,
>> Please find attached the trac-all.log file. Thank you very much for your
>> help.
>> Bahram
>>
>> 2015-08-17 19:31 GMT+02:00 Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>:
>>
>>   Hi Bahram - Can you please send us your entire trac-all.log file?
>> Thanks!
>>
>>   a.y
>>
>>   On Fri, 14 Aug 2015, B M wrote:
>>
>> Dear experts,
>> I have the last version of tTrakula. i did the first step with
>>   trac-all -prep -c
>> bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
>> This worked properly to the end as shown below:
>> trac-preproc finished without error at Fri Aug 14 17:31:29
>> CEST 2015
>>
>> However looking at logfile i found following errors:
>> flirt -in
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz
>> -ref
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz
>> -out
>>
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
>> -applyxfm -init
>>
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat
>> -interp nearestneighbour
>> terminate called after throwing an instance of
>> 'NEWMAT::SingularException'
>> Abort (core dumped)
>>
>> OR
>>
>> Loading brain mask of output subject from
>>
>> /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
>> niiRead(): error opening file
>>
>> /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
>> ERROR: Could not read
>>
>> /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
>>
>>
>> AND as i tried the next step i got the following error:
>>
>> bm@bm-linux:~$ trac-all -bedp -c
>> bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
>> INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/
>> INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/
>> Actual FREESURFER_HOME /usr/local/freesurfer
>> WARN: Running FSL's bedbost locally - this might take a while
>> WARN: It is recommended to run this step on a cluster
>> bedpostx_mgh -n 2
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri
>> /usr/local/freesurfer/bin/bedpostx_mgh: 131:
>> /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "("
>> unexpected
>>
>> Could you please advise me what to do?
>> Best
>>
>> Bahram
>>
>>
>> ___
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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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>> in error
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>> properly
>> dispose of the e-mail.
>>
>>
>>
>>
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>
>
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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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anat2diff.bbr.mat
Description: application/extension-mat


anat2mni.mat
Description: application/extension-mat
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Re: [Freesurfer] Trakula

2015-08-19 Thread Anastasia Yendiki


Hi Bahram - There are some errors in there related to registration files. 
Can you please send these files?


bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat

Thanks,
a.y

On Tue, 18 Aug 2015, B M wrote:


Hi Anastasia,
Please find attached the trac-all.log file. Thank you very much for your help.
Bahram

2015-08-17 19:31 GMT+02:00 Anastasia Yendiki :

  Hi Bahram - Can you please send us your entire trac-all.log file? Thanks!

  a.y

  On Fri, 14 Aug 2015, B M wrote:

Dear experts,
I have the last version of tTrakula. i did the first step with
  trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
This worked properly to the end as shown below:
trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015

However looking at logfile i found following errors:
flirt -in 
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz 
-ref
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out

bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
 -applyxfm -init

bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat 
-interp nearestneighbour
terminate called after throwing an instance of 
'NEWMAT::SingularException'
Abort (core dumped)

OR

Loading brain mask of output subject from

/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
niiRead(): error opening file

/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
ERROR: Could not read

/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz


AND as i tried the next step i got the following error:

bm@bm-linux:~$ trac-all -bedp -c 
bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/
INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/
Actual FREESURFER_HOME /usr/local/freesurfer
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 131: 
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "("
unexpected

Could you please advise me what to do?
Best

Bahram


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Re: [Freesurfer] Trakula

2015-08-18 Thread B M
Hi Anastasia,
Please find attached the trac-all.log file. Thank you very much for your
help.
Bahram

2015-08-17 19:31 GMT+02:00 Anastasia Yendiki :

>
> Hi Bahram - Can you please send us your entire trac-all.log file? Thanks!
>
> a.y
>
>
> On Fri, 14 Aug 2015, B M wrote:
>
> Dear experts,
>> I have the last version of tTrakula. i did the first step with
>>   trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
>> This worked properly to the end as shown below:
>> trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015
>>
>> However looking at logfile i found following errors:
>> flirt -in
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz
>> -ref
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
>> -applyxfm -init
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat
>> -interp nearestneighbour
>> terminate called after throwing an instance of 'NEWMAT::SingularException'
>> Abort (core dumped)
>>
>> OR
>>
>> Loading brain mask of output subject from
>>
>> /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
>> niiRead(): error opening file
>> /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
>> ERROR: Could not read
>> /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
>>
>>
>> AND as i tried the next step i got the following error:
>>
>> bm@bm-linux:~$ trac-all -bedp -c
>> bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
>> INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/
>> INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/
>> Actual FREESURFER_HOME /usr/local/freesurfer
>> WARN: Running FSL's bedbost locally - this might take a while
>> WARN: It is recommended to run this step on a cluster
>> bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri
>> /usr/local/freesurfer/bin/bedpostx_mgh: 131:
>> /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected
>>
>> Could you please advise me what to do?
>> Best
>>
>> Bahram
>>
>>
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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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> error
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> dispose of the e-mail.
>
>
Fri Aug 14 17:22:48 CEST 2015
/home/bm
/usr/local/freesurfer/bin/trac-all
-prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
Subject P01-a
SUBJECTS_DIR bmdaten/Auswertung/ALS-Review/Trakula/
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
bm
bm-linux
Linux bm-linux 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  256954 
maxlocks unlimited
maxsignal256954 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:  32909372   309815561927816  0 776952   25756624
-/+ buffers/cache:4447980   28461392
Swap:124999676   9000  124990676


Program versions:
$Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $
mri_convert --all-info 
ProgramName: mri_convert  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2015/08/14-15:22:48-GMT  BuildTimeStamp: Aug 16 2014 05:13:24  CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $  User: bm  Machine: bm-linux  Platform: Linux  PlatformVersion: 3.11.0-26-generic  CompilerName: GCC  CompilerVersion: 30400 
FLIRT version 6.0
$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
$Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2015/08/14-15:22:48-GMT  BuildTimeStamp: Feb  2 2013 22:46:06  CVS:   User: bm  Machine: bm-linux  Platform: Linux  PlatformVersion: 3.11.0-26-generic  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2015/08/14-15:22:48-GMT  BuildTimeStamp: May 23 2014 05:15:35  CVS:   User: bm  Machine: bm-linux  Platform:

Re: [Freesurfer] Trakula

2015-08-17 Thread Anastasia Yendiki


Hi Bahram - Can you please send us your entire trac-all.log file? Thanks!

a.y

On Fri, 14 Aug 2015, B M wrote:


Dear experts,
I have the last version of tTrakula. i did the first step with
  trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
This worked properly to the end as shown below:
trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015

However looking at logfile i found following errors:
flirt -in 
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz 
-ref
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
 -applyxfm -init
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat 
-interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
Abort (core dumped)

OR

Loading brain mask of output subject from
/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
niiRead(): error opening file 
/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
ERROR: Could not read 
/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz


AND as i tried the next step i got the following error:

bm@bm-linux:~$ trac-all -bedp -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/
INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/
Actual FREESURFER_HOME /usr/local/freesurfer
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: 
Syntax error: "(" unexpected

Could you please advise me what to do?
Best

Bahram

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addressed. If you believe this e-mail was sent to you in error and the e-mail
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dispose of the e-mail.


[Freesurfer] Trakula

2015-08-14 Thread B M
Dear experts,
I have the last version of tTrakula. i did the first step with
  trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
This worked properly to the end as shown below:
trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015

However looking at logfile i found following errors:
flirt -in
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz
-ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
-applyxfm -init
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat
-interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
Abort (core dumped)

OR

Loading brain mask of output subject from
/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
niiRead(): error opening file
/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
ERROR: Could not read
/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz


AND as i tried the next step i got the following error:

bm@bm-linux:~$ trac-all -bedp -c
bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/
INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/
Actual FREESURFER_HOME /usr/local/freesurfer
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 131:
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected

Could you please advise me what to do?
Best

Bahram
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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] 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
 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
 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
wrong!
           Thank you!

 

Re: [Freesurfer] trakula segmentation fault

2012-04-25 Thread Viviana Siless
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/**
>> 4531ddb4948dff7223febc5a5b4f7e**7d/testData.tar.gzLet
>>  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
>>
>>   

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 
 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 
 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
    

Re: [Freesurfer] trakula segmentation fault

2012-04-23 Thread Viviana Siless
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/**
>> 4531ddb4948dff7223febc5a5b4f7e**7d/testData.tar.gzLet
>>  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 r

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 
 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/lh.atr_PP_roi1.flt.nii.gz
  dlabel/

Re: [Freesurfer] trakula segmentation fault

2012-04-17 Thread Viviana Siless
Hi Anastasia,
My mistake with the expiration date.
Please try with this link:
https://transfert.inria.fr/fichiers/0b1013b5de0fc0cc9e8dd2d6101a054b/testData.tar.gz

Thanks!

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


On Tue, Apr 17, 2012 at 6:03 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Viviana - I was away from email for some time and it looks like the
> uploaded file has expired. Could you reupload it? I apologize for the delay.
>
> Thanks,
> a.y
>
>
> On Fri, 6 Apr 2012, Viviana Siless wrote:
>
>  Hi Anastasia,
>> Here is the data: https://transfert.inria.fr/**fichiers/**
>> 4531ddb4948dff7223febc5a5b4f7e**7d/testData.tar.gzLet
>>  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 dlabe

Re: [Freesurfer] trakula segmentation fault

2012-04-06 Thread Viviana Siless
Hi Anastasia,
Here is the data:
https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gzLet
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/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

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



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