date:20160522

Re: [Freesurfer] DTI error

2016-05-22 Thread Jasmin Alves

Correct.

On Sunday, May 22, 2016, Anastasia Yendiki 
wrote:

>
> No idea, sorry. You used the -c option with the previous steps of trac-all
> and didn't see this error, correct?
>
> On Sun, 22 May 2016, Jasmin Alves wrote:
>
> Hi Anastasia,
>> Perhaps I was asking for advice regarding the wrong step in trac-all, do
>> you
>> have any ideas why I am still receiving the following error:
>>
>> ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt
>>
>> This occurs when I do trac-all -path –c dmrirc1_sim.txt
>>
>> I tried looking at posts from previous mailing lists, and found no match
>> to
>> this problem.
>>
>>
>> Thank you,
>>
>> Jasmin
>>
>>
>> On Sun, May 22, 2016 at 5:53 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Ok, then you can ignore the error that you see when you run the
>>   bedpost step.
>>
>>   `On Sun, 22 May 2016, Jasmin Alves wrote:
>>
>>   Sorry for the mix-up. All of the bedpost output files are
>>   generated as well
>>   both 1 and 2 of each file.
>>
>>   On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki
>>    wrote:
>>
>> These are output files from the -prep step. I'm
>>   asking about
>> output files from the bedpost step, since that's
>>   where you're
>> encountering the error.
>>
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard
>>
>>
>> .edu_fswiki_trac-2Dall-23Outputsfromtrac-2Dall-2Dbedp=DQIDaQ=clK7kQUTWt
>>
>>
>> AVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=7c1gaW5UpDUs-D
>>
>>
>> f4uqLGaiN1YKi8WpD7PUUFUH_Yh_8=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA
>>
>> =
>> What's in the dmri.bedpostX/ directory?
>>
>> On Sun, 22 May 2016, Jasmin Alves wrote:
>>
>>   Output files are being generated, ie.
>>1. dtifit_FA.nii.gz - Fractional Anisotropy
>>2. dtifit_MD.nii.gz - Mean Diffusivity
>>3. dtifit_MO.nii.gz - Mode of the Anisotropy
>>4. dtifit_S0.nii.gz - Non-Diffusion weighted
>>   image
>>5. dtifit_L1.nii.gz - Primary Eigenvalue
>>6. dtifit_L2.nii.gz - Secondary Eigenvalue
>>7. dtifit_L3.nii.gz - Tertiary Eigenvalue
>>8. dtifit_V1.nii.gz - Primary Eigenvector
>>9. dtifit_V2.nii.gz - Secondary Eigenvector
>>   10. dtifit_V3.nii.gz - Tertiary Eigenvector
>>   But it seems the bedpost process gets cut
>>   short and
>>   then,  the trac-all path
>>   step won't work. I have ran it a few times and
>>   the
>>   bedpost step ends at the
>>   same point.
>>
>>
>>   On Sun, May 22, 2016 at 3:24 PM, Anastasia
>>   Yendiki
>>    wrote:
>>
>> But do you see the output files from the
>>   previous step? The
>> outputs from each step are described on
>>   the
>>   wiki.
>>
>> On Sun, 22 May 2016, Jasmin Alves wrote:
>>
>>   Hi Anastasia,
>>   Thank you for the reply, when I do
>>   just
>>   let it run,
>>   I get the following
>>   error when I try to do trac-all
>>   -path –c
>>   dmrirc1_sim.txt
>>
>>   I get the following error:
>>
>>   ERROR: flag –c unrecognized
>>
>>   -path –c dmrirc1_sim.txt
>>
>>
>>   Thanks,
>>
>>   Jasmin
>>
>>
>>   On Sun, May 22, 2016 at 1:51 AM,
>>   Anastasia Yendiki
>>   
>>   wrote:
>>
>> Hi Jasmin - Check if things
>>   are
>>   running
>>   despite that error. Are
>> output files being
>>   generated?
>>
>> a.y
>>
>> On Sat, 21 May 2016, Jasmin
>>   Alves
>>   wrote:
>>
>>
>>   Dear Freesurfer,
>>
>>   While doing the
>>   bedpost step
>>   for
>>   TRAC-all ( trac-all
>>   -bedp -c
>>   dmrirc1_sim.txt) I
>>   received
>>   the
>>   following error:
>>
>>
>>
>>

Re: [Freesurfer] DTI error

2016-05-22 Thread Anastasia Yendiki



No idea, sorry. You used the -c option with the previous steps of trac-all 
and didn't see this error, correct?


On Sun, 22 May 2016, Jasmin Alves wrote:


Hi Anastasia,
Perhaps I was asking for advice regarding the wrong step in trac-all, do you
have any ideas why I am still receiving the following error:

ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt

This occurs when I do trac-all -path –c dmrirc1_sim.txt

I tried looking at posts from previous mailing lists, and found no match to
this problem.


Thank you,

Jasmin


On Sun, May 22, 2016 at 5:53 PM, Anastasia Yendiki
 wrote:

  Ok, then you can ignore the error that you see when you run the
  bedpost step.

  `On Sun, 22 May 2016, Jasmin Alves wrote:

  Sorry for the mix-up. All of the bedpost output files are
  generated as well
  both 1 and 2 of each file. 

  On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki
   wrote:

        These are output files from the -prep step. I'm
  asking about
        output files from the bedpost step, since that's
  where you're
        encountering the error.

https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard

.edu_fswiki_trac-2Dall-23Outputsfromtrac-2Dall-2Dbedp=DQIDaQ=clK7kQUTWt

AVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=7c1gaW5UpDUs-D

f4uqLGaiN1YKi8WpD7PUUFUH_Yh_8=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA

        =
        What's in the dmri.bedpostX/ directory?

        On Sun, 22 May 2016, Jasmin Alves wrote:

              Output files are being generated, ie.
               1. dtifit_FA.nii.gz - Fractional Anisotropy
               2. dtifit_MD.nii.gz - Mean Diffusivity
               3. dtifit_MO.nii.gz - Mode of the Anisotropy
               4. dtifit_S0.nii.gz - Non-Diffusion weighted
  image
               5. dtifit_L1.nii.gz - Primary Eigenvalue
               6. dtifit_L2.nii.gz - Secondary Eigenvalue
               7. dtifit_L3.nii.gz - Tertiary Eigenvalue
               8. dtifit_V1.nii.gz - Primary Eigenvector
               9. dtifit_V2.nii.gz - Secondary Eigenvector
              10. dtifit_V3.nii.gz - Tertiary Eigenvector
              But it seems the bedpost process gets cut
  short and
              then,  the trac-all path
              step won't work. I have ran it a few times and
  the
              bedpost step ends at the
              same point. 


              On Sun, May 22, 2016 at 3:24 PM, Anastasia
  Yendiki
               wrote:

                    But do you see the output files from the
              previous step? The
                    outputs from each step are described on
  the
              wiki.

                    On Sun, 22 May 2016, Jasmin Alves wrote:

                          Hi Anastasia,
                          Thank you for the reply, when I do
  just
              let it run,
                          I get the following
                          error when I try to do trac-all
  -path –c
                          dmrirc1_sim.txt

                          I get the following error:

                          ERROR: flag –c unrecognized

                          -path –c dmrirc1_sim.txt


                          Thanks,

                          Jasmin 


                          On Sun, May 22, 2016 at 1:51 AM,
              Anastasia Yendiki
                          
  wrote:

                                Hi Jasmin - Check if things
  are
              running
                          despite that error. Are
                                output files being
  generated?

                                a.y

                                On Sat, 21 May 2016, Jasmin
  Alves
              wrote:


                                      Dear Freesurfer,

                                      While doing the
  bedpost step
              for
                          TRAC-all ( trac-all
                                      -bedp -c
                                      dmrirc1_sim.txt) I
  received
              the
                          following error:

                                     
                         
              /Applications/freesurfer/bin/bedpostx_mgh:
  line 345:
                                      kill: (51042) - No
  such
                                      process

                                      Any ideas?

                                      Thank you,
                                      Jasmin 

                                      Jasmin
  AlvesPredoctoral

Re: [Freesurfer] DTI error

2016-05-22 Thread Jasmin Alves

Hi Anastasia,

Perhaps I was asking for advice regarding the wrong step in trac-all, do
you have any ideas why I am still receiving the following error:

ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt

This occurs when I do trac-all -path –c dmrirc1_sim.txt

I tried looking at posts from previous mailing lists, and found no match to
this problem.


Thank you,

Jasmin

On Sun, May 22, 2016 at 5:53 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Ok, then you can ignore the error that you see when you run the bedpost
> step.
>
>
> `On Sun, 22 May 2016, Jasmin Alves wrote:
>
> Sorry for the mix-up. All of the bedpost output files are generated as well
>> both 1 and 2 of each file.
>>
>> On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki
>>  wrote:
>>
>>   These are output files from the -prep step. I'm asking about
>>   output files from the bedpost step, since that's where you're
>>   encountering the error.
>>
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard
>>
>> .edu_fswiki_trac-2Dall-23Outputsfromtrac-2Dall-2Dbedp=DQIDaQ=clK7kQUTWt
>>
>> AVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=7c1gaW5UpDUs-D
>>
>> f4uqLGaiN1YKi8WpD7PUUFUH_Yh_8=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA
>>   =
>>   What's in the dmri.bedpostX/ directory?
>>
>>   On Sun, 22 May 2016, Jasmin Alves wrote:
>>
>> Output files are being generated, ie.
>>  1. dtifit_FA.nii.gz - Fractional Anisotropy
>>  2. dtifit_MD.nii.gz - Mean Diffusivity
>>  3. dtifit_MO.nii.gz - Mode of the Anisotropy
>>  4. dtifit_S0.nii.gz - Non-Diffusion weighted image
>>  5. dtifit_L1.nii.gz - Primary Eigenvalue
>>  6. dtifit_L2.nii.gz - Secondary Eigenvalue
>>  7. dtifit_L3.nii.gz - Tertiary Eigenvalue
>>  8. dtifit_V1.nii.gz - Primary Eigenvector
>>  9. dtifit_V2.nii.gz - Secondary Eigenvector
>> 10. dtifit_V3.nii.gz - Tertiary Eigenvector
>> But it seems the bedpost process gets cut short and
>> then,  the trac-all path
>> step won't work. I have ran it a few times and the
>> bedpost step ends at the
>> same point.
>>
>>
>> On Sun, May 22, 2016 at 3:24 PM, Anastasia Yendiki
>>  wrote:
>>
>>   But do you see the output files from the
>> previous step? The
>>   outputs from each step are described on the
>> wiki.
>>
>>   On Sun, 22 May 2016, Jasmin Alves wrote:
>>
>> Hi Anastasia,
>> Thank you for the reply, when I do just
>> let it run,
>> I get the following
>> error when I try to do trac-all -path –c
>> dmrirc1_sim.txt
>>
>> I get the following error:
>>
>> ERROR: flag –c unrecognized
>>
>> -path –c dmrirc1_sim.txt
>>
>>
>> Thanks,
>>
>> Jasmin
>>
>>
>> On Sun, May 22, 2016 at 1:51 AM,
>> Anastasia Yendiki
>>  wrote:
>>
>>   Hi Jasmin - Check if things are
>> running
>> despite that error. Are
>>   output files being generated?
>>
>>   a.y
>>
>>   On Sat, 21 May 2016, Jasmin Alves
>> wrote:
>>
>>
>> Dear Freesurfer,
>>
>> While doing the bedpost step
>> for
>> TRAC-all ( trac-all
>> -bedp -c
>> dmrirc1_sim.txt) I received
>> the
>> following error:
>>
>>
>>
>> /Applications/freesurfer/bin/bedpostx_mgh: line 345:
>> kill: (51042) - No such
>> process
>>
>> Any ideas?
>>
>> Thank you,
>> Jasmin
>>
>> Jasmin AlvesPredoctoral
>> Student
>> Medical Biology Graduate
>> Program
>> University of Southern
>> California
>> jal...@usc.edu
>>
>>
>>
>>
>>
>> ___
>>   Freesurfer mailing list
>>   Freesurfer@nmr.mgh.harvard.edu
>>
>>

Re: [Freesurfer] DTI error

2016-05-22 Thread Anastasia Yendiki



Ok, then you can ignore the error that you see when you run the bedpost 
step.


`On Sun, 22 May 2016, Jasmin Alves wrote:


Sorry for the mix-up. All of the bedpost output files are generated as well
both 1 and 2 of each file. 

On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki
 wrote:

  These are output files from the -prep step. I'm asking about
  output files from the bedpost step, since that's where you're
  encountering the error.

https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard
.edu_fswiki_trac-2Dall-23Outputsfromtrac-2Dall-2Dbedp=DQIDaQ=clK7kQUTWt
AVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=7c1gaW5UpDUs-D
f4uqLGaiN1YKi8WpD7PUUFUH_Yh_8=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA
  =
  What's in the dmri.bedpostX/ directory?

  On Sun, 22 May 2016, Jasmin Alves wrote:

Output files are being generated, ie.
 1. dtifit_FA.nii.gz - Fractional Anisotropy
 2. dtifit_MD.nii.gz - Mean Diffusivity
 3. dtifit_MO.nii.gz - Mode of the Anisotropy
 4. dtifit_S0.nii.gz - Non-Diffusion weighted image
 5. dtifit_L1.nii.gz - Primary Eigenvalue
 6. dtifit_L2.nii.gz - Secondary Eigenvalue
 7. dtifit_L3.nii.gz - Tertiary Eigenvalue
 8. dtifit_V1.nii.gz - Primary Eigenvector
 9. dtifit_V2.nii.gz - Secondary Eigenvector
10. dtifit_V3.nii.gz - Tertiary Eigenvector
But it seems the bedpost process gets cut short and
then,  the trac-all path
step won't work. I have ran it a few times and the
bedpost step ends at the
same point. 


On Sun, May 22, 2016 at 3:24 PM, Anastasia Yendiki
 wrote:

      But do you see the output files from the
previous step? The
      outputs from each step are described on the
wiki.

      On Sun, 22 May 2016, Jasmin Alves wrote:

            Hi Anastasia,
            Thank you for the reply, when I do just
let it run,
            I get the following
            error when I try to do trac-all -path –c
            dmrirc1_sim.txt

            I get the following error:

            ERROR: flag –c unrecognized

            -path –c dmrirc1_sim.txt


            Thanks,

            Jasmin 


            On Sun, May 22, 2016 at 1:51 AM,
Anastasia Yendiki
             wrote:

                  Hi Jasmin - Check if things are
running
            despite that error. Are
                  output files being generated?

                  a.y

                  On Sat, 21 May 2016, Jasmin Alves
wrote:


                        Dear Freesurfer,

                        While doing the bedpost step
for
            TRAC-all ( trac-all
                        -bedp -c
                        dmrirc1_sim.txt) I received
the
            following error:

                       
           
/Applications/freesurfer/bin/bedpostx_mgh: line 345:
                        kill: (51042) - No such
                        process

                        Any ideas?

                        Thank you,
                        Jasmin 

                        Jasmin AlvesPredoctoral
Student 
                        Medical Biology Graduate
Program 
                        University of Southern
California
                        jal...@usc.edu 



                 
           
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Re: [Freesurfer] DTI error

2016-05-22 Thread Jasmin Alves

Sorry for the mix-up. All of the bedpost output files are generated as well
both 1 and 2 of each file.

On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> These are output files from the -prep step. I'm asking about output files
> from the bedpost step, since that's where you're encountering the error.
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_trac-2Dall-23Outputsfromtrac-2Dall-2Dbedp=DQIDaQ=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=7c1gaW5UpDUs-Df4uqLGaiN1YKi8WpD7PUUFUH_Yh_8=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA=
> What's in the dmri.bedpostX/ directory?
>
> On Sun, 22 May 2016, Jasmin Alves wrote:
>
> Output files are being generated, ie.
>>  1. dtifit_FA.nii.gz - Fractional Anisotropy
>>  2. dtifit_MD.nii.gz - Mean Diffusivity
>>  3. dtifit_MO.nii.gz - Mode of the Anisotropy
>>  4. dtifit_S0.nii.gz - Non-Diffusion weighted image
>>  5. dtifit_L1.nii.gz - Primary Eigenvalue
>>  6. dtifit_L2.nii.gz - Secondary Eigenvalue
>>  7. dtifit_L3.nii.gz - Tertiary Eigenvalue
>>  8. dtifit_V1.nii.gz - Primary Eigenvector
>>  9. dtifit_V2.nii.gz - Secondary Eigenvector
>> 10. dtifit_V3.nii.gz - Tertiary Eigenvector
>>
>> But it seems the bedpost process gets cut short and then,  the trac-all
>> path
>> step won't work. I have ran it a few times and the bedpost step ends at
>> the
>> same point.
>>
>>
>> On Sun, May 22, 2016 at 3:24 PM, Anastasia Yendiki
>>  wrote:
>>
>>   But do you see the output files from the previous step? The
>>   outputs from each step are described on the wiki.
>>
>>   On Sun, 22 May 2016, Jasmin Alves wrote:
>>
>> Hi Anastasia,
>> Thank you for the reply, when I do just let it run,
>> I get the following
>> error when I try to do trac-all -path –c
>> dmrirc1_sim.txt
>>
>> I get the following error:
>>
>> ERROR: flag –c unrecognized
>>
>> -path –c dmrirc1_sim.txt
>>
>>
>> Thanks,
>>
>> Jasmin
>>
>>
>> On Sun, May 22, 2016 at 1:51 AM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Jasmin - Check if things are running
>> despite that error. Are
>>   output files being generated?
>>
>>   a.y
>>
>>   On Sat, 21 May 2016, Jasmin Alves wrote:
>>
>>
>> Dear Freesurfer,
>>
>> While doing the bedpost step for
>> TRAC-all ( trac-all
>> -bedp -c
>> dmrirc1_sim.txt) I received the
>> following error:
>>
>>
>> /Applications/freesurfer/bin/bedpostx_mgh: line 345:
>> kill: (51042) - No such
>> process
>>
>> Any ideas?
>>
>> Thank you,
>> Jasmin
>>
>> Jasmin AlvesPredoctoral Student
>> Medical Biology Graduate Program
>> University of Southern California
>> jal...@usc.edu
>>
>>
>>
>>
>> ___
>>   Freesurfer mailing list
>>   Freesurfer@nmr.mgh.harvard.edu
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e
>>
>>
>> du_mailman_listinfo_freesurfer=DQIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8
>>
>>
>> p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=_YHMcYTHXxIXmxZsQ6qCykG0PXDj2RSyadSYv
>>
>>
>> Jp8mKI=fkP_flwCTRv-7FzQB1kw0eRwApBybsAjJNxNF8VH9RQ=
>>
>>
>>   The information in this e-mail is intended
>> only for the person
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>>   and the e-mail
>>   contains patient information, please contact
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>>   Compliance HelpLine at
>>
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>>
>>
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>>
>>
>> KTyqa6rNRHLug=_YHMcYTHXxIXmxZsQ6qCykG0PXDj2RSyadSYvJp8mKI=ZCxo2mqb7_uBl
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>> Jasmin AlvesPredoctoral Student
>> Medical Biology Graduate Program
>> University of Southern California
>> jal...@usc.edu
>>
>>
>>
>> ___

Re: [Freesurfer] DTI error

2016-05-22 Thread Anastasia Yendiki



These are output files from the -prep step. I'm asking about output files 
from the bedpost step, since that's where you're encountering the error.


https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputsfromtrac-all-bedp

What's in the dmri.bedpostX/ directory?

On Sun, 22 May 2016, Jasmin Alves wrote:


Output files are being generated, ie.
 1. dtifit_FA.nii.gz - Fractional Anisotropy
 2. dtifit_MD.nii.gz - Mean Diffusivity
 3. dtifit_MO.nii.gz - Mode of the Anisotropy
 4. dtifit_S0.nii.gz - Non-Diffusion weighted image
 5. dtifit_L1.nii.gz - Primary Eigenvalue
 6. dtifit_L2.nii.gz - Secondary Eigenvalue
 7. dtifit_L3.nii.gz - Tertiary Eigenvalue
 8. dtifit_V1.nii.gz - Primary Eigenvector
 9. dtifit_V2.nii.gz - Secondary Eigenvector
10. dtifit_V3.nii.gz - Tertiary Eigenvector
But it seems the bedpost process gets cut short and then,  the trac-all path
step won't work. I have ran it a few times and the bedpost step ends at the
same point. 


On Sun, May 22, 2016 at 3:24 PM, Anastasia Yendiki
 wrote:

  But do you see the output files from the previous step? The
  outputs from each step are described on the wiki.

  On Sun, 22 May 2016, Jasmin Alves wrote:

Hi Anastasia,
Thank you for the reply, when I do just let it run,
I get the following
error when I try to do trac-all -path –c
dmrirc1_sim.txt

I get the following error:

ERROR: flag –c unrecognized

-path –c dmrirc1_sim.txt


Thanks,

Jasmin 


On Sun, May 22, 2016 at 1:51 AM, Anastasia Yendiki
 wrote:

      Hi Jasmin - Check if things are running
despite that error. Are
      output files being generated?

      a.y

      On Sat, 21 May 2016, Jasmin Alves wrote:


            Dear Freesurfer,

            While doing the bedpost step for
TRAC-all ( trac-all
            -bedp -c
            dmrirc1_sim.txt) I received the
following error:

           
/Applications/freesurfer/bin/bedpostx_mgh: line 345:
            kill: (51042) - No such
            process

            Any ideas?

            Thank you,
            Jasmin 

            Jasmin AlvesPredoctoral Student 
            Medical Biology Graduate Program 
            University of Southern California
            jal...@usc.edu 



     
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--
Jasmin AlvesPredoctoral Student 
Medical Biology Graduate Program 
University of Southern California
jal...@usc.edu 



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Re: [Freesurfer] DTI error

2016-05-22 Thread Jasmin Alves

Output files are being generated, ie.


   1. dtifit_FA.nii.gz - Fractional Anisotropy
   2. dtifit_MD.nii.gz - Mean Diffusivity
   3. dtifit_MO.nii.gz - Mode of the Anisotropy
   4. dtifit_S0.nii.gz - Non-Diffusion weighted image
   5. dtifit_L1.nii.gz - Primary Eigenvalue
   6. dtifit_L2.nii.gz - Secondary Eigenvalue
   7. dtifit_L3.nii.gz - Tertiary Eigenvalue
   8. dtifit_V1.nii.gz - Primary Eigenvector
   9. dtifit_V2.nii.gz - Secondary Eigenvector
   10. dtifit_V3.nii.gz - Tertiary Eigenvector

But it seems the bedpost process gets cut short and then,  the trac-all
path step won't work. I have ran it a few times and the bedpost step ends
at the same point.


On Sun, May 22, 2016 at 3:24 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> But do you see the output files from the previous step? The outputs from
> each step are described on the wiki.
>
>
> On Sun, 22 May 2016, Jasmin Alves wrote:
>
> Hi Anastasia,
>> Thank you for the reply, when I do just let it run, I get the following
>> error when I try to do trac-all -path –c dmrirc1_sim.txt
>>
>> I get the following error:
>>
>> ERROR: flag –c unrecognized
>>
>> -path –c dmrirc1_sim.txt
>>
>>
>> Thanks,
>>
>> Jasmin
>>
>>
>> On Sun, May 22, 2016 at 1:51 AM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Jasmin - Check if things are running despite that error. Are
>>   output files being generated?
>>
>>   a.y
>>
>>   On Sat, 21 May 2016, Jasmin Alves wrote:
>>
>>
>> Dear Freesurfer,
>>
>> While doing the bedpost step for TRAC-all ( trac-all
>> -bedp -c
>> dmrirc1_sim.txt) I received the following error:
>>
>> /Applications/freesurfer/bin/bedpostx_mgh: line 345:
>> kill: (51042) - No such
>> process
>>
>> Any ideas?
>>
>> Thank you,
>> Jasmin
>>
>> Jasmin AlvesPredoctoral Student
>> Medical Biology Graduate Program
>> University of Southern California
>> jal...@usc.edu
>>
>>
>>
>>   ___
>>   Freesurfer mailing list
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>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e
>>
>> du_mailman_listinfo_freesurfer=DQIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8
>>
>> p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=_YHMcYTHXxIXmxZsQ6qCykG0PXDj2RSyadSYv
>>   Jp8mKI=fkP_flwCTRv-7FzQB1kw0eRwApBybsAjJNxNF8VH9RQ=
>>
>>
>>   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
>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli
>>
>> anceline=DQIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0
>>
>> KTyqa6rNRHLug=_YHMcYTHXxIXmxZsQ6qCykG0PXDj2RSyadSYvJp8mKI=ZCxo2mqb7_uBl
>>   K06A4PzG2Oc3tXOOfY5nkuRQDxr1-g=  . 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.
>>
>>
>>
>>
>> --
>> Jasmin AlvesPredoctoral Student
>> Medical Biology Graduate Program
>> University of Southern California
>> jal...@usc.edu
>>
>>
>>
> ___
> Freesurfer mailing list
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>
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> addressed. If you believe this e-mail was sent to you in error and the
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-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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Re: [Freesurfer] DTI error

2016-05-22 Thread Anastasia Yendiki



But do you see the output files from the previous step? The outputs from 
each step are described on the wiki.


On Sun, 22 May 2016, Jasmin Alves wrote:


Hi Anastasia,
Thank you for the reply, when I do just let it run, I get the following
error when I try to do trac-all -path –c dmrirc1_sim.txt

I get the following error:

ERROR: flag –c unrecognized

-path –c dmrirc1_sim.txt


Thanks,

Jasmin 


On Sun, May 22, 2016 at 1:51 AM, Anastasia Yendiki
 wrote:

  Hi Jasmin - Check if things are running despite that error. Are
  output files being generated?

  a.y

  On Sat, 21 May 2016, Jasmin Alves wrote:


Dear Freesurfer,

While doing the bedpost step for TRAC-all ( trac-all
-bedp -c
dmrirc1_sim.txt) I received the following error:

/Applications/freesurfer/bin/bedpostx_mgh: line 345:
kill: (51042) - No such
process

Any ideas?

Thank you,
Jasmin 

Jasmin AlvesPredoctoral Student 
Medical Biology Graduate Program 
University of Southern California
jal...@usc.edu 



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--
Jasmin AlvesPredoctoral Student 
Medical Biology Graduate Program 
University of Southern California
jal...@usc.edu 


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Re: [Freesurfer] DTI error

2016-05-22 Thread Jasmin Alves

Hi Anastasia,

Thank you for the reply, when I do just let it run, I get the following
error when I try to do trac-all -path –c dmrirc1_sim.txt

I get the following error:

ERROR: flag –c unrecognized

-path –c dmrirc1_sim.txt


Thanks,

Jasmin

On Sun, May 22, 2016 at 1:51 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Jasmin - Check if things are running despite that error. Are output
> files being generated?
>
> a.y
>
> On Sat, 21 May 2016, Jasmin Alves wrote:
>
>
>> Dear Freesurfer,
>>
>> While doing the bedpost step for TRAC-all ( trac-all -bedp -c
>> dmrirc1_sim.txt) I received the following error:
>>
>> /Applications/freesurfer/bin/bedpostx_mgh: line 345: kill: (51042) - No
>> such
>> process
>>
>> Any ideas?
>>
>> Thank you,
>> Jasmin
>>
>> Jasmin AlvesPredoctoral Student
>> Medical Biology Graduate Program
>> University of Southern California
>> jal...@usc.edu
>>
>>
>>
> ___
> Freesurfer mailing list
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>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DQIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=_YHMcYTHXxIXmxZsQ6qCykG0PXDj2RSyadSYvJp8mKI=fkP_flwCTRv-7FzQB1kw0eRwApBybsAjJNxNF8VH9RQ=
>
>
> 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
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> HelpLine at
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-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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Re: [Freesurfer] DTI error

2016-05-22 Thread Anastasia Yendiki



Hi Jasmin - Check if things are running despite that error. Are output 
files being generated?


a.y

On Sat, 21 May 2016, Jasmin Alves wrote:



Dear Freesurfer,

While doing the bedpost step for TRAC-all ( trac-all -bedp -c
dmrirc1_sim.txt) I received the following error:

/Applications/freesurfer/bin/bedpostx_mgh: line 345: kill: (51042) - No such
process

Any ideas?

Thank you,
Jasmin 

Jasmin AlvesPredoctoral Student 
Medical Biology Graduate Program 
University of Southern California
jal...@usc.edu 


___
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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] DTI error

Re: [Freesurfer] DTI error

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Re: [Freesurfer] DTI error

Re: [Freesurfer] DTI error

Re: [Freesurfer] DTI error

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