Re: [Freesurfer] bvecs error from Tracula

[Anastasia Yendiki]

Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 
3-column format? 
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula


Thanks,
a.y

On Mon, 15 Jul 2013, amirhossein manzouri wrote:


Dear Experts, 
I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get 
the attached bval and bvec file which the bvec one is wrong so the process exits
with error in dtifit. I have also attached  original bvec and bval.

--
Best regards,
Amirhossein Manzouri 

 


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Re: [Freesurfer] bvecs error from Tracula

[amirhossein manzouri]

Hi Anastasia,
I have tried both , 3-row and 3-column format and still wrong bvecc and
bval from flip4fsl. Could you please send me a sample of your original
files so I can compare?


On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of
> 3-column format? http://surfer.nmr.mgh.harvard.**
> edu/fswiki/FsTutorial/Tracula
>
> Thanks,
> a.y
>
>
> On Mon, 15 Jul 2013, amirhossein manzouri wrote:
>
>  Dear Experts,
>> I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step
>> I get the attached bval and bvec file which the bvec one is wrong so the
>> process exits
>> with error in dtifit. I have also attached  original bvec and bval.
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>
>>
>
> 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.
>



-- 
Best regards,
Amirhossein Manzouri
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Re: [Freesurfer] bvecs error from Tracula

[Anastasia Yendiki]

Hi Amirhossein - I'm attaching sample files.

a.y

On Tue, 16 Jul 2013, amirhossein manzouri wrote:


Hi Anastasia, 
I have tried both , 3-row and 3-column format and still wrong bvecc and bval
from flip4fsl. Could you please send me a sample of your original files so I
can compare?


On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki
 wrote:

  Hi Amirhossein - Are your original bvecs/bvals in 3-row format
  instead of 3-column format?
  http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

  Thanks,
  a.y

  On Mon, 15 Jul 2013, amirhossein manzouri wrote:

Dear Experts, 
I am running trac-all -prep -c dmrirc on my DWI
data. After flip4fsl step I get the attached bval
and bvec file which the bvec one is wrong so the
process exits
with error in dtifit. I have also attached  original
bvec and bval.

--
Best regards,
Amirhossein Manzouri 

 





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.




--
Best regards,
Amirhossein Manzouri 

 


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Re: [Freesurfer] bvecs error from Tracula

[amirhossein manzouri]

Thanks Anastasia,
IT HELPED!


On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Amirhossein - I'm attaching sample files.
>
> a.y
>
>
> On Tue, 16 Jul 2013, amirhossein manzouri wrote:
>
>  Hi Anastasia,
>> I have tried both , 3-row and 3-column format and still wrong bvecc and
>> bval
>> from flip4fsl. Could you please send me a sample of your original files
>> so I
>> can compare?
>>
>>
>> On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Amirhossein - Are your original bvecs/bvals in 3-row format
>>   instead of 3-column format?
>>   
>> http://surfer.nmr.mgh.harvard.**edu/fswiki/FsTutorial/Tracula
>>
>>   Thanks,
>>   a.y
>>
>>   On Mon, 15 Jul 2013, amirhossein manzouri wrote:
>>
>> Dear Experts,
>> I am running trac-all -prep -c dmrirc on my DWI
>> data. After flip4fsl step I get the attached bval
>> and bvec file which the bvec one is wrong so the
>> process exits
>> with error in dtifit. I have also attached  original
>> bvec and bval.
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>
>>
>>
>> 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.
>>
>>
>>
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>


-- 
Best regards,
Amirhossein Manzouri
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Re: [Freesurfer] bvecs error from Tracula

[Anastasia Yendiki]

Good to hear! Can you please share with all of us what was wrong with your 
original files? It may help others who have the same problem in the 
future. Thanks!


On Wed, 17 Jul 2013, amirhossein manzouri wrote:


Thanks Anastasia, 
IT HELPED!


On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki 

wrote:

  Hi Amirhossein - I'm attaching sample files.

  a.y

  On Tue, 16 Jul 2013, amirhossein manzouri wrote:

Hi Anastasia, 
I have tried both , 3-row and 3-column format and still
wrong bvecc and bval
from flip4fsl. Could you please send me a sample of your
original files so I
can compare?


On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki
 wrote:

      Hi Amirhossein - Are your original bvecs/bvals in
3-row format
      instead of 3-column format?
     
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

      Thanks,
      a.y

      On Mon, 15 Jul 2013, amirhossein manzouri wrote:

            Dear Experts, 
            I am running trac-all -prep -c dmrirc on my
DWI
            data. After flip4fsl step I get the attached
bval
            and bvec file which the bvec one is wrong so
the
            process exits
            with error in dtifit. I have also attached
 original
            bvec and bval.

            --
            Best regards,
            Amirhossein Manzouri 

             





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.




--
Best regards,
Amirhossein Manzouri 

 





--
Best regards,
Amirhossein Manzouri 

 


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Re: [Freesurfer] bvecs error from Tracula

[amirhossein manzouri]

The format of my bval file was wrong so I edited your file and tried and it
worked, also bvec should be in three columns as you have mentioned before.


On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Good to hear! Can you please share with all of us what was wrong with your
> original files? It may help others who have the same problem in the future.
> Thanks!
>
>
> On Wed, 17 Jul 2013, amirhossein manzouri wrote:
>
>  Thanks Anastasia,
>> IT HELPED!
>>
>>
>> On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>
>> wrote:
>>
>>   Hi Amirhossein - I'm attaching sample files.
>>
>>   a.y
>>
>>   On Tue, 16 Jul 2013, amirhossein manzouri wrote:
>>
>> Hi Anastasia,
>> I have tried both , 3-row and 3-column format and still
>> wrong bvecc and bval
>> from flip4fsl. Could you please send me a sample of your
>> original files so I
>> can compare?
>>
>>
>> On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Amirhossein - Are your original bvecs/bvals in
>> 3-row format
>>   instead of 3-column format?
>>
>> 
>> http://surfer.nmr.mgh.harvard.**edu/fswiki/FsTutorial/Tracula
>>
>>   Thanks,
>>   a.y
>>
>>   On Mon, 15 Jul 2013, amirhossein manzouri wrote:
>>
>> Dear Experts,
>> I am running trac-all -prep -c dmrirc on my
>> DWI
>> data. After flip4fsl step I get the attached
>> bval
>> and bvec file which the bvec one is wrong so
>> the
>> process exits
>> with error in dtifit. I have also attached
>>  original
>> bvec and bval.
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>
>>
>>
>> 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.
>>
>>
>>
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>
>>
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>


-- 
Best regards,
Amirhossein Manzouri
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Re: [Freesurfer] bvecs error from Tracula

[amirhossein manzouri]

Dear Anastasia,
I am trying to download the
dmri_5.1_snow_leopard.tar.gz
from
FreeSurfer website to solve memory problem but it is not available. Would
you please check the source to the link?


On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri <
a.h.manzo...@gmail.com> wrote:

> The format of my bval file was wrong so I edited your file and tried and
> it worked, also bvec should be in three columns as you have mentioned
> before.
>
>
> On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki <
> ayend...@nmr.mgh.harvard.edu> wrote:
>
>>
>> Good to hear! Can you please share with all of us what was wrong with
>> your original files? It may help others who have the same problem in the
>> future. Thanks!
>>
>>
>> On Wed, 17 Jul 2013, amirhossein manzouri wrote:
>>
>>  Thanks Anastasia,
>>> IT HELPED!
>>>
>>>
>>> On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki <
>>> ayend...@nmr.mgh.harvard.edu>
>>> wrote:
>>>
>>>   Hi Amirhossein - I'm attaching sample files.
>>>
>>>   a.y
>>>
>>>   On Tue, 16 Jul 2013, amirhossein manzouri wrote:
>>>
>>> Hi Anastasia,
>>> I have tried both , 3-row and 3-column format and still
>>> wrong bvecc and bval
>>> from flip4fsl. Could you please send me a sample of your
>>> original files so I
>>> can compare?
>>>
>>>
>>> On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki
>>>  wrote:
>>>
>>>   Hi Amirhossein - Are your original bvecs/bvals in
>>> 3-row format
>>>   instead of 3-column format?
>>>
>>> http://surfer.nmr.mgh.harvard.**
>>> edu/fswiki/FsTutorial/Tracula
>>>
>>>   Thanks,
>>>   a.y
>>>
>>>   On Mon, 15 Jul 2013, amirhossein manzouri wrote:
>>>
>>> Dear Experts,
>>> I am running trac-all -prep -c dmrirc on my
>>> DWI
>>> data. After flip4fsl step I get the attached
>>> bval
>>> and bvec file which the bvec one is wrong so
>>> the
>>> process exits
>>> with error in dtifit. I have also attached
>>>  original
>>> bvec and bval.
>>>
>>> --
>>> Best regards,
>>> Amirhossein Manzouri
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> 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.
>>>
>>>
>>>
>>>
>>> --
>>> Best regards,
>>> Amirhossein Manzouri
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Best regards,
>>> Amirhossein Manzouri
>>>
>>>
>>>
>>>
>>>
>
>
> --
> Best regards,
> Amirhossein Manzouri
>
>
>
>


-- 
Best regards,
Amirhossein Manzouri
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Re: [Freesurfer] bvecs error from Tracula

[Anastasia Yendiki]

Hi Amirhossein - That fix applied only to the 5.1 version. I'd recommend 
using the 5.3 version for tracula. Are you getting a memory error, and if 
so with which version?


Thanks,
a.y

On Mon, 22 Jul 2013, amirhossein manzouri wrote:


Dear Anastasia, 
I am trying to download the dmri_5.1_snow_leopard.tar.gz from FreeSurfer
website to solve memory problem but it is not available. Would you please
check the source to the link? 


On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri
 wrote:
  The format of my bval file was wrong so I edited your file and
  tried and it worked, also bvec should be in three columns as you
  have mentioned before.


On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki
 wrote:

  Good to hear! Can you please share with all of us what was
  wrong with your original files? It may help others who
  have the same problem in the future. Thanks!

  On Wed, 17 Jul 2013, amirhossein manzouri wrote:

Thanks Anastasia, 
IT HELPED!


On Tue, Jul 16, 2013 at 5:25 PM, Anastasia
Yendiki 
wrote:

      Hi Amirhossein - I'm attaching sample
files.

      a.y

      On Tue, 16 Jul 2013, amirhossein
manzouri wrote:

            Hi Anastasia, 
            I have tried both , 3-row and
3-column format and still
            wrong bvecc and bval
            from flip4fsl. Could you please
send me a sample of your
            original files so I
            can compare?


            On Mon, Jul 15, 2013 at 7:44 PM,
Anastasia Yendiki
            
wrote:

                  Hi Amirhossein - Are your
original bvecs/bvals in
            3-row format
                  instead of 3-column format?
                 
           
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

                  Thanks,
                  a.y

                  On Mon, 15 Jul 2013,
amirhossein manzouri wrote:

                        Dear Experts, 
                        I am running trac-all
-prep -c dmrirc on my
            DWI
                        data. After flip4fsl
step I get the attached
            bval
                        and bvec file which
the bvec one is wrong so
            the
                        process exits
                        with error in dtifit.
I have also attached
             original
                        bvec and bval.

                        --
                        Best regards,
                        Amirhossein Manzouri 

                         





            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.




            --
            Best regards,
            Amirhossein Manzouri 

             





--
Best regards,
Amirhossein Manzouri 

 





--
Best regards,
Amirhossein Manzouri 

 




--
Best regards,
Amirhossein Manzouri 

 


___
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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] bvecs error from Tracula

[amirhossein manzouri]

Hi,
Yes I am getting the memory error with version 5.3, exactly the one that is
reported in this link:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.html
Thanks,


On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Amirhossein - That fix applied only to the 5.1 version. I'd recommend
> using the 5.3 version for tracula. Are you getting a memory error, and if
> so with which version?
>
> Thanks,
> a.y
>
>
> On Mon, 22 Jul 2013, amirhossein manzouri wrote:
>
>  Dear Anastasia,
>> I am trying to download the dmri_5.1_snow_leopard.tar.**gz from
>> FreeSurfer
>> website to solve memory problem but it is not available. Would you please
>> check the source to the link?
>>
>>
>> On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri
>>  wrote:
>>   The format of my bval file was wrong so I edited your file and
>>   tried and it worked, also bvec should be in three columns as you
>>   have mentioned before.
>>
>>
>> On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Good to hear! Can you please share with all of us what was
>>   wrong with your original files? It may help others who
>>   have the same problem in the future. Thanks!
>>
>>   On Wed, 17 Jul 2013, amirhossein manzouri wrote:
>>
>> Thanks Anastasia,
>> IT HELPED!
>>
>>
>> On Tue, Jul 16, 2013 at 5:25 PM, Anastasia
>> Yendiki 
>> wrote:
>>
>>   Hi Amirhossein - I'm attaching sample
>> files.
>>
>>   a.y
>>
>>   On Tue, 16 Jul 2013, amirhossein
>> manzouri wrote:
>>
>> Hi Anastasia,
>> I have tried both , 3-row and
>> 3-column format and still
>> wrong bvecc and bval
>> from flip4fsl. Could you please
>> send me a sample of your
>> original files so I
>> can compare?
>>
>>
>> On Mon, Jul 15, 2013 at 7:44 PM,
>> Anastasia Yendiki
>> 
>> wrote:
>>
>>   Hi Amirhossein - Are your
>> original bvecs/bvals in
>> 3-row format
>>   instead of 3-column format?
>>
>>
>> 
>> http://surfer.nmr.mgh.harvard.**edu/fswiki/FsTutorial/Tracula
>>
>>   Thanks,
>>   a.y
>>
>>   On Mon, 15 Jul 2013,
>> amirhossein manzouri wrote:
>>
>> Dear Experts,
>> I am running trac-all
>> -prep -c dmrirc on my
>> DWI
>> data. After flip4fsl
>> step I get the attached
>> bval
>> and bvec file which
>> the bvec one is wrong so
>> the
>> process exits
>> with error in dtifit.
>> I have also attached
>>  original
>> bvec and bval.
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>
>>
>>
>> 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.
>>
>>
>>
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>
>>
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>
>>
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>


-- 
Best regards,
Amirhossein Manzou

Re: [Freesurfer] bvecs error from Tracula

[amirhossein manzouri]

Hi,
The content is : freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
Can it help?


On Mon, Jul 22, 2013 at 10:31 PM, Z K  wrote:

> Hello Amirhossein,
>
> Can you please provide me with the contents of build-stamp.txt in the
> /Applications/freesurfer directory?
>
> -Zeke
>
>
> On 07/22/2013 04:23 PM, amirhossein manzouri wrote:
>
>> Hi,
>> Yes I am getting the memory error with version 5.3, exactly the one that
>> is reported in this link:
>> https://mail.nmr.mgh.harvard.**edu/pipermail//freesurfer/**
>> 2011-July/019392.html
>> Thanks,
>>
>>
>> On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki
>> > >
>> wrote:
>>
>>
>> Hi Amirhossein - That fix applied only to the 5.1 version. I'd
>> recommend using the 5.3 version for tracula. Are you getting a
>> memory error, and if so with which version?
>>
>> Thanks,
>> a.y
>>
>>
>> On Mon, 22 Jul 2013, amirhossein manzouri wrote:
>>
>> Dear Anastasia,
>> I am trying to download the dmri_5.1_snow_leopard.tar.__gz from
>>
>> FreeSurfer
>> website to solve memory problem but it is not available. Would
>> you please
>> check the source to the link?
>>
>>
>> On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri
>> mailto:a.h.manzo...@gmail.com**>> wrote:
>>The format of my bval file was wrong so I edited your
>> file and
>>tried and it worked, also bvec should be in three columns
>> as you
>>have mentioned before.
>>
>>
>> On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki
>> > 
>> >
>> wrote:
>>
>>Good to hear! Can you please share with all of us what was
>>wrong with your original files? It may help others who
>>have the same problem in the future. Thanks!
>>
>>On Wed, 17 Jul 2013, amirhossein manzouri wrote:
>>
>>  Thanks Anastasia,
>>  IT HELPED!
>>
>>
>>  On Tue, Jul 16, 2013 at 5:25 PM, Anastasia
>>  Yendiki > > >>
>>
>>  wrote:
>>
>>Hi Amirhossein - I'm attaching sample
>>  files.
>>
>>a.y
>>
>>On Tue, 16 Jul 2013, amirhossein
>>  manzouri wrote:
>>
>>  Hi Anastasia,
>>  I have tried both , 3-row and
>>  3-column format and still
>>  wrong bvecc and bval
>>  from flip4fsl. Could you please
>>  send me a sample of your
>>  original files so I
>>  can compare?
>>
>>
>>  On Mon, Jul 15, 2013 at 7:44 PM,
>>  Anastasia Yendiki
>>  > > >>
>>
>>  wrote:
>>
>>Hi Amirhossein - Are your
>>  original bvecs/bvals in
>>  3-row format
>>instead of 3-column format?
>>
>>
>> http://surfer.nmr.mgh.harvard.**__edu/fswiki/FsTutorial/**Tracula
>>
>> 
>> 
>> >
>>
>>Thanks,
>>a.y
>>
>>On Mon, 15 Jul 2013,
>>  amirhossein manzouri wrote:
>>
>>  Dear Experts,
>>  I am running trac-all
>>  -prep -c dmrirc on my
>>  DWI
>>  data. After flip4fsl
>>  step I get the attached
>>  bval
>>  and bvec file which
>>  the bvec one is wrong so
>>  the
>>  process exits
>>  with error in dtifit.
>>  I have also attached
>>   original
>>  bvec and bval.
>>
>>  --
>>  Best regards,
>>  Amirhossein Manzouri
>>
>>
>>
>>
>>
>>

Re: [Freesurfer] bvecs error from Tracula

[amirhossein manzouri]

Hi ZeKe,
I am getting this error during Tracula procedure somewhere between
bbregister!
BR
On Jul 24, 2013 5:42 PM, "Z K"  wrote:

> Hello Amir,
>
> According to the log file you've attached, recon-all finished to
> completion without any errors. Are you sure you are encountering a memory
> error? If so, why?
>
> -Zeke
>
> On 07/24/2013 11:28 AM, amirhossein manzouri wrote:
>
>> Kindly find attached the recon-all.log
>>
>>
>> On Wed, Jul 24, 2013 at 4:50 PM, Z K > >
>> wrote:
>>
>> Hello Amir,
>>
>> Thanks for that... could you also please provide the recon-all.log
>> file? It will be located in
>> $SUBJECT_DIR/subject_name/__**scripts/recon-all.log
>>
>> -Zeke
>>
>>
>> On 07/24/2013 03:01 AM, amirhossein manzouri wrote:
>>
>> Hi,
>> The content is :
>> freesurfer-Darwin-snowleopard-**__i686-stable-pub-v5.3.0
>> Can it help?
>>
>>
>> On Mon, Jul 22, 2013 at 10:31 PM, Z K
>> mailto:zkauf...@nmr.mgh.**
>> harvard.edu >
>> 
>> 
>> >>
>> wrote:
>>
>>  Hello Amirhossein,
>>
>>  Can you please provide me with the contents of
>> build-stamp.txt in
>>  the /Applications/freesurfer directory?
>>
>>  -Zeke
>>
>>
>>  On 07/22/2013 04:23 PM, amirhossein manzouri wrote:
>>
>>  Hi,
>>  Yes I am getting the memory error with version 5.3,
>> exactly the
>>  one that
>>  is reported in this link:
>> https://mail.nmr.mgh.harvard._**___edu/pipermail//freesurfer/_**
>> ___2011-July/019392.html
>>
>>
>> > 2011-July/019392.html
>> > 2011-July/019392.html
>> >>
>>  Thanks,
>>
>>
>>  On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki
>>  > > >
>>  
>> > >>
>>  > __ha**r__vard.edu<
>> http://harvard.edu>
>>
>>  
>> 
>> > wrote:
>>
>>
>>   Hi Amirhossein - That fix applied only to the 5.1
>> version. I'd
>>   recommend using the 5.3 version for tracula. Are
>> you getting a
>>   memory error, and if so with which version?
>>
>>   Thanks,
>>   a.y
>>
>>
>>   On Mon, 22 Jul 2013, amirhossein manzouri wrote:
>>
>>   Dear Anastasia,
>>   I am trying to download the
>>  dmri_5.1_snow_leopard.tar.__gz from
>>
>>   FreeSurfer
>>   website to solve memory problem but it is not
>>  available. Would
>>   you please
>>   check the source to the link?
>>
>>
>>   On Wed, Jul 17, 2013 at 5:51 PM, amirhossein
>> manzouri
>>   >  > __>
>>  > 
>>
>>  > __>__>> wrote:
>>  The format of my bval file was wrong so
>> I edited
>>  your
>>   file and
>>  tried and it worked, also bvec should be
>> in
>>  three columns
>>   as you
>>  have mentioned before.
>>
>>
>>   On Wed, Jul 17, 2013 at 5:11 PM, Anastasia
>> Yendiki
>>   > > >
>>  
>> > >>
>>   > __ha**r__vard.edu<
>> http://harvard.edu>
>>
>>  
>> 
>> > wrote:
>>
>>  Go

Re: [Freesurfer] bvecs error from Tracula

[Anastasia Yendiki]

Hi Amirhossein - If your error happens when bbregister is run, then it's 
not the error that the dmri_5.1_snow_leopard.tar.gz fix was meant to 
address. In any case that fix is not relevant to you b/c you're using 5.3 
and not 5.1. Can you please send your trac-all.log to establish where 
exactly the error is happening?


Thanks,
a.y

On Thu, 25 Jul 2013, amirhossein manzouri wrote:



Hi ZeKe,
I am getting this error during Tracula procedure somewhere between
bbregister!
BR

On Jul 24, 2013 5:42 PM, "Z K"  wrote:
  Hello Amir,

  According to the log file you've attached, recon-all finished to
  completion without any errors. Are you sure you are encountering
  a memory error? If so, why?

  -Zeke

  On 07/24/2013 11:28 AM, amirhossein manzouri wrote:
Kindly find attached the recon-all.log


On Wed, Jul 24, 2013 at 4:50 PM, Z K
mailto:zkauf...@nmr.mgh.harvard.edu>> wrote:

    Hello Amir,

    Thanks for that... could you also please provide
the recon-all.log
    file? It will be located in
   
$SUBJECT_DIR/subject_name/__scripts/recon-all.log

    -Zeke


    On 07/24/2013 03:01 AM, amirhossein manzouri
wrote:

        Hi,
        The content is :
       
freesurfer-Darwin-snowleopard-__i686-stable-pub-v5.3.0
        Can it help?


        On Mon, Jul 22, 2013 at 10:31 PM, Z K
        mailto:zkauf...@nmr.mgh.harvard.edu>
        >>
wrote:

             Hello Amirhossein,

             Can you please provide me with the
contents of
        build-stamp.txt in
             the /Applications/freesurfer directory?

             -Zeke


             On 07/22/2013 04:23 PM, amirhossein
manzouri wrote:

                 Hi,
                 Yes I am getting the memory error
with version 5.3,
        exactly the
                 one that
                 is reported in this link:
       
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/01
9392.html


       
>
                 Thanks,


                 On Mon, Jul 22, 2013 at 8:15 PM,
Anastasia Yendiki
                 mailto:ayend...@nmr.mgh.harvard.edu>
               
 >
                 __har__vard.edu


               
 
__>
                 

                 __>__>>
wrote:
                                 The format of my
 

Re: [Freesurfer] bvecs error from Tracula

[Anastasia Yendiki]

Hi Amirhossein - The memory error doesn't occur when bbregister is 
running, but when dmri_train is running and loading the atlas data. You 
seem to have the snow leopard version of freesurfer installed, based on 
your build stamp (freesurfer-Darwin-snowleopard-__i686-stable-pub-v5.3.0). 
What version of the operating system do you have on your computer and how 
much memory?


Thanks,
a.y

On Mon, 29 Jul 2013, amirhossein manzouri wrote:


Hi, 
Kindly find attched the trac-all.log !


On Thu, Jul 25, 2013 at 6:25 PM, Anastasia Yendiki
 wrote:

  Hi Amirhossein - If your error happens when bbregister is run,
  then it's not the error that the dmri_5.1_snow_leopard.tar.gz
  fix was meant to address. In any case that fix is not relevant
  to you b/c you're using 5.3 and not 5.1. Can you please send
  your trac-all.log to establish where exactly the error is
  happening?

  Thanks,
  a.y

  On Thu, 25 Jul 2013, amirhossein manzouri wrote:


Hi ZeKe,
I am getting this error during Tracula procedure
somewhere between
bbregister!
BR

On Jul 24, 2013 5:42 PM, "Z K"
 wrote:
      Hello Amir,

      According to the log file you've attached,
recon-all finished to
      completion without any errors. Are you sure
you are encountering
      a memory error? If so, why?

      -Zeke

      On 07/24/2013 11:28 AM, amirhossein manzouri
wrote:
            Kindly find attached the recon-all.log


            On Wed, Jul 24, 2013 at 4:50 PM, Z K
            mailto:zkauf...@nmr.mgh.harvard.edu>>
wrote:

                Hello Amir,

                Thanks for that... could you also
please provide
            the recon-all.log
                file? It will be located in
               
           
$SUBJECT_DIR/subject_name/__scripts/recon-all.log

                -Zeke


                On 07/24/2013 03:01 AM, amirhossein
manzouri
            wrote:

                    Hi,
                    The content is :
                   
           
freesurfer-Darwin-snowleopard-__i686-stable-pub-v5.3.0
                    Can it help?


                    On Mon, Jul 22, 2013 at 10:31
PM, Z K
                    mailto:zkauf...@nmr.mgh.harvard.edu>
                   
>>
            wrote:

                         Hello Amirhossein,

                         Can you please provide me
with the
            contents of
                    build-stamp.txt in
                         the
/Applications/freesurfer directory?

                         -Zeke


                         On 07/22/2013 04:23 PM,
amirhossein
            manzouri wrote:

                             Hi,
                             Yes I am getting the
memory error
            with version 5.3,
                    exactly the
                             one that
                             is reported in this
link:
                  
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/0
1
            9392.html


                  
>
                             Thanks,


                             On Mon, Jul 22, 2013 at
8:15 PM,
            Anastasia Yendiki
                           
 mailto:ayend...@nmr.mgh.harvard.edu>
                           
             >
                           
 __har__vard.edu