Re: [Freesurfer] Tracula bedpostx error
Hi Prad - I'm guessing the tutorial was generated with an earlier version
of bedpostx, tracula, or a combination of both. So I wouldn't expect to
find the exact same values. As long as things run and the files are
generated, it looks like you're fine.
Best,
a.y
On Mon, 7 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote:
> Hi Anastasia,
>
> Thank you for clarifying that. I have a follow up question.
>
> To avoid this error while running the ball and stick model fit( Syntax error:
> "(" unexpected), I ran it locally using "bedpostx $path_to_dmri".
>
> The results of the overall path statistics differ from those in the tutorial.
> I've attached my results for the left ILF (pathstats.overall_redone.txt) and
> the tutorial results (pathstats.overall_original.txt)
>
> Is this difference due to running them on different machines or is because I
> had to run the bedpostx command directly ?
>
> Thanks!
> -Prad
> ___
>
> _
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia Yendiki
> <ayend...@nmr.mgh.harvard.edu>
> Sent: Monday, March 7, 2016 10:19 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Tracula bedpostx error
>
> Hi Prad - What will affect the speed is whether you run it locally on your
> computer (in which case it'll process one slice after the other) or on a
> cluster (in which case all the slices will be processed in parallel on
> different nodes of the cluster). This is the case regardless of the
> version that you use.
>
> Best,
>
> a.y
>
> On Sun, 6 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote:
>
>>
>>
>> Hello Anastasia,
>>
>> I have been trying to run through the tutorial with one of the subjects from
>> the tutorial(elmo.2008) to familiarize myself with Tracula.
>> The preprocessing step seems to have been completed without any errors (Log
>> file attached).However, when I proceed with the ball and stick model fit
>> step, I get the following error
>>
>> bedpostx_mgh -n 2 /home/biba1/testing_tracula/diffusion/elmo.2008/dmri
>> /apps/freesurfer/bin/bedpostx_mgh: 131: /apps/freesurfer/bin/bedpostx_mgh:
>> Syntax error: "(" unexpected. I'm running the tutorial locally on Ubuntu
>> 12.04 with FSL 5.0.9.
>>
>> In an earlier post where the same error was
>> encountered(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html)
>> you recommended
>> running bedpostx directly.
>>
>> Would this impact the results or run time in any way? and is there something
>> I can do to fix this error if it is likely to take much longer?
>>
>>
>> Thanks!
>>
>> -Prad
>>
>>
>>
>>
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Re: [Freesurfer] Tracula bedpostx error
Hi Anastasia,
Thank you for clarifying that. I have a follow up question.
To avoid this error while running the ball and stick model fit( Syntax error:
"(" unexpected), I ran it locally using "bedpostx $path_to_dmri".
The results of the overall path statistics differ from those in the tutorial.
I've attached my results for the left ILF (pathstats.overall_redone.txt) and
the tutorial results (pathstats.overall_original.txt)
Is this difference due to running them on different machines or is because I
had to run the bedpostx command directly ?
Thanks!
-Prad
___
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>
Sent: Monday, March 7, 2016 10:19 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula bedpostx error
Hi Prad - What will affect the speed is whether you run it locally on your
computer (in which case it'll process one slice after the other) or on a
cluster (in which case all the slices will be processed in parallel on
different nodes of the cluster). This is the case regardless of the
version that you use.
Best,
a.y
On Sun, 6 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote:
>
>
> Hello Anastasia,
>
> I have been trying to run through the tutorial with one of the subjects from
> the tutorial(elmo.2008) to familiarize myself with Tracula.
> The preprocessing step seems to have been completed without any errors (Log
> file attached).However, when I proceed with the ball and stick model fit
> step, I get the following error
>
> bedpostx_mgh -n 2 /home/biba1/testing_tracula/diffusion/elmo.2008/dmri
> /apps/freesurfer/bin/bedpostx_mgh: 131: /apps/freesurfer/bin/bedpostx_mgh:
> Syntax error: "(" unexpected. I'm running the tutorial locally on Ubuntu
> 12.04 with FSL 5.0.9.
>
> In an earlier post where the same error was
> encountered(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html)
> you recommended
> running bedpostx directly.
>
> Would this impact the results or run time in any way? and is there something
> I can do to fix this error if it is likely to take much longer?
>
>
> Thanks!
>
> -Prad
>
>
>
>
# Title Pathway Statistics
#
# generating_program /usr/local/freesurfer/dev/bin/dmri_pathstats
# cvs_version
# cmdline /usr/local/freesurfer/dev/bin/dmri_pathstats --intrc
/space/freesurfer/subjects/diffusion_tutorial/elmo.2008/dpath/lh.ilf_AS_avg33_mni_bbr
--dtbase /space/freesurfer/subjects/diffusion_tutorial/elmo.2008/dmri/dtifit
--path lh.ilf --subj elmo.2008 --out
/space/freesurfer/subjects/diffusion_tutorial/elmo.2008/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt
--outvox
/space/freesurfer/subjects/diffusion_tutorial/elmo.2008/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.byvoxel.txt
# sysname Linux
# hostname compute-0-29
# machine x86_64
# user ayendiki
# anatomy_type pathway
#
# subjectname elmo.2008
# pathwayname lh.ilf
#
Count 1500
Volume 902
Len_Min 36
Len_Max 83
Len_Avg 53.2167
Len_Center 54
AD_Avg 0.00137149
AD_Avg_Weight 0.00137135
AD_Avg_Center 0.00132052
RD_Avg 0.000618602
RD_Avg_Weight 0.000615934
RD_Avg_Center 0.000625125
MD_Avg 0.000869563
MD_Avg_Weight 0.000867741
MD_Avg_Center 0.000856922
FA_Avg 0.482952
FA_Avg_Weight 0.484575
FA_Avg_Center 0.453493
# Title Pathway Statistics
#
# generating_program /apps/freesurfer/bin/dmri_pathstats
# cvs_version
# cmdline /apps/freesurfer/bin/dmri_pathstats --intrc
/home/biba1/testing_tracula/diffusion/elmo.2008/dpath/lh.ilf_AS_avg33_mni_bbr
--dtbase /home/biba1/testing_tracula/diffusion/elmo.2008/dmri/dtifit --path
lh.ilf --subj elmo.2008 --out
/home/biba1/testing_tracula/diffusion/elmo.2008/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt
--outvox
/home/biba1/testing_tracula/diffusion/elmo.2008/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.byvoxel.txt
# sysname Linux
# hostname BIBAStation1
# machine x86_64
# user biba1
# anatomy_type pathway
#
# subjectname elmo.2008
# pathwayname lh.ilf
#
Count 1500
Volume 1261
Len_Min 33
Len_Max 86
Len_Avg 56.282
Len_Center 59
AD_Avg 0.00133899
AD_Avg_Weight 0.00133384
AD_Avg_Center 0.0013349
RD_Avg 0.000625518
RD_Avg_Weight 0.000628174
RD_Avg_Center 0.000615722
MD_Avg 0.000863341
MD_Avg_Weight 0.000863395
MD_Avg_Center 0.000855447
FA_Avg 0.463227
FA_Avg_Weight 0.459711
FA_Avg_Center 0.467562
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] Tracula bedpostx error
Hi Prad - What will affect the speed is whether you run it locally on your
computer (in which case it'll process one slice after the other) or on a
cluster (in which case all the slices will be processed in parallel on
different nodes of the cluster). This is the case regardless of the
version that you use.
Best,
a.y
On Sun, 6 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote:
Hello Anastasia,
I have been trying to run through the tutorial with one of the subjects from
the tutorial(elmo.2008) to familiarize myself with Tracula.
The preprocessing step seems to have been completed without any errors (Log
file attached).However, when I proceed with the ball and stick model fit
step, I get the following error
bedpostx_mgh -n 2 /home/biba1/testing_tracula/diffusion/elmo.2008/dmri
/apps/freesurfer/bin/bedpostx_mgh: 131: /apps/freesurfer/bin/bedpostx_mgh: Syntax error:
"(" unexpected. I'm running the tutorial locally on Ubuntu
12.04 with FSL 5.0.9.
In an earlier post where the same error was
encountered(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html)
you recommended
running bedpostx directly.
Would this impact the results or run time in any way? and is there something I
can do to fix this error if it is likely to take much longer?
Thanks!
-Prad
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
