Hi Bruce,


Sure, please see highlighted below part of screen output showing the error. Since I ran the command within a screen sesison I have saved executed screen session to a log file. Find attached log file with output of entire run. Please let me know if any other files are required and if attached log file could be interpreted.


Read individual LTAs
Writing  LTA to file ped1_base_to_ped1_0.lta...
mri_concatenate_lta successful.

 mri_concatenate_lta -invert1 ped1_1_to_ped1_base.lta identity.nofile ped1_base_to_ped1_1.lta

invert the first LTA before applying it
Read individual LTAs
Writing  LTA to file ped1_base_to_ped1_1.lta...  
mri_concatenate_lta successful.

 mri_concatenate_lta -invert1 ped1_2_to_ped1_base.lta identity.nofile ped1_base_to_ped1_2.lta

invert the first LTA before applying it
Read individual LTAs
Writing  LTA to file ped1_base_to_ped1_2.lta...  
mri_concatenate_lta successful.

 mri_concatenate_lta -invert1 ped1_3_to_ped1_base.lta identity.nofile ped1_base_to_ped1_3.lta

invert the first LTA before applying it
Read individual LTAs
Writing  LTA to file ped1_base_to_ped1_3.lta...  
mri_concatenate_lta successful.

 mri_concatenate_lta -invert1 ped1_4_to_ped1_base.lta identity.nofile ped1_base_to_ped1_4.lta

invert the first LTA before applying it
Read individual LTAs
Writing  LTA to file ped1_base_to_ped1_4.lta...  
mri_concatenate_lta successful.
#--------------------------------------------
#@# MotionCor Wed Jul 26 14:04:13 EDT 2017

 mri_add_xform_to_header -c /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/talairach.xfm /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/orig.mgz /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/orig.mgz

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Wed Jul 26 14:04:14 EDT 2017
/shared_data2/sneha/MSKCC_Processed/ped1_base/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

Linux gizmo 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s ped1_base exited with ERRORS at Wed Jul 26 14:04:17 EDT 2017

For more details, see the log file /shared_data2/sneha/MSKCC_Processed/ped1_base/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Thanks,

Sneha

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Sent: Monday, August 7, 2017 2:02:27 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case
 
Hi Sneha

can you include the output as text instead of an image?

thanks
Bruce
On Mon, 7 Aug 2017,
Sneha Pandya wrote:

>
> Hi Bruce,
>
>
> Please find attached recon-all.log file and I used following command to run the base:
>
>
> recon-all -base ped1_base -tp ped1_0 -tp ped1_1 -tp ped1_2 -tp ped1_3 -tp ped1_4 -all
>
>
> Following is the screen shot of output showing the error:
>
> [IMAGE]
>
> Thanks,
> Sneha
>
> ________________________________________________________________________________________________________________________________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> Sent: Monday, August 7, 2017 1:43:01 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case  
> Hi Sneha
>
> can you send us the commad you ran and the full screen output inluding
> the error and also the recon-all.log?
>
> cheers
> Bruce
>
> On Mon, 7
> Aug 2017, Sneha Pandya wrote:
>
> >
> > Dear team,
> >
> >
> > I have completed cross-sectional pipeline on my pediatric case with a baseline and 4 follow up time points between 4-7 years of age. However, I was not able
> to
> > run longitudinal pipeline on it as the base template creation failed with some topological errors. I assume this failure is due to large eTIV changes within
> 4-7
> > years of age.
> >
> >
> > I wanted to compare cortical thickness map of follow-up time points to its baseline using qdec. However, I was not able to as running qdec with single subject
> > failed with 0 dof error. Can you'll please suggest how can I generate cortical thickness map between follow-up and baseline scans for this subject if qdec is
> > not an option.
> >
> >
> > Thanks,
> >
> > Sneha
> >
> >
> >
> >
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