Re: [Freesurfer] HippocampalSubfields only generates lh

2016-01-21 Thread Eugenio Iglesias 
Hi Jiook, 
the log file says that the analysis of the left side did complete. Were the 
output files written? 
Cheers, 
Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Jiook Cha"  
To: "iglesias"  
Cc: "Freesurfer support list"  
Sent: Wednesday, January 20, 2016 2:16:36 AM 
Subject: HippocampalSubfields only generates lh 

Hi Iglesias, 

I recently tried HippocampalSubfields in freesurfer 6.0. It only completed 
hippocampal segmentation for the left hemisphere, but not the right. 

Under scripts folder, recon-all.error says: 
/ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/recon-all 
PWD /ifs/scratch/pimri/posnerlab/1anal/osa/fs2/B03/label 
CMD /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/segmentSF_T1.sh 
/ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/MCRv80 
/ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer B03 
/ifs/scratch/pimri/posnerlab/1anal/osa/fs2 left 

So it seems as left hippocampus failed the pipeline didn’t try the right 
hippocampus. 

Attached is hippocampal-subfields-T1.log. Do you have any idea what’s happening 
here? 












Best, 

Jiook 






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Re: [Freesurfer] HippocampalSubfields only generates lh

2016-01-21 Thread Eugenio Iglesias 
Sorry, it wasn't clear from the previous email whether the left hemi had 
completed or not. 
Can you please send me the recon-all log file? 
Cheers, 
/E 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Jiook Cha"  
To: "Eugenio Iglesias"  
Cc: "iglesias" , "Freesurfer support list" 
 
Sent: Thursday, January 21, 2016 12:32:46 PM 
Subject: Re: HippocampalSubfields only generates lh 

Yes they were. 



On Jan 21, 2016, at 06:14, Eugenio Iglesias < e.igles...@bcbl.eu > wrote: 




Hi Jiook, 
the log file says that the analysis of the left side did complete. Were the 
output files written? 
Cheers, 
Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Jiook Cha" < cha.ji...@gmail.com > 
To: "iglesias" < igles...@nmr.mgh.harvard.edu > 
Cc: "Freesurfer support list" < freesurfer@nmr.mgh.harvard.edu > 
Sent: Wednesday, January 20, 2016 2:16:36 AM 
Subject: HippocampalSubfields only generates lh 

Hi Iglesias, 

I recently tried HippocampalSubfields in freesurfer 6.0. It only completed 
hippocampal segmentation for the left hemisphere, but not the right. 

Under scripts folder, recon-all.error says: 
/ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/recon-all 
PWD /ifs/scratch/pimri/posnerlab/1anal/osa/fs2/B03/label 
CMD /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/segmentSF_T1.sh 
/ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/MCRv80 
/ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer B03 
/ifs/scratch/pimri/posnerlab/1anal/osa/fs2 left 

So it seems as left hippocampus failed the pipeline didn’t try the right 
hippocampus. 

Attached is hippocampal-subfields-T1.log. Do you have any idea what’s happening 
here? 












Best, 

Jiook 






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. 



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Re: [Freesurfer] HippocampalSubfields only generates lh

2016-01-21 Thread Jiook Cha 
Yes they were. 



> On Jan 21, 2016, at 06:14, Eugenio Iglesias  wrote:
> 
> Hi Jiook,
> the log file says that the analysis of the left side did complete. Were the 
> output files written?
> Cheers,
> Eugenio
> 
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
> 
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
> 
> From: "Jiook Cha" 
> To: "iglesias" 
> Cc: "Freesurfer support list" 
> Sent: Wednesday, January 20, 2016 2:16:36 AM
> Subject: HippocampalSubfields only generates lh
> 
> Hi Iglesias,
> 
> I recently tried HippocampalSubfields in freesurfer 6.0. It only completed 
> hippocampal segmentation for the left hemisphere, but not the right. 
> 
> Under scripts folder, recon-all.error says:
>   /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/recon-all
> PWD /ifs/scratch/pimri/posnerlab/1anal/osa/fs2/B03/label
> CMD 
> /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/segmentSF_T1.sh 
> /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/MCRv80 
> /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer B03 
> /ifs/scratch/pimri/posnerlab/1anal/osa/fs2 left
> 
> So it seems as left hippocampus failed the pipeline didn’t try the right 
> hippocampus.
> 
> Attached is hippocampal-subfields-T1.log. Do you have any idea what’s 
> happening here?
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Best,
> 
> Jiook
> 
> 
> 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.
> 
> 
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The information in this e-mail is intended only for the person to whom it is
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