Re: [Freesurfer] HippocampalSubfields only generates lh
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. ___ 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.
Re: [Freesurfer] HippocampalSubfields only generates lh
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. ___ 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.
Re: [Freesurfer] HippocampalSubfields only generates lh
Yes they were. > On Jan 21, 2016, at 06:14, Eugenio Iglesiaswrote: > > 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. > > ___ 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.