[Freesurfer] asking for literature
Hello, Could anybody please point me to a paper/asbtract showing meaningful improvement of pial surface segmentation using additional T2 or Flair images in the recon-all procedure? Thanks, Jiook ᐧ ___ 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.
[Freesurfer] hippocampal subfields analysis took 10 min
Dear Eugenio, I had to run the hippocampal subfield segmentation analysis in Freesurfer v6 manually by running segmentSF_T1.sh program. When I call it through recon-all, it only processed the left hemisphere but not the right. The issue is that running segmentSF only took 10 min per hemisphere. I didn't use multicores. Although the analysis resulted in all the files correctly, I am just concerned if running this manually completed the analysis prematurely. Sincerely, Jiook ᐧ ___ 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 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.
[Freesurfer] Post-doctoral Research Position at Columbia University
Post-doctoral Research Position at Columbia University A postdoctoral research position is currently available at Columbia University and the New York State Psychiatric Institute. Candidates must have completed a PhD in clinical, developmental, or cognitive neuroscience, or a related field. Research focuses on translational and developmental neuroimaging. Candidate should be interested in multimodal MRI techniques, attentional and related disorders in children and young adults, and the development of biomarkers of treatment response. Candidates with experience in the following areas are preferred: a) Computer programming skills (e.g., in C/C++, Python, MATLAB) b) Facility in operating of one or more common neuroimaging packages (e.g., AFNI, FSL, or SPM) Applicants should email their CV to Jonathan Posner, MD: jep2...@columbia.edu ___ 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.
