Yes, you have so specify it separately. Cheers, /Eugenio
Juan Eugenio Iglesias Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 19 Sep 2016, at 14:13, pierre deman <deman.pie...@gmail.com<mailto:deman.pie...@gmail.com>> wrote: Hi, I have a short question about the additional T2 scan as well. If I perform the full recon-all; recon-all -s mySubject -i myT1.nii -T2 myT2.nii -T2pial -all -hippocampal-subfields-T1T2 do I still have to precise myT2scan.nii.gz T2 for using the t2 for the hippocampal subfields as well ? or it will automatically take the t2 precised for the t2pial ? Cheers, Pierre On Mon, Sep 5, 2016 at 4:13 PM, Iglesias, Eugenio <e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>> wrote: The same one; just change the input file and the analysis ID - T2: recon-all -s mySubject -hippocampal-subfields-T1T2 myT2scan.nii.gz T2 - FLAIR: recon-all -s mySubject -hippocampal-subfields-T1T2 myFLAIRscan.nii.gz FLAIR Cheers, /Eugenio Juan Eugenio Iglesias Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com<http://www.jeiglesias.com/> http://cmictig.cs.ucl.ac.uk/ On 5 Sep 2016, at 15:10, Vaz pandolfo, Renata <r...@njit.edu<mailto:r...@njit.edu>> wrote: Dear FS experts, I have a question about the "segmentation with an additional scan - multispectral segmentation" on the hippocampal sf segmentation, FS dev. 6.0. For controls on which I had already run recon-all -all, I added the T2 sequence with the following command: recon-all -s <subject_name> \ -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID> Now, if I want to do the same thing with FLAIR as the additional input, which flag should I use? Thank you, Renata _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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. -- DEMAN Pierre Mobile : +33 7 82 57 80 94
_______________________________________________ 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.
