Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}
Thanks for the quick reply. I'll re-run my subjects with the -FLAIR flag.
Joe
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 02 February 2017 22:56 To: Freesurfer support list Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6)
Hi Joe
there are slight differences, and for sure we reserve the right to use the knowledge that it is a FLAIR scan in the algorithms, so you should probably rerun
cheers Bruce On Thu, 2 Feb 2017, Joe Necus (PGR) wrote:
Hello,
I am running recon-all on the latest version of freesurfer (Version 6) and would like to know whether there is any difference between using the -T2 -T2Pial and -Flair flags.
I am currently running recon-all with a T1 and FLAIR image, but have used the -T2 -T2pial flags and would like to know whether I need to go back and instead re-run with the -FLAIR flag instead.
Thanks a lot,
Joe
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - Harvard Universityhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
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 mycompliancereport.comhttp://www.partners.org/complianceline www.partners.org ComplianceLine engages in the business of providing 24-hour toll-free hotlines for the reporting and tracking of compliance concerns to assist in the identification of possible unethical, illegal or questionable behavior.
but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Erik
Eugenio can confirm, but I don't think the subfield stuff cares. The -hippocampal-subfields-T1T2 means use multiple inputs, but it doesn't assume anything about the distribution of intensities in them.
cheers Bruce On Fri, 3 Feb 2017, Erik O'Hanlon wrote:
Hi Experts,
Just flowing on from Joe's question, I have run my analysis without the T2 or FLAIR flag but have specificed the T2 which is a FLAIR image for the hippocampal subfield options. I have used
recon-all -all -3T -s /sub008 -hippocampal-subfields-T1T2 /sub008/sub_008_T2.nii.gz T2Flair
Should I have used -hippocampal-subfields-T1FLAIR instead? Can I change this and simply rerun without the need to do everything from scratch. I have T2 and FLAIR images that I havent used for pial correction, can I add that in too and if so which is best teh T2 or the FLAIR or both?
Thanks and as always, really appreciate the help
Cheers
Erik
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Joe Necus (PGR) [J.Necus2@newcastle.ac.uk] Sent: 03 February 2017 10:56 To: Freesurfer support list Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}
Thanks for the quick reply. I'll re-run my subjects with the -FLAIR flag.
Joe
Erik O'Hanlon Postdoctoral researcher
[IMAGE]
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 02 February 2017 22:56 To: Freesurfer support list Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) Hi Joe
there are slight differences, and for sure we reserve the right to use the knowledge that it is a FLAIR scan in the algorithms, so you should probably rerun
cheers Bruce On Thu, 2 Feb 2017, Joe Necus (PGR) wrote:
Hello,
I am running recon-all on the latest version of freesurfer (Version 6) and would like to know whether there is any difference between using the -T2 -T2Pial and -Flair flags.
I am currently running recon-all with a T1 and FLAIR image, but have used the -T2 -T2pial flags and would like to know whether I need to go back and instead re-run with the -FLAIR flag instead.
Thanks a lot,
Joe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - Harvard University mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
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 MailScanner has detected a possible fraud attempt from "www.partners.org" claiming to be mycompliancereport.com www.partners.org ComplianceLine engages in the business of providing 24-hour toll-free hotlines for the reporting and tracking of compliance concerns to assist in the identification of possible unethical, illegal or questionable behavior.
but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Thanks Bruce,
Much appreciated
Best regards
Erik ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 03 February 2017 15:18 To: Freesurfer support list Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}
Hi Erik
Eugenio can confirm, but I don't think the subfield stuff cares. The -hippocampal-subfields-T1T2 means use multiple inputs, but it doesn't assume anything about the distribution of intensities in them.
cheers Bruce On Fri, 3 Feb 2017, Erik O'Hanlon wrote:
Hi Experts,
Just flowing on from Joe's question, I have run my analysis without the T2 or FLAIR flag but have specificed the T2 which is a FLAIR image for the hippocampal subfield options. I have used
recon-all -all -3T -s /sub008 -hippocampal-subfields-T1T2 /sub008/sub_008_T2.nii.gz T2Flair
Should I have used -hippocampal-subfields-T1FLAIR instead? Can I change this and simply rerun without the need to do everything from scratch. I have T2 and FLAIR images that I havent used for pial correction, can I add that in too and if so which is best teh T2 or the FLAIR or both?
Thanks and as always, really appreciate the help
Cheers
Erik
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Joe Necus (PGR) [J.Necus2@newcastle.ac.uk] Sent: 03 February 2017 10:56 To: Freesurfer support list Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}
Thanks for the quick reply. I'll re-run my subjects with the -FLAIR flag.
Joe
Erik O'Hanlon Postdoctoral researcher
[IMAGE]
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 02 February 2017 22:56 To: Freesurfer support list Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) Hi Joe
there are slight differences, and for sure we reserve the right to use the knowledge that it is a FLAIR scan in the algorithms, so you should probably rerun
cheers Bruce On Thu, 2 Feb 2017, Joe Necus (PGR) wrote:
Hello,
I am running recon-all on the latest version of freesurfer (Version 6) and would like to know whether there is any difference between using the -T2 -T2Pial and -Flair flags.
I am currently running recon-all with a T1 and FLAIR image, but have used the -T2 -T2pial flags and would like to know whether I need to go back and instead re-run with the -FLAIR flag instead.
Thanks a lot,
Joe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - Harvard University mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
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 MailScanner has detected a possible fraud attempt from "www.partners.org" claiming to be mycompliancereport.com www.partners.org ComplianceLine engages in the business of providing 24-hour toll-free hotlines for the reporting and tracking of compliance concerns to assist in the identification of possible unethical, illegal or questionable behavior.
but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi! recon-all -all -3T -s /sub008 -hippocampal-subfields-T1T2 /sub008/sub_008_T2.nii.gz T2Flair looks good. The flag -hippocampal-subfields-T1FLAIR does not even exist ;-) Cheers, /Eugenio
Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
On 3 Feb 2017, at 11:32, Erik O'Hanlon <erikohanlon@rcsi.iemailto:erikohanlon@rcsi.ie> wrote:
recon-all -all -3T -s /sub008 -hippocampal-subfields-T1T2 /sub008/sub_008_T2.nii.gz T2Flair
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Erik O'Hanlon -
Iglesias Gonzalez, Eugenio -
Joe Necus (PGR)