Re: [Freesurfer] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
Hi Yoon - The update is here: http://freesurfer.net/fswiki/Tracula#Updates There will also be a new freesurfer release in the next couple of months, but I don't anticipate making more changes to longitudinal tracula before that, so this should be the same as in the future 5.4 version. a.y On Wed, 23 Jul 2014, Yoonho Chung wrote: Thank you for your input. Before we go ahead and reprocess our recon and DTI data with FS v 5.3 we were wondering if you plan an update on the TRACULA DTI longitudinal stream anytime soon. I think I saw somewhere in the email chain that this is likely to happen soon with additional features and bug fixes. If so, I think it would be worth the wait. Thank you! Yoon On May 22, 2014, at 5:37 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Yoon - If you are getting an error from longitudinal tracula, do check the tracula updates at the link that I gave you in my previous email. As for 5.2 recon-all, others can chime in here, but like I said it is not recommended to use it. Sorry about that. a.y On Thu, 22 May 2014, Yoonho Chung wrote: Thanks for the quick response! If I already have all the T1 data processed using recon-all with FS v5.2, do you think it is okay to switch the stream to FS v.5.3 and run Tracula? - without having to do the recon-all again for the T1 data? It is because I am also experiencing DTI longitudinal error due to the OS issue (according to other threads). And if possible, I would like to avoid having to redo all the recons if we have to switch it to v5.3. Thanks again! Yoon 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
Re: [Freesurfer] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
Hi Yoon - No, in the current code the assumption is that the b-values are the same for all subjects in the study. One scenario where this wouldn't be the case is if different DWI volumes are removed for different subjects because of excessive motion, and we'll be able to handle this in the next version. a.y On Fri, 30 May 2014, Chung, Yoonho wrote: Thanks for the tip. Another question. In the dmrirc file, can we also define multiple bval file? (like how in the example-dmrirc long- you can set multiple bvecs.txt using 'set bveclist'? In the example, option for specifying multiple bval files is not shown. Thank you Yoon On May 22, 2014, at 5:37 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Yoon - If you are getting an error from longitudinal tracula, do check the tracula updates at the link that I gave you in my previous email. As for 5.2 recon-all, others can chime in here, but like I said it is not recommended to use it. Sorry about that. a.y On Thu, 22 May 2014, Yoonho Chung wrote: Thanks for the quick response! If I already have all the T1 data processed using recon-all with FS v5.2, do you think it is okay to switch the stream to FS v.5.3 and run Tracula? - without having to do the recon-all again for the T1 data? It is because I am also experiencing DTI longitudinal error due to the OS issue (according to other threads). And if possible, I would like to avoid having to redo all the recons if we have to switch it to v5.3. Thanks again! Yoon 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
Re: [Freesurfer] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
Thanks for the tip. Another question. In the dmrirc file, can we also define multiple bval file? (like how in the example-dmrirc long- you can set multiple bvecs.txt using 'set bveclist'? In the example, option for specifying multiple bval files is not shown. Thank you Yoon On May 22, 2014, at 5:37 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Yoon - If you are getting an error from longitudinal tracula, do check the tracula updates at the link that I gave you in my previous email. As for 5.2 recon-all, others can chime in here, but like I said it is not recommended to use it. Sorry about that. a.y On Thu, 22 May 2014, Yoonho Chung wrote: Thanks for the quick response! If I already have all the T1 data processed using recon-all with FS v5.2, do you think it is okay to switch the stream to FS v.5.3 and run Tracula? - without having to do the recon-all again for the T1 data? It is because I am also experiencing DTI longitudinal error due to the OS issue (according to other threads). And if possible, I would like to avoid having to redo all the recons if we have to switch it to v5.3. Thanks again! Yoon 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
[Freesurfer] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
Hi Anastasia, I have a large set of freesurfer recons (T1) already processed through FS version 5.2 longitudinal stream while ago. However, I see now that there is an advantage of using Tracula 5.3 longitudinal stream for DTI longitudinal analysis. Do you know if I run the DWI data using 5.3 TRACULA longitudinal stream - if it will work with recons that are processed with 5.2? Thanks! Y ___ 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] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
Hi Yoonho - Tracula did not change at all between the 5.2 and 5.3 releases. It was recon-all that changed, and in fact 5.3 was released to correct a bug in 5.2, so it is not recommended to use 5.2 recon-all. For info about tracula versions, see: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates Hope this helps, a.y On Wed, 21 May 2014, Chung, Yoonho wrote: Hi Anastasia, I have a large set of freesurfer recons (T1) already processed through FS version 5.2 longitudinal stream while ago. However, I see now that there is an advantage of using Tracula 5.3 longitudinal stream for DTI longitudinal analysis. Do you know if I run the DWI data using 5.3 TRACULA longitudinal stream - if it will work with recons that are processed with 5.2? Thanks! Y ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
