Re: [Freesurfer] Longitudinal difference...
Hola Gonzalo, field strength affects T1, so different field strengths (e.g., 1.5T vs 3.0T) give somewhat different T1 contrast, which Freesurfer uses to estimate surfaces and boundaries to then thickness and volumes. You would have probably found also morphometric differences even if you would have scanned the same subject on the different scanners in a short time window, as we showed in Han et al., Neuroimage 2006 and Jovicich et al. Neuroimage 2009. For both cross-sectional and longitudinal studies it is adviced to not mix MRI field strengths. Best, Jorge On 19/05/2015 20:36, Gonzalo Rojas Costa wrote: Hi: We have GE 1.5T MRI fspgr volumetric acquisition of a MS patient (39 years old) and a Siemens 3T MRI mprage acquisition of the same patient three years after (42 years old)... we processed that images to got the volume of some structures that we need and compare... but, we found that multiple brain structures are bigger in the 42 year old images: right hypocampus (3187-3755), right cerebral white matter (151164-172448), right Cerebellum-White-Matter (12652-14902), right Cerebellum-Cortex (48812-51935), etc... And a similar situation occurs in left hemisphere... The Intracranial volumen in both cases is: 1348899,976 and 1332590,755197... Why is the difference in volumen in the structures in both studies ?... Why is always bigger at 42 years old than 39 years old?... Any technical problem ?... We got a similar difference by normalizing with ICV... Sincerely, Gonzalo Rojas Costa ___ 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 fellowship: cortical integration timescales across the ventral stream
*Post-doctoral fellowship: cortical integration timescales across the ventral stream* We are looking for postdoc candidates for a European Union financed project investigating how temporal integration properties change at different levels of the processing hierarchy for meaningful objects, scenes and events. The fellow would work together with David Melcher and Scott Fairhall. Specifically, we are seeking a postdoc with advanced expertise in fMRI as demonstrated by two first author fMRI publications. Salary would be in the range of circa 24,000 – 30,000 euro (net) per year, commensurate with experience. The Center for Mind/Brain Sciences (CIMeC, http://web.unitn.it/en/cimec) at the University of Trento offers a vibrant research setting with state-of-the-art neuroimaging methodologies, including a research-only MRI scanner, MEG, EEG and TMS, as well as behavioral, eye tracking and motion tracking laboratories. Melcher Active Perception Lab: http://r.unitn.it/en/cimec/map FairLab: theFairLab.org http://thefairlab.org/ For informal inquiries about this position email: david (dot) melcher (AT) unitn (dot) it ___ 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] papers on reliability of volume of indivdual cortical parcellation regions
Hi Mehul, here is one such paper: http://www.ncbi.nlm.nih.gov/pubmed/23668971 see Table 7. Cheers, jorge On 24/05/2014 19:31, Mehul Sampat wrote: Hi Folks, I was able to find a number of papers looking at the reliability of cortical thickness of individual regions (ex: https://surfer.nmr.mgh.harvard.edu/pub/articles/reliability_wonderlick.pdf) I was wondering if there are any papers that have looked at the reliability of the volumes of the individual cortical parcellation regions ? Thanks Mehul -- Jorge Jovicich, Ph.D. MR Lab Head Center for Mind Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovic...@unitn.it http://www.cimec.unitn.it/ http://polorovereto.unitn.it/~jovicich ___ 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] use 1 vs. 2 T1 acquisitions
Hello Stacey, this issue came up recently, please find attached some responses. I hope this helps. Cheers, Jorge On 21/03/2014 21:56, Stacey M Schaefer wrote: Hello freesurfer gurus, We acquire 2 BRAVO T1s on a GE 3T during the same scan session on most of our study participants, but because of various issues, occasionally only get 1 T1/participant. I've been processing the data combining both T1s when we have 2 and using just 1 T1 when that was all we had thinking it would be best to use the highest quality data as possible (more is better rational), especially given the old FS recommendation that multiple acquisitions were better. However, after perusing recent course materials, I came across the suggestion in one of the powerpoints to always be consistent across subjects using either 1 or 2. Is that the most recent recommendation - if we don't have 2 acquisitons on everyone to pick the one with best contrast and only use 1 T1/participant? If so, can you explain why? Thanks for your advice! Stacey Schaefer -- --- Stacey M. Schaefer, Ph.D. Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Ave Rm T127 Madison, WI 53705 Waisman Phone: 608-263-9321 ___ 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. -- Jorge Jovicich, Ph.D. MR Lab Coordinator Center for Mind Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovic...@unitn.it http://www.cimec.unitn.it/ http://polorovereto.unitn.it/~jovicich ---BeginMessage--- thanks Jorge, nice to see that someone quantified this :) Bruce On Tue, 7 Jan 2014, Jorge Jovicich wrote: Hi Hai, I agree with Bruce. In a recent paper (http://www.ncbi.nlm.nih.gov/pubmed/23668971), for a variety of 3T vendor and coil configurations, we confirmed previous findings that averaging two within-session uncorrupted MPRAGE scans did not significantly improve across session reproducibility. In you case just choose the best one of the two. Is it worth acquiring two MPRAGES then? Tricky. Maybe you can go for only a single acquistion if your MR operator is experienced to distinguish what level of artifact will be unacceptable for the target analysis and deserves a repeated acquisition in case of unacceptable quality. Otherwise, one may fix two acquisitions in the protocol and use the best of them. Nevertheless, the operators should always be paying attention to the data quality during the acquisition to decide if some type of intervention can help. cheers, jorge On 06/01/2014 21:38, Bruce Fischl wrote: Hi Hai it really depends on your coil and field strength, and whether either is motion-corrupted. For 3T 32 channel data our somewhat ad hoc opinion is that one is better than two (due to blurring induced by interpolation), but it's really a case-by-case decision. sorry that there isn't an easier answer Bruce On Mon, 6 Jan 2014, Hai Pan wrote: Hello, FreeSurfer experts, We made two T1 scans for each subject at each session, will they be helpful for better recon-all results? Shall I average them and process the averaged T1 image? Let me know please. Thank you, Hai ___ 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. ---End Message--- ___ 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
Re: [Freesurfer] Are two T1 scans helpful for better recon-all?
Hi Hai, I agree with Bruce. In a recent paper (http://www.ncbi.nlm.nih.gov/pubmed/23668971), for a variety of 3T vendor and coil configurations, we confirmed previous findings that averaging two within-session uncorrupted MPRAGE scans did not significantly improve across session reproducibility. In you case just choose the best one of the two. Is it worth acquiring two MPRAGES then? Tricky. Maybe you can go for only a single acquistion if your MR operator is experienced to distinguish what level of artifact will be unacceptable for the target analysis and deserves a repeated acquisition in case of unacceptable quality. Otherwise, one may fix two acquisitions in the protocol and use the best of them. Nevertheless, the operators should always be paying attention to the data quality during the acquisition to decide if some type of intervention can help. cheers, jorge On 06/01/2014 21:38, Bruce Fischl wrote: Hi Hai it really depends on your coil and field strength, and whether either is motion-corrupted. For 3T 32 channel data our somewhat ad hoc opinion is that one is better than two (due to blurring induced by interpolation), but it's really a case-by-case decision. sorry that there isn't an easier answer Bruce On Mon, 6 Jan 2014, Hai Pan wrote: Hello, FreeSurfer experts, We made two T1 scans for each subject at each session, will they be helpful for better recon-all results? Shall I average them and process the averaged T1 image? Let me know please. Thank you, Hai ___ 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. -- Jorge Jovicich, Ph.D. MR Lab Coordinator Center for Mind Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovic...@unitn.it http://www.cimec.unitn.it/ http://polorovereto.unitn.it/~jovicich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
