[Freesurfer] global measures of volume bug
External Email - Use Caution Dear FS experts, I came across this post about a bug related to global measures of volume from version 6.0: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed I have two questions that I hope someone can clarify: 1) This bug does not affect measures of cortical thickness or area, or specific subcortical volumes, correct? 2) For longitudinally processed data, is it sufficient to run the proposed solution (recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 -wmparc -balabels) on the longitudinal data, or do we need to first do it on the cross-sectionally processed data? Best regards, Christian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] hippocampal subfields in younger populations
Dear FreeSurfer and hippocampal subfield segmentation developers, I have noted that the FS6.0 hippocampal subfield segmentation procedure was developed using scans of older adult brains. Has the application of this method to kids, adolescents and/or young adults in any way been validated? Or do you have any thoughts regarding such use of the method? I would think this would be an issue for young kids that have markedly different brain volumes, but not for older kids and young adults that differ less dramatically from older adults. But I would greatly appreciate any input regarding this. Best regards, Christian ___ 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] longHippoSubfields
Hi again Eugenio, Sorry for the picky follow-up question regarding the longitudinal hippocampal subfields processing, but do you suggest that when the official version 6 comes out, we rerun everything (including the standard FS long processing) or would it be ok to just rerun the hippocampal part (on scan processed with 5.3)? For us, the first option might necessitate a new round of QC, which would be very time consuming for a large longitudinal dataset. regards, Christian From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Christian Krog Tamnes <c.k.tam...@psykologi.uio.no> Sent: 30 November 2016 15:57 To: Freesurfer support list Subject: Re: [Freesurfer] longHippoSubfields We will get the beta for now then. Thanks Eugenio! regards, Christian From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Eugenio <e.igles...@ucl.ac.uk> Sent: 30 November 2016 15:46 To: Freesurfer support list Subject: Re: [Freesurfer] longHippoSubfields Hi Christian, I believe you were unlucky enough to download the dev version during the days that this module was broken. I would strongly suggest that you either download the beta version of 6.0 or wait until the official release of this version, which should be happening soon. 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 30 Nov 2016, at 14:26, Christian Krog Tamnes <c.k.tam...@psykologi.uio.no<mailto:c.k.tam...@psykologi.uio.no>> wrote: Dear Juan and FreeSurfer team, We are trying to test out the longitudinal hippocampus subfield segmentation pipeline, but can't seem to run/find the script (longHippoSubfieldsT1.sh). We have done the standard processing in v5.3 and have the following dev version: freesurfer-Linux-centos6_x86_64-dev-20160914-bdac8bc. Sorry for the basic question, but do we simply need a later dev build? Best regards, Christian ___ 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. ___ 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] longHippoSubfields
We will get the beta for now then. Thanks Eugenio! regards, Christian From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Eugenio <e.igles...@ucl.ac.uk> Sent: 30 November 2016 15:46 To: Freesurfer support list Subject: Re: [Freesurfer] longHippoSubfields Hi Christian, I believe you were unlucky enough to download the dev version during the days that this module was broken. I would strongly suggest that you either download the beta version of 6.0 or wait until the official release of this version, which should be happening soon. 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 30 Nov 2016, at 14:26, Christian Krog Tamnes <c.k.tam...@psykologi.uio.no<mailto:c.k.tam...@psykologi.uio.no>> wrote: Dear Juan and FreeSurfer team, We are trying to test out the longitudinal hippocampus subfield segmentation pipeline, but can't seem to run/find the script (longHippoSubfieldsT1.sh). We have done the standard processing in v5.3 and have the following dev version: freesurfer-Linux-centos6_x86_64-dev-20160914-bdac8bc. Sorry for the basic question, but do we simply need a later dev build? Best regards, Christian ___ 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. ___ 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] longHippoSubfields
Dear Juan and FreeSurfer team, We are trying to test out the longitudinal hippocampus subfield segmentation pipeline, but can't seem to run/find the script (longHippoSubfieldsT1.sh). We have done the standard processing in v5.3 and have the following dev version: freesurfer-Linux-centos6_x86_64-dev-20160914-bdac8bc. Sorry for the basic question, but do we simply need a later dev build? Best regards, Christian ___ 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] ICV for adolescent and young adult in longitudinal stream
Dear Martin and FS experts, I have a small follow-up question regarding the post below. Given a young sample where ICV is still growing, that I want to control for this and that the data look ok: Can I use the cross-sectional ICV as a covariate in analyses on the longitudinal data? Or will this introduce any bias? In other words, does “the longitudinal stream assumes head size is fixed across time” affect the estimated long values when this assumption is incorrect? Best regards, Christian K Tamnes From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Martin Reuter mreu...@nmr.mgh.harvard.edu Sent: 14 October 2014 17:23 To: Freesurfer support list Subject: Re: [Freesurfer] ICV for adolescent and young adult in longitudinal stream Hi Knut, the longitudinal stream assumes head size is fixed across time. That is why we report only one ICV (the one from the within subject template) in all time points. If in your data heads are growing still, you can still use the longitudinal stream, but need to be carefully inspecting your data (e.g. are surfaces OK in both time points, is the skull strip good etc). You can also read out the individual ICV on each time point when looking at the cross sectional directories (first step of the long pipeline), there in aseg. stats are the ICV's for each time point. Best, Martin On 10/13/2014 12:24 PM, Knut J Bjuland wrote: Dear FreeSurfer export, I have used the longitudinal stream in FreeSurfer. However, when I extracted the ICV for adolescents and young adult, I get the same number for those subjects that are present at two-time points. Will registration to a common space cause the change in ICV? Can this change explain why the icv is equal at 15 and 19 years of age for all my subjects with two-time points? Best regards, Knut Jørgen Bjuland PhD candidate NTNU Trondheim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
