[Freesurfer] Weighted Average of Cortical Thickness
Hi, I had 2 questions relating to measuring global mean cortical thickness with the weighting factor of surface area bh.thickness = ( (lh.thickness * lh.surfarea) + (rh.thickness * rh.surfarea) ) / (lh.surfarea + rh.surfarea) 1.) If this weighting is recommended, then shouldn't it be performed for each vertex in an exploratory whole brain group analyses (e.g., for one vertex in left hemi: lh.thickness*lh.surfarea)/(lh.surfarea). 2.) Are there any references that come to mind to cite in regards to this normalization technique? I see that this following paper uses normalization (but was wondering if you would recommend any others): Vuoksimaa, E., Panizzon, M. S., Chen, C.-H., Fiecas, M., Eyler, L. T., Fennema-Notestine, C., … Kremen, W. S. (2015). The Genetic Association Between Neocortical Volume and General Cognitive Ability Is Driven by Global Surface Area Rather Than Thickness. *Cerebral Cortex (New York, NY)* , *25*(8), 2127–2137. http://doi.org/10.1093/cercor/bhu018 Best, Mike ___ 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] Ascii file of thickness overlay with vertex index and coordinates
Hi, I was wondering how I would go about getting the vertex index and coordinates in one ascii file for a thickness overlay file. With mri_convert using the --asci+crsf option it outputs the vertex index only. Now I want to get the coordinates of each index...Is this possible? I may be misunderstanding something Could this info be extracted with converting a surface (e.g., inflated) with mris_convert? If so, where can I find info on how to read the ascii surface files. In other words, what I'm trying to do is for each vertex: Best, Mike -- Michael Kranz Graduate Research Assistant |Beckman Institute University of Illinois 314-323-1329 ___ 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] fslmaths like utility for surface overlays?
Thanks!! These options do the trick On Wed, Mar 29, 2017 at 2:03 AM, Michael Kranz <mbkr...@gmail.com> wrote: > Hi, > > Is there a way to create a subject specific overlay with an intensity > value of 1 (or another constant value across the entire cortical mantle)? > (I'm thinking a command like fslmaths in FSL but on the surface for each > vertex). > > Best, > Mike > > > -- > Michael Kranz > Graduate Research Assistant |Beckman Institute University of Illinois > 314-323-1329 <(314)%20323-1329> > -- Michael Kranz Graduate Research Assistant |Beckman Institute University of Illinois 314-323-1329 ___ 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] fslmaths like utility for surface overlays?
Hi, Is there a way to create a subject specific overlay with an intensity value of 1 (or another constant value across the entire cortical mantle)? (I'm thinking a command like fslmaths in FSL but on the surface for each vertex). Best, Mike -- Michael Kranz Graduate Research Assistant |Beckman Institute University of Illinois 314-323-1329 ___ 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] Whole brain mediation analysis
Hi, I was wondering if you guys had any suggestions for developing a whole brain mediation analysis through Freesurfer or can think of any examples (e.g., does thickness mediate the relationship between age and cognition)? It looks like SPM has something (whole brain mediation analysis), and given the outputs from mri_glmfit, it seems like it would be possible with Freesurfer. Best, Mike -- Michael Kranz Graduate Research Assistant | Beckman Institute University of Illinois 314-323-1329 ___ 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] Comparing aparc labels with volume ROIs in MNI152 2mm space
Hi guys, I want to overlay an ROI mask created in FSL in the MNI152 2mm volume space (from a metaanalysis) with the aparc labels in Freesurfer to compare the two ROI schemes (so I can have justification for picking some of the Freesurfer ROIs for analyses). I'm thinking of running the MNI152 2mm brain through Freesurfer reconstruction and then mapping the volume defined ROI to this surface. Is this the best way to do this, and if so, how should I calculate the registration matrix in order to use the mri_vol2surf? I'm guessing there's a much easier way though… Thanks, Mike ___ 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] Longitudinal fMRI analysis
Hi, I have two groups and two time points (pre and post). I want to investigate group*time interactions in an fMRI task taken at both time points. I have run all the subjects through first level FEAT analyses in FSL as well as the longitudinal Freesurfer pipeline. I'm thinking of registering the FEAT first level analyses to the each corresponding longitudinal time point first. Then, if I want to do a group level analysis, can I still use the longitudinal two stage process or is this just designed for structural measures ( http://freesurfer.net/fswiki/LongitudinalTwoStageModel)? Or, would you suggest another approach for group analysis for longitudinal fMRI data taking advantage of Freesurfer? Thanks, Mike Kranz ___ 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] mris__label__calc intersect error in longitudinal qcache
Hi, I'm having trouble figuring out following problem: For one subject (out of 200), I get the following error (this error only persists for the right hemisphere-- left hemisphere works fine for this subject). mris_label_calc intersect /SUBJECTS_DIR/sub2.long.subt/label/rh.cortex.label /SUBJECTS_DIR/subt/label/rh.long.cortex.label /SUBJECTS_DIR/subt/label/rh.long.cortex.label ERROR -11 : mris_label_calc intersect did not work? *subt is base and sub2 is second time point .* Do you guys have any experience with this error and problems that it may have been caused by? I've tried re-running the longitudinal stream from scratch and the error still persists. I've visually checked the images and all segmentations were accurate. Thanks, Mike Kranz ___ 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] Longitudinal data for cross sectional individual differences study
Hi Freesurfers, Just wanted to verify: I have ran my subjects through the longitudinal processing stream (two time points a couple weeks apart). I want to predict cognitive performance (from the first time point) with Freesurfer stats. As I have the longitudinal data available, would it be better to use longitudinally processed stats (as opposed to the cross sectional stats)? I ask because I'm not aware of any publications that do this... Thanks much, Mike Kranz Michael Kranz Graduate Research Assistant | Beckman Institute University of Illinois 314-323-1329 ___ 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] Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011
Hi all, I was wondering how I could go about getting anatomical stats for the different regions from the Choi2012 and Buckner 2011 parcellations. The Yeo 2011 cortical parcellation files were available in the fsaverage folders and I could get stats and labels for those, but I couldn't figure out how to get stats on these other two. Thanks, Mike Kranz ___ 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] Curvature/folding stats
Hi all, What's the difference between the curvature and folding measures outputted in the aparc stats files (i.e. mean, gaussian, folding index, and curvature index)? Additionally, which measures are the most reliable for individual differences? Thanks, Mike Michael Kranz Graduate Research Assistant |Beckman Institute University of Illinois 314-323-1329 ___ 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] Brodmann Area Atlas
Hi all, Is there a place where I could find an atlas with all of the Brodmann areas? Or is the one available with a portion of the areas the only existing atlas? Thanks, Mike ___ 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] Brodmann Area Atlas
Nvm just read an old thread. Sorry about that. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019825.html On Fri, Aug 16, 2013 at 11:24 AM, Michael Kranz mbkr...@gmail.com wrote: Hi all, Is there a place where I could find an atlas with all of the Brodmann areas? Or is the one available with a portion of the areas the only existing atlas? Thanks, Mike -- Michael Kranz Lab Manager | LBC Lab Beckman Institute University of Illinois 314-323-1329 ___ 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] Cerebellum Subcortical edits
Although the cerebellum isn't part of my primary analyses, I thought it would be interesting to compare cerebellum volume with my other subcortical measures (eg caudate and putamen) in predicting video game skill acquisition. Also, I was flirting with the idea of using Buckner's cerebellum and striatum parcellations as well. On Thu, Aug 1, 2013 at 8:22 AM, Martin Kavec martin.ka...@gmail.com wrote: Hi Michael, It looks like lateral venous sinuses are included in this subject and as Bruce says, since the intensity is very close to cerebellar cortex, they are difficult to distinguish. It depends on what you are after in your analysis if you need to take care or not. Regards, Martin Sent from my iPad On 31.7.2013, at 23:23, Michael Kranz mbkr...@gmail.com wrote: Hi guys, I was just wondering approximately how often the aseg volume will need manual edits. I know the tutorial says very rarely but I noticed that most of my subjects have non-brain matter (I think) incorrectly labelled as cerebellum. Attached is a pic of what I mean.aseg.png Thanks, Mike ___ 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. -- Michael Kranz Lab Manager | LBC Lab Beckman Institute University of Illinois 314-323-1329 ___ 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] Processing Multiple Subjects
Hi all, If I process more subjects than the recommended amount given my number of cores and memory, will this affect the stats/surfaces or just slow the process down? I'm asking due to the sensitivity of workstations and also I seem to be getting slightly different stats sometimes when I re-submit to recon-all but haven't pin pointed the reason yet. Thanks, Mike ___ 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.
