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30132 discussions

FW: Consistency between volumes in fsaverage and subject data?
by Jensen, Sarah 07 Oct '13

07 Oct '13

Hi Bruce, Thanks for getting back to me! I am using my own ROIs, created based on an ALE (Activation Likelihood Estimation) conducted in the gingerALE software, and dividing the ALE map into smaller clusters in Marsbar (SPM). I then applied the ROIs to the surface based registration(fsaverage registration) and turned these into label files (mri_cor2label) and extracted volumes from my participants (mri_label2label) I noticed that some of my biggest ROIs didn't come out with the larges volumes in my final data and started looking at the correlations of my volumes across the different steps. I found the volumes of my templates in SPM (Marsbar) and after the projection to fsaverage were highly correlated although the ROIs where much smaller in fsavarage. But there was no correlation between my ROIs in fsaverage and my extracted data (based on 500 participants). I did not correct for the reduced surface area in these analyses, so thanks a lot for making me aware of this. Can you by any chance direct me to a reference for this? And do you think I should expect a correlation between the templates in fsaverage my data if I do this? I am not interested in there correlations as such, but ran these analyses to check my data because I am worried something might have gone wrong. Thanks a lot! Best, Sarah ________________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Sent: 07 October 2013 13:21 To: Jensen, Sarah Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Consistency between volumes in fsaverage and subject data? Hi Sarah what ROIs do you mean? And did you correct for the reduced surface area in fsaverage w.r.t. the individual surfaces? If not, it's not surprising that fsaverage ROIs have less surface area. It is an average surface and less folded than any individual. cheers Bruce On Mon, 7 Oct 2013, Jensen, Sarah wrote: > > Hi Freesurfer users, > > > I am analysing some volumetric data and have noticed that the volumes I > extract from my participants are very different from the volumes of my > templates in fsaverage space. I for instance have two ROIs that stand out as > big (about 6-8 times larger that the other ROIS) in fsaverage space, but > come out as almost indistinguishable from the other ROIs in my data. When I > sort my ROIs according to size there seems to be no consistency between the > size in fsaverage space and my subjects, and the correlation between the > volume in fsaverage and my subjects is about .05 - 0.1. > > > I am new to freesurfer, and would intuitively expect greater consistency > between the ROIs in fsaverage and the subjects. Has anyone else had similar > experiences, and is this lack of consistency between volumes in fsaverage > space and participant data perfectly normal? > > > Thanks, > > > Sarah > > > 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.

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Consistency between volumes in fsaverage and subject data?
by Jensen, Sarah 07 Oct '13

07 Oct '13

Hi Freesurfer users, I am analysing some volumetric data and have noticed that the volumes I extract from my participants are very different from the volumes of my templates in fsaverage space. I for instance have two ROIs that stand out as big (about 6-8 times larger that the other ROIS) in fsaverage space, but come out as almost indistinguishable from the other ROIs in my data. When I sort my ROIs according to size there seems to be no consistency between the size in fsaverage space and my subjects, and the correlation between the volume in fsaverage and my subjects is about .05 - 0.1. I am new to freesurfer, and would intuitively expect greater consistency between the ROIs in fsaverage and the subjects. Has anyone else had similar experiences, and is this lack of consistency between volumes in fsaverage space and participant data perfectly normal? Thanks, Sarah

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Re: [Freesurfer] DOSS contrast - one group, 3 covariates
by Anita van Loenhoud 07 Oct '13

07 Oct '13

Thank you Doug!

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Re: [Freesurfer] symmetric template in freesurfer
by Douglas Greve 06 Oct '13

06 Oct '13

Yes, it is released. See https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi doug ps. Please remember to post to the list. Thanks! On 10/6/13 11:10 PM, Xinian Zuo wrote: > Hi Doug -- Hope all is well. I am writing to follow up my previous > question about the symmetric templates of brain surfaces. I noticed > that HCP released data contain some preprocessed data projected onto a > symmetric surface template. Have freesurfer already completed this > development or still in progress? If achieve this success, would you > please guide me the use of this template. In moving my analyses from > volume to surface (both are symmetric spaces), two things are keys of > the transformation: transform individual surfaces into the fs symm > surface template, and how project a 4D functional data onto the symm > surface template. We really appreciate if you can give some > suggestions on these two implementations in Freesurfer. Best regards, > Xi-Nian. > > > On Sat, May 5, 2012 at 12:19 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Yes, we will be releasing a version of FS with the new software in > a few weeks (hopefully the end of May). > doug > > > On 05/03/2012 07:28 PM, Xinian Zuo wrote: > > Dear Douglas, I hope all is well. Just writing to ask if the > template > progressed well. Doing some functional analysis and want to > move them > to be on the surface :) Best regards, Xi-Nian. > > On Sat, Oct 2, 2010 at 3:05 AM, Xinian Zuo<zuoxinian(a)gmail.com > <mailto:zuoxinian@gmail.com>> wrote: > > wow, really a good news. looking forward to see it :) > > Xinian > > > On Fri, Oct 1, 2010 at 2:51 PM, Douglas N > Greve<greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > wrote: > > :) I hope not. There's a guy here who's primed to work > on it after the > grant deadlines have passed. > > doug > > Xinian Zuo wrote: > > Thanks for sharing this information, need another > 3 years? :) > > On Wed, Sep 29, 2010 at 11:57 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > We are in the middle of creating one (but have > been for about 3 > years:). > > doug > > > Xinian Zuo wrote: > > Hi Douglas, > > Hope all is well. Thanks for help to > answer my questions > before. I am working on some cortical > homotopic measures and > want to switch them into freesurfer. I am > not very sure if > there is a symmetric template/surface in > freesurfer in the new > release (5.0). Does fs team has any plan > to develop one? If > so, it would be very helpful to study > features of both > structural and functional homotopy. > > Best regards, > -- Xinian Zuo, Ph.D > Associate Research Scientist > Institute for Pediatric Neuroscience > NYU Child Study Center > 215 Lexington Ave., 14th Floor > New York, NY 10016 > Phone: (212) 263 2485 > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > 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. > > > > > -- > Xinian Zuo, Ph.D > Associate Research Scientist > Institute for Pediatric Neuroscience > NYU Child Study Center > 215 Lexington Ave., 14th Floor > New York, NY 10016 > Phone: (212) 263 2485 > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > -- > Xinian Zuo, Ph.D > Associate Research Scientist > Institute for Pediatric Neuroscience > NYU Child Study Center > 215 Lexington Ave., 14th Floor > New York, NY 10016 > Phone: (212) 263 2485 > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- > Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn) > Google Scholar Citations: > http://scholar.google.com/citations?user=a3-gVGMAAAAJ&hl=en

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LGI mean value per hemisphere
by Jane Garrison 06 Oct '13

06 Oct '13

Hi I have a question related to calculation of the local gyrification index using FreeSurfer. I have computed the LGI and checked the results successfully. I can get mean values of LGI for different ROI's using the command: mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats But I would also like to get a single mean value of LGI for each hemisphere. Please could you advise how best to find this. Thanks and best wishes Jane Garrison

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MPRAGE SNR
by Yang, Daniel 04 Oct '13

04 Oct '13

Dear FreeSurfer Experts, Is there a way to estimate the SNR in MPRAGE scans besides using wm-anat-snr ? For examples, I read that SNR is improved in multiecho MPRAGE and I am wondering how that is computed? Thanks! Daniel

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Help with mri_copy_values
by Jonathan Holt 04 Oct '13

04 Oct '13

I'm trying to apply voxel deletions made to the brainmask.mgz to the wm.mgz. As I understand it, if I run mri_copy_values brainmask.mgz 0 wm.mgz all of the 0 value voxels, or the deleted voxels in braibmask.mgz will be applied to the wm.mgz (provided they have the same geometry or some such). it seems to run properly and says voxels copied from input to output volume but when I load in tkmedit or freeview the wm.mgz still contains voxels where there are none in the brainmask.mgz any ideas? jon

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Error when running mris_anatomical_stats
by Tara Ann Miskovich 04 Oct '13

04 Oct '13

Hello Freesurfer experts, I am having difficulty when trying to extract LGI values from a specific label I made. mris_anatomical seems to work when I run it with an annotation, so I am not sure why I am having this error. mris_anatomical_stats -l sub200/label/lh.precuneus.label -t sub200/surf/lh.pial_lgi -f sub200/stats/lh.precuneus_lgi.stats sub200 lh This is the output: limiting computations to label sub200/label/lh.trait_precuneus.label. using thickness file sub200/surf/lh.pial_lgi. reading volume /media/LGI/LGI/sub200/mri/wm.mgz... reading input surface /media/LGI/LGI/sub200/surf/lh.white... reading input pial surface /media/LGI/LGI/sub200/surf/lh.pial... reading input white surface /media/LGI/LGI/sub200/surf/lh.white... Segmentation fault (core dumped) Thank you for the help! Tara

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Global thickness calculation
by Mollie Bayda 04 Oct '13

04 Oct '13

Hi, I am trying to calculate whole-brain mean cortical thickness in each individual subject for correction of regional mean thicknesses. I see on the wiki that this is recommended to be done by: bh.thickness = (lh.thickness X lh.area) + (rh.thickness X rh.area) / (lh.area +rh.area) In my table I see lh and rh total area but I do not see lh and rh thickness. All I see is mean thicknesses for each region. Are the total rh and lh mean thicknesses supposed to appear in the table? Thanks!

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LGI longitudinal data
by Tricia Merkley 04 Oct '13

04 Oct '13

Hi, Is it possible to run the LGI on data that has already been longitudinally processed? For example, when I try to run: recon-all -s subject001.long.subject001_base -localGI I get the following error: ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters: \' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists. This is using v5.1.0, and no, I'm not trying to re-run a longitudinal time point. Just the LGI. I'd appreciate any suggestions! Thanks so much, Tricia

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