[Freesurfer] working with cluster annotations in fs-fast
Hi folks, I'm trying to split a cluster from mri_glmfit-sim into two separate regions. (Ginormous blob of activation across multiple structures of interest...) I've gotten to the point of generating a new annotation with the separate labels for my separate regions, but am stuck getting a "cluster size" for the new labels. It looks like one can't use mris_anatomical_stats on fsaverage... but something like that must be happening inside of mri_glmfit-sim to get cluster sizes? What's the best way to get these values for my new annotation? (Or is this a terrible idea for some reason I haven't yet considered?) Thanks! Abby Noyce -- Abigail Noyce, Ph.D. Department of Psychological & Brain Sciences Boston University ano...@bu.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] (no subject)
Hi Doug et al, I would like to get a different cluster summary stat out of mri_glmfit-sim. Rather than size, I'd like to use the "sum of t-scores" (after Maris & Oostenwald 2007, for example). That is, set a cluster inclusion threshold, and then for each cluster of adjacent vertices that clear the threshold, sum their t-scores. For the permutation significance testing, then, the largest such clusterwise sum would be the statistic used to generate the null distribution... I'm happy to write my own scripts, but can't figure out where to try to pull this number out. Thanks! Abby Noyce ___ 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] mirroring fsaverage labels between hemispheres
Hi, I have pored over (I think) all of the mailing list postings about cross-hemisphere mapping and I can't quite figure out how to do this. I have a bunch of labels on fsaverage, and I want to be able to check/visualize the relationship between lh and rh versions of the labels. I can do mri_label2label to map from fsaverage to fsaverage_sym, but that doesn't do the right thing, and fsaverage doesn't have the same kind of xhemi registration structure that "normal" subjects get with surfreg --xhemi. I guess I could back-project onto a normal subject and then project to fsaverage_sym, but that seems like an unnecessary step. How can I get mirror-projected labels from fsaverage on fsaverage_sym? Thanks! Abby -- Abigail L. Noyce, Ph.D. Psychological & Brain Sciences Boston University ano...@bu.edu 617-440-3640 ___ 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] Freesurfer Digest, Vol 170, Issue 1
> Date: Mon, 2 Apr 2018 14:55:47 -0400 > From: Douglas Greve > Subject: Re: [Freesurfer] mirroring fsaverage labels between > hemispheres > > If you have a label defined on the lh or rh of fsaverage, you can map it > to the contralateral hemi with something like > > mris_apply_reg --src-label lh.your.label --streg lh.sphere.left_right > rh.sphere.left_right --trg rh.your.label > > where the left_right files are in fsaverage/surf > My fsaverage doesn't seem to have those registrations (we're still on 5.3) - I have lh.sphere, lh.sphere.reg, and lh.sphere.reg.avg but nothing with the .left_right suffix. -a -- Abigail L. Noyce, Ph.D. Psychological & Brain Sciences Boston University ano...@bu.edu 617-440-3640 ___ 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] mirroring fsaverage labels between hemispheres
Still stuck - I downloaded the bin for mris_left_right_register from https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_left_right_register and ran it from the fsaverage surf directory: $PROJECTDIR/mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right (Yes, it really should be in $FREESURFER_HOME, but I don't think that's the problem.) it fails with: $Id: mris_left_right_register.c,v 1.2 2011/12/16 20:49:37 greve Exp $ $Id: mrisurf.c,v 1.781 2016/06/13 21:20:50 fischl Exp $ reading lh surface from lh.sphere... reading rh surface from rh.sphere... MRISreadCurvature: could not open ./rh.inflated.H No such file or directory /r2/users/fspace2/abby/AV_6rois/3_experiment/3_analysis/scripts/problabels/mris_left_right_register: could not read curvature file './rh.inflated.H' No such file or directory There is indeed no rh.inflated.H (or lh.inflated.H) in the surf directory. What's my next piece of backtracking? Thanks, Abby > Date: Tue, 3 Apr 2018 15:36:22 -0400 > From: "Douglas N. Greve" > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 170, Issue 1 > To: > Message-ID: <39459d44-cf44-6a53-1f0f-2eab5c471...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8"; format=flowed > > you can generate them with > > cd $FREESURFER_HOME/subjects/fsaverage/surf > > mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right > rh.sphere.left_right > > should take less than an hour to run > > On 04/03/2018 03:28 PM, Abigail Noyce wrote: > > > > Date: Mon, 2 Apr 2018 14:55:47 -0400 > > From: Douglas Greve > <mailto:dgr...@mgh.harvard.edu>> > > Subject: Re: [Freesurfer] mirroring fsaverage labels between > > ? ? ? ? hemispheres > > > > If you have a label defined on the lh or rh of fsaverage, you can > > map it > > to the contralateral hemi with something like > > > > mris_apply_reg --src-label lh.your.label --streg lh.sphere.left_right > > rh.sphere.left_right --trg rh.your.label > > > > where the left_right files are in fsaverage/surf > > > > > > My fsaverage doesn't seem to have those registrations (we're still on > > 5.3) - I have lh.sphere, lh.sphere.reg, and lh.sphere.reg.avg but > > nothing with the .left_right suffix. > > > > -a > > -- > > Abigail L. Noyce, Ph.D. > > Psychological & Brain Sciences > > Boston University > > > > ano...@bu.edu <mailto:ano...@bu.edu> > > 617-440-3640 <(617)%20440-3640> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Message: 9 > Date: Tue, 3 Apr 2018 16:01:45 -0400 > From: "Douglas N. Greve" > Subject: Re: [Freesurfer] Surface label to volume and then back to > surface > To: > Message-ID: <1600e55a-3097-8455-cb9a-7725ce6e3...@mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252"; format=flowed > > Hi David, I've tried to answer your questions below. > > doug > > > On 03/30/2018 01:48 PM, David Beeler wrote: > > Hi all, > > Sorry in advance, this is a bit of an annoying one! > > > > I am trying to use freesurfer's automatically generated MT label as a > > parcel to constrain activity measured during a functional MT > > localizer. I am currently doing my analysis in the volume and I'd like > > to transform the MT surface label into the subject's volume functional > > space (i.e. the same space as the sig.nii.gz for a particular > > contrast), take the voxels in sig.nii.gz that are within the MT label, > > and project them back onto the surface (preferably to be viewed as an > > overlay with freeview). I will eventually run the analysis on the > > surface as well (making this much less roundabout, but I also use > > volume parcels so understanding how to correctly go between the volume > > and surface is important to me). > > > > In my pipeline I start off by running preproc-sess, then I register > > and transform my preprocessed functional data (fmcpr.nii.gz) to the > > subject's anatomical (without upsampling). After doing mkanalysis and > > mkcontrast, I run selxavg on this volume. So the functional data is > > aligned with the anatomical, but still has low res dimensions. > > > > If it's not too much to ask, would it be possible to provide the > > specific commands to do all thes
