Freesurfer

freesurfer@nmr.mgh.harvard.edu

30088 discussions

group difference thickness map
by Miranka Wirth 12 Apr '12

12 Apr '12

Dear freesurfers, I am trying to create a map that shows the vertex-wise magnitude of thinning (f.e.) between two groups, similar to Fig5 in Dickerson et al., 2009. I know how to extract the group-average thickness map from the beta.mg (mri_convert beta.mgh group1.mgh --frame 0 etc.), assuming that this is the way to construct the figure. Is there an easy way in freesurfer to compute the difference between these to group-average maps? Thank you for sharing. Miranka

2 1

mri_label2vol
by Johnson 12 Apr '12

12 Apr '12

Hi Can someone tell me please in*_details_*what does this line do? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz thanks -- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgadel2(a)uic.edu

3 16

Re: [Freesurfer] Resampling volumes from functional to anatomical space
by Lingqiang Kong 12 Apr '12

12 Apr '12

sorry. meant to sent to the list, too. L > Hi Bruce, > > Yes that's what I wanted! The --fstarg flag uses the > $SUBJECTS_DIR/$subj/mri/orig.mgz as the targ so in my case it would be the > same as using --targ $SUBJECTS_DIR/$subj/mri/T1.mgz. > > So I guessed it had worked from the beginning but I had mistakenly thought > that it didn't. It just looked different to my eyes because the functional > contrast sig.nii looked one size bigger than the T1 structural and a lot > of stuff seems to be outside the brain (now I take it that it's normal to > look this way?). > > > Thank you so much for your clarification. I was really confused about what > mri_vol2vol was doing. > > Lingqiang > >> Hi Lingqiang >> >> do you mean in voxel register with the anatomy, with the same voxel >> dimensions, etc...? If so I think you can specify --targ \ >> $SUBJECTS_DIR/$subject/mri/T1.mgz >> >> or you mri_convert with -rl <path to T1.mgz> >> >> cheers >> Bruce >> >> >> On Thu, 12 Apr 2012, Lingqiang Kong wrote: >> >>> Hi Surfers, >>> >>> I am trying to resample a GLM analysis contrast overalay ('sig.nii') >>> back >>> to individual subject anatomical space (T1.mgz). The functional scans >>> and >>> the anatomical scans were acquired on two different days and were >>> co-registered with register.dat. The T1.mgz has high resolution and the >>> sig.nii has low resolution. >>> >>> I used >>> mri_vol2vol --mov sig.nii --fstarg --reg register.dat --o sig_high.nii >>> >>> trying to generate a new overlay 'sig_high.nii' which is aligned with >>> T1.mgz. >>> >>> However, this only generated the appropriate tranformation but did not >>> really "MOVE" the sig_high.nii to align with the T1.mgz. (I checked >>> using >>> tkregister2 and also with loading all three files in Matlab using >>> MRIread()). The sig_high.nii is aligned with sig.nii instead of T1.mgz. >>> >>> In the end, I want to load them in Matlab by MRIread and have the new >>> sig_high.nii aligned with T1.mgz. How do I do that? >>> >>> >>> Thank you. >>> >>> Lingqiang >>> >>> >>> >>> >> >> >> > > > -- > Lingqiang Kong > Ph.D candidate > Auditory Neuroscience Laboratory > Perceptual Neuroimaging Laboratory > Boston University > > 677 Beacon St. > Boston, MA 02215 > http://www.cns.bu.edu/~shinn/ANL/index.html > http://people.bu.edu/fmri/ > -- Lingqiang Kong Ph.D candidate Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/

1 0

Re: [Freesurfer] Mapping pf fsaverage surface to native volume
by Douglas N Greve 12 Apr '12

12 Apr '12

The template specifies the output geometry. When you specify --identity, you specify a particular transformation between the volume and the surface, so you can't change the target volume without specifying a different transform. I'm at a bit of a loss as to why this is not working. What is your tkmedit command? doug On 04/05/2012 06:04 AM, René Besseling wrote: > Hi Doug, > > I'm using tksurfer to visualize the surface maps; this looks OK for > both the original map overlaid on fsaverage and the mapped surface > (generated using mri_surf2surf) overlaid on subj01. The mapping from > surface to cortical ribbon also works well for fsaverage but goes > haywire for subj01, see pics in attachment. > > I noticed that mri_surf2vol gives different results when using > different --template volumes. Why is that? I assumed that the > --template image essentially provides the range of voxel coordinates > to which the surface values can be mapped. In other words: when > providing a template with a bigger field of view, I'd expect the > center of the resulting output to look the same as the output > generating when using a small FOV template. Does it matter whether you > write your output as .mgz or .nii? > > Best regards, > > Rene > > On Wed, Apr 4, 2012 at 10:42 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > How are you visualizing the results? Can you send a pic? You should be > using tkmedit. > doug > > On 04/04/2012 09:59 AM, René Besseling wrote: > > Dear Freesurfer users, > > > > I've been trying to map a Qdec contrast sig.mgh to the native volume > > of a subject using mri_surf2surf (to get from Qdec fsaverage surface > > to native surface) and mri_surf2vol (to map from native surface to > > native volume cortical ribbon). However, the last step goes wrong: I > > get a nii with the same range of values as were in the surface, but > > the nonzero voxels are scattered all over, so I guess there is > > something wrong with the surface-to-voxel coordinate mapping. > Below is > > my code, any ideas on what goes wrong? > > > > Best regards, > > > > Rene > > > > mri_surf2surf --hemi rh --srcsubject fsaverage --noreshape --sval > > sig.mgh --trgsubject subj01 --tval sig_2subj01.mgh > > > > mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon > > --identity sub01 --template subj01/mri/orig.mgz --o > > sig_2subj01_volumetric.nii > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > 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 <tel:617-724-2358> > Fax: 617-726-7422 <tel: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> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

2 2

How can I get the mean thickness of the significant cluster
by zhang mingxia 12 Apr '12

12 Apr '12

Dear Freesurfer experts, I have done the whole brain analysis and get some significant clusters. How can I get the mean thickness of these clusters of every subject? Thank you very much. Mingxia Zhang

2 1

Resampling volumes from functional to anatomical space
by Lingqiang Kong 12 Apr '12

12 Apr '12

Hi Surfers, I am trying to resample a GLM analysis contrast overalay ('sig.nii') back to individual subject anatomical space (T1.mgz). The functional scans and the anatomical scans were acquired on two different days and were co-registered with register.dat. The T1.mgz has high resolution and the sig.nii has low resolution. I used mri_vol2vol --mov sig.nii --fstarg --reg register.dat --o sig_high.nii trying to generate a new overlay 'sig_high.nii' which is aligned with T1.mgz. However, this only generated the appropriate tranformation but did not really "MOVE" the sig_high.nii to align with the T1.mgz. (I checked using tkregister2 and also with loading all three files in Matlab using MRIread()). The sig_high.nii is aligned with sig.nii instead of T1.mgz. In the end, I want to load them in Matlab by MRIread and have the new sig_high.nii aligned with T1.mgz. How do I do that? Thank you. Lingqiang -- Lingqiang Kong Ph.D candidate Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/

3 2

summing across FIR timepoints
by Ellen Lau 12 Apr '12

12 Apr '12

Hi, We ran a first-level FIR analysis on our functional data with selxavg3-sess, which outputs a single ces.nii file for each subject containing the contrast images for all timepoints. Now we would like to create an image representing the sum of a subset of these images in a time-window of interest (e.g. contrast4s + contrast6s + contrast8s) and then bring this single 4-8s contrast for each subject forward to the second-level (presumably by concatenating these summed 4-8s images into a single file that mri_glmfit will accept). Could someone advise us on the best way to do these two steps? thanks, Ellen

2 1

aseg.mgz
by Steven Thomas Korycinski 12 Apr '12

12 Apr '12

Freesurfer users, Can anyone tell me if the subcortical segmentation shown in TkMedit (aseg.mgz) is subject-specific or a general outline of structure labels in Talairach space for all subjects? Also, are the statistics provided in aseg.stats based directly on the aseg.mgz or something else? Thanks, Steve

2 1

changing data structure
by Anthony Dick 12 Apr '12

12 Apr '12

Hello, I am running the rebuild_gca_atlas.csh program and got the following error for seg_edited.mgz, which is the manually defined file imported from a different program outside of freesurfer. mri_ca_train: segmentation file <path>/seg_edited.mgz is not type UCHAR or FLOAT Is there a way to redefine the data structure? Anthony -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 (try this first) Lab Phone: 305-348-9057 or 305-348-9055 Fax: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://www.fiu.edu/~adick Lab Webpage: http://dcn.fiu.edu

3 2

FreeView doesn't load surfaces
by Domenico M. Mezzapesa 12 Apr '12

12 Apr '12

Dear FreeSurfer experts, I have a problem using FreeView: it can load volume without problems, but when I try to load surface it crash. The error is: MatrixMultiply: m2 is null! No such file or directory Best regards Domenico M Mezzapesa Invita i tuoi amici e Tiscali ti premia! Il consiglio di un amico vale più di uno spot in TV. Per ogni nuovo abbonato 30 € di premio per te e per lui! Un amico al mese e parli e navighi sempre gratis: http://freelosophy.tiscali.it/

3 2

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer