[Freesurfer] Create brain outline from pial surface

doesn't work for this goal. Any suggestions would be appreciated. Best, Liang -- Liang Wang, PhD Institute of Psychology Chinese Academy of Sciences Beijing 100101, China ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Create brain outline from pial surface

Thanks Bruce. I applied mri_binarize to brainmask.mgz with specified threshold and got many holes in the mask. In addition, brainmask.mgz includes the cerebellum. I would like to only create the brain (cerebral cortex) outline based on the pial surface. Thanks. Best, Liang -- Liang Wang, PhD

[Freesurfer] Coordinate transformation between raw space and freesurfer confirm space

Hi, I need to convert a vast amount of coordinates (voxel unit: i, j, k) in raw space to freesurfer space (256*256*256 FOV). Could someone give some suggestions how to solve it? Thanks, Liang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu h

Re: [Freesurfer] Coordinate transformation between raw space and freesurfer confirm space

cheers > Brce > > > > On Sun, 9 Sep 2012, liang wang wrote: > > Hi, >> I need to convert a vast amount of coordinates (voxel unit: i, j, k) in >> raw space to freesurfer space (256*256*256 FOV). Could >> someone give some suggestions how to solve it? >>

[Freesurfer] Anatomical variation between individual surface and average template

output a file which characterizes this type of anatomical variation. Could someone point me which file it is and how to use it to create a group-level measure in order to clear display somewhere has large variation. Thanks. Best, Liang -- Liang Wang, PhD Neuroscience of Attention and Perception

Re: [Freesurfer] Anatomical variation between individual surface and average template

e of the inflated > surface, the sulc and mean curvature of the white surface. > > cheers > Bruce > > > On Thu, 13 Sep 2012, liang wang wrote: > > Dear FS folkers, >> I am working on a functional probabilistic atlas. I find that some >> functional >> r

Re: [Freesurfer] Anatomical variation between individual surface and average template

that lh.sulc seems to be smoothed. Thanks. Best, Liang 2012/9/14 Bruce Fischl > yes, you can use mris_make_template to generate these results (it's what > we used to create the tif files in the first place) > > On Fri, 14 Sep 2012, liang wang wrote: > > Dear Bruce, >

[Freesurfer] --reg in mri_vol2surf

Hi Experts, At subject level, I want to convert a functional volume (in a subject's native space) to this subject's native surface. The functional volume has been registered to this subject T1 images in native space. I know "mri_vol2surf' would do the job but unsure how to generate the registrati

Re: [Freesurfer] --reg in mri_vol2surf

he results does not look right. Any suggestions for these questions would be very appreciated! -Liang On Fri, Dec 5, 2014 at 5:40 PM, Bruce Fischl wrote: > Hi Liang > > try bbregister. > > cheers > Bruce > > On Fri, 5 Dec 2014, Liang Wang wrote: > > Hi Experts, >&

Re: [Freesurfer] --reg in mri_vol2surf

match up. It won't be easy. Your bbregister command is not going to work > for sure, you cannot use --init-header (which should only be used for > two MRIs acquired in the same session). Try --init-fsl or --init-spm. > Most PET tracers have an effective T2 weighting > > > > On

[Freesurfer] mris_calc or other calculators

Hi experts, I have cortical thickness on fsaverage surfaces (?h.thickness_on_fsaverage.mgh) from a group of individuals. I'd like to create a volume (.mgh) that represents group mean or sd or other descriptive statistics. I know mris_calc can do similar job but wonder if there is more straightforw

Re: [Freesurfer] mris_calc or other calculators

Cool! Thanks Doug! -Liang On Wed, Dec 10, 2014 at 3:05 PM, Douglas N Greve wrote: > > You can use mri_concat, something like > > mri_concat file1.mgh file2.mgh --mean --o mean.mgh > > > > On 12/10/2014 04:00 PM, Liang Wang wrote: > > Hi experts, > > > &

[Freesurfer] Extracting ROIs from aparc.a2009s+aseg.mgz

command: tkmedit subjid orig -aux brain -aparc.a2009s+aseg.mgz, but can correctly display . Any advise would be appreciated. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Av

Re: [Freesurfer] Extracting ROIs from aparc.a2009s+aseg.mgz

l. > > To display aparc.a2009s+aseg.mgz in tkmedit, you can do: > tkmedit subjid orig.mgz -segmentation aparc.a2005s+aseg.mgz > > Allison > -- > > On Wed, 10 Mar 2010, liang wang wrote: > > Hi FS experts, >> >> Does anyone know how to extract these ROIs (includi

Re: [Freesurfer] Extracting ROIs from aparc.a2009s+aseg.mgz

harvard.edu/fswiki/FsTutorial/MultiModalRegistration > > Having the aparc divided up isn't necessary to do them though. > Allison > > -- > > On Thu, 11 Mar 2010, liang wang wrote: > > Hi Allison, >> >> Thanks. I have used the command line below to separatel

[Freesurfer] How to transform brain.mgz back to native space

advance. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail

Re: [Freesurfer] How to transform brain.mgz back to native space

those instructions instead. > Allison > > -- > > On Sat, 13 Mar 2010, Bruce Fischl wrote: > > Hi Liang, >> >> you should just be able to use the -rl (reslice like) option in >> mri_convert and give the orig/001.mgz as the target. >> >> cheers

[Freesurfer] Extracting time series from aparc.a2009s+aseg.mgz

Hi FSusers, Is there a way to extract averaged BOLD signal from the identified cortical regions in aparc.a2009s+aseg.mgz. Thanks Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West

[Freesurfer] Which way is better for mapping automatic segmentations

/bold.feat --aseg aparc.a2009s+aseg cd /drive3/TEST/BOLD/bold.feat/reg/freesurfer *BNC006 .aseg-in-fun.nii.gz* and *aparc.a2009s+aseg.nii.gz* are outputs from the first and second one, respectively. Does anyone give me some suggestion about which method is suitable to my situation. Best, Liang -- Liang

[Freesurfer] Displaying significant difference with a threshold of cluster size

;true" difference. I don't know how to make it by a selected threshold of cluster size . Any suggestions would be appreciated. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 9

Re: [Freesurfer] Displaying significant difference with a threshold of cluster size

by cluster-based threshold method. Is it a acceptable way? Liang 2010/7/11 Douglas N Greve > You should correct for multiple comparisons using cluster-wise correction. > See the tutorials on group analysis on our wiki. > > doug > > liang wang wrote: > >> Hi, &

[Freesurfer] Creating table of segmentation volumes

was 745 mm^3 in the aseg.stats, but 729 mm^3 in the wmparc.stats. I am not sure why they are different and which file should be selected to represent the volumes. I am appreciated for any suggestions. Best, Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry

[Freesurfer] A region loss in the ?h.aparc.stats

ctx-lh-insula). I am creating a figure to show all these ROIs. Hence I am curious why there is not the insula shown. I am appreciated if anyone could give me a hand for solving this seemly conflicting information. Thanks so much. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab

Re: [Freesurfer] A region loss in the ?h.aparc.stats

all these ROIs. Hence I am >> curious why there is not the insula shown. >> > What is where the insula should be? > I think that the insula should be displayed in the ?h.aparc.annot, because ?h.aparc.stats reports several surface measurements of this regions. But I can't

Re: [Freesurfer] A region loss in the ?h.aparc.stats

t and find existence of the insula inside each subject's file. I don't know what's the wrong during the average process. I am looking forward to your suggestions. Thanks. Liang 2010/7/13 liang wang > Hi > > >> >>> Also, when using tksurfer to present ?h.aparc.anno

[Freesurfer] Extracting fMRI time course and computing correlations among them

tions from the average output (obtained from make_average_subject), or the parcellations based on each subject. I would next compute functional connectivity between these regions. I am appreciated for any suggestions. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psych

[Freesurfer] Creating aparc.a2009s+aseg.mgz for the averaged data

y make_average_surface file is updated by Nick's new one. And it does not include ribbon.mgz before updating. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouv

Re: [Freesurfer] Extracting fMRI time course and computing correlations among them

ely use the individuals. Use mri_vol2surf to convert the motion > corrected (and otherwise unsmoothed) fmri time courses to the > surface. Then use mri_segstats with the --avgwf and --annot options > to compute the mean time course over the parcellations. > > doug > > > > &

Re: [Freesurfer] Extracting fMRI time course and computing correlations among them

27;t amount > for much. > > doug > > liang wang wrote: > >> Dear Doug, >> >> Thanks for your comments. However, I am worried about the different number >> of voxels within each parcellation between subjects, if extracting fmri time >> course from individ

Re: [Freesurfer] Creating aparc.a2009s+aseg.mgz for the averaged data

distance youraveragesubject > > Note this when you make the aparc+aseg in this way, it should only be > used when visualizing data on the mni305 brain. Don't extract volumes, > etc. If you want to use one of the surface parcellations, do a > surface-based analysis. > > doug &g

[Freesurfer] Creating a label

obtained by mri_cor2label seemingly includes more tiny, disperse vertices. Does anyone know what's happening? Thanks. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue

[Freesurfer] Transforming aseg.mgz to DTI space

rsely apply this transformation file. I tried to use --apply_inverse_transform in mri_convert, but it doesn't work. Any suggestions would be appreciated. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addi

[Freesurfer] Errors for talairach transformation

, pval=0. < threshold=0.0050) Linux node37.cluster 2.6.18-128.el5 #1 SMP Wed Jan 21 10:41:14 EST 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ph exited with ERRORS at Wed Nov 17 10:15:36 EST 2010 -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscie

Re: [Freesurfer] Errors for talairach transformation

reason. Try > running mri_info on the dicoms to see if there is something strange in them > > > On Wed, 17 Nov 2010, liang wang wrote: > > Hi FSusers, >> >> The terminal displays errors when I run "recon-all -autorecon1 -subjid >> ..." >> to

Re: [Freesurfer] Errors for talairach transformation

hl > can you try running recon-all directly on the dicoms? Also, it's probably > pretty noisy at .5mm in-plane - how does it look? Is it whole brain? > > > On Wed, 17 Nov 2010, liang wang wrote: > > Hi Bruce, >> >> I run the command on a NIFTI image con