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] Create brain outline from pial surface

, but it 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 https

Re: [Freesurfer] --reg in mri_vol2surf

, Liang Wang wrote: Hi Bruce, Thanks a lot for the suggestions! Here are some followup questions. 1) The functional volume was PET data and anatomical data have been processed with Freesurfer. I run the bbregister as: bbregister --mov PET.nii --s subject_name --reg register.dat --t1

[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

Re: [Freesurfer] mris_calc or other calculators

Cool! Thanks Doug! -Liang On Wed, Dec 10, 2014 at 3:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu 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, I have cortical thickness

Re: [Freesurfer] --reg in mri_vol2surf

suggestions for these questions would be very appreciated! -Liang On Fri, Dec 5, 2014 at 5:40 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Liang try bbregister. cheers Bruce On Fri, 5 Dec 2014, Liang Wang wrote: Hi Experts, At subject level, I want to convert a functional

[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

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

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 regions (particular along a big sulcus) show quite high probability value

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 fis...@nmr.mgh.harvard.edu 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, Thanks

[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] Coordinate transformation between raw space and freesurfer confirm space

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? Thanks, Liang The information in this e-mail is intended

[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

[Freesurfer] Errors for talairach transformation

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 Neuroscience Institute

Re: [Freesurfer] Errors for talairach transformation

for some 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 get a skull-stripped brain image. The processing exits

Re: [Freesurfer] Errors for talairach transformation

...@nmr.mgh.harvard.edu 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 converted by dicom files. The image can

[Freesurfer] Transforming aseg.mgz to DTI space

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 Addiction Services

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

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 individual parcellation result. Also, I am using the following combined

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

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 On Sat, 17 Jul 2010, liang wang wrote: Hi, When

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

, liang wang wrote: Hi, Does anyone know one of studies which uses the parcellations (aparc or aparc.a2009s) Freesurfer provides to extract fMRI time course from each subject's fMRI data. Reading the instructions in Freesurfer Wiki, I know how to do that. However, I am not sure whether I should

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

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 Psychiatry

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

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 Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext

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

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 wangl...@gmail.com Hi Also, when using tksurfer to present ?h.aparc.annot, I can not find the insula

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

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 find it. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab

[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

[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

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

to follow 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 Bruce On Fri, 12 Mar 2010, liang wang wrote: Hi FS experts

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

/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 separately create many label files, each of which include vertex number

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

in 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.com

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

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 (including all gyral and sulci) from the image aparc.a2009s+aseg.mgz. I

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

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