Hi Allison,

Thanks. I have used the command line below to separately create many label files, each of which include vertex number and XYZ coordinates. mri_annotation2label --subject BNC006 --hemi lh --labelbase aparc.a2009

Sorry for not declaring my intention previously. What I actually want to do is utilizing the gray ROIs recorded in aparc.a2009s+aseg.mgz to generate the average time courses of each ROI from BOLD fMRI scanned from the same subject. Can you give some advice how to accurately make it. Also, I am worried the registeration issues across different modality images.

Best, Liang

2010/3/11 Allison Stevens astevens@nmr.mgh.harvard.edu

Liang, mri_annotation2label will separate all the ROIs in the ?h.aparc.a2009s.annot - is this what you need? I'm not sure what you mean by "mask image based on this image using 1, 2". You can merge or split labels as well.

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 (including all gyral and sulci) from the image <aparc.a2009s+aseg.mgz>. I just want to create a mask image based on this image by using 1, 2, .. to code different brain areas. Thanks for your solutions.

Also, I can not display the image 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

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.

Hi Allison,

Thanks for the website you provide me. Through reading, I understand how to averaged extract contrast effect size in each ROI generated by FreeSurfer (e.g. aparc.a2009s+aseg.mgz). You know, the contrast image is a 3D file for each subject. However, BOLD data usually is a 4D image (i.e. 3D + time course). I try to use the following commands to carry out what I need (Let me say *BNC006 *is a subject ID, *example_func.nii.gz* a motion correction template and *filtered_func.nii.gz* a 4D BOLD data with realigment to example.nii.gz). Note that The below id is just to test whether there is a correct output.

$ bbregister --mov example_func.nii.gz --bold --s BNC006 --init-fsl --reg register.dat $ mri_vol2vol --mov filtered_func.nii.gz --reg register.dat --fstarg --interp nearnest --o filtered_func.anat.mgh $ mri_segstats --seg $SUBJECTS_DIR/BNC006/mri/aparc.a2009s+aseg.mgz --ctab $FREESURFER/FreeSurferColorLUT.txt --id \ 11101 --id 11105 --i fitered_fun.anat.mgh --sum filter.stats

The fist two lines run fine, but the last one seems stop after displaying loading filter_fun.anat.mgh.

Your any suggests will be appreciated.

Best, Liang

2010/3/12 Allison Stevens astevens@nmr.mgh.harvard.edu

Liang, We have a very good tutorial which takes you through what you would like to do. It's located here:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividua...

There is also some information on registration here: https://surfer.nmr.mgh.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 separately create many label files, each of which include vertex number and XYZ coordinates. mri_annotation2label --subject BNC006 --hemi lh --labelbase aparc.a2009

Sorry for not declaring my intention previously. What I actually want to do is utilizing the gray ROIs recorded in aparc.a2009s+aseg.mgz to generate the average time courses of each ROI from BOLD fMRI scanned from the same subject. Can you give some advice how to accurately make it. Also, I am worried the registeration issues across different modality images.

Best, Liang

2010/3/11 Allison Stevens astevens@nmr.mgh.harvard.edu

Liang,

...

mri_annotation2label will separate all the ROIs in the ?h.aparc.a2009s.annot - is this what you need? I'm not sure what you mean by "mask image based on this image using 1, 2". You can merge or split labels as well.

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 (including all gyral and sulci) from the image <aparc.a2009s+aseg.mgz>. I just want to create a mask image based on this image by using 1, 2, .. to code different brain areas. Thanks for your solutions.

Also, I can not display the image 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

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.