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 <[email protected]> > 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/MultiModalFmriIndividual > > 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 <[email protected]> >> >> 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. >>> >>> >>> >> >> >> -- 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: [email protected]
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