What is the problem with the orientation? The little letters indicate that the orientation is correct. fslview ignores the orientation when displaying so it might come out upside down.
On 07/05/2016 01:35 PM, Sabin Khadka wrote: > > Hi Doug, As you suggested I mapped fmri into the anatomical space using > > mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o > fmcpr.anat.nii.gz > > The orientation of fmcpr.anat.nii.gz seem to have some problem (see > below). However the label seems to be correct. I am a bit confused > here. Do I need to tranform the file somehow? > > fmcpr.nii.gz > > Inline image 1 > > fmcpr.anat.nii.gz > > Inline image 2 > > > > Cheers, > Sabin Khadka > > On Thu, Jun 23, 2016 at 11:28 AM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > After you run preproc-sess, there will be a file called > register.dof6.dat. Map fmri into the anatomical space, something like > > mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat > --o fmcpr.anat.nii.gz > > Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz > > However, I don't think that the aseg has those cerebellum > parcellations. > > On 6/21/16 5:52 PM, Sabin Khadka wrote: >> Hi Yeo- Thanks very much for your answer. Yes the data is in >> mni305 space. I process my fmri data with >> >> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 >> -fwhm 6 -per-run -stc odd >> and then to extract ROI time series values I did >> >> mri_segstats --annot fsaverage rh aparc --i >> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid >> 2000 --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt >> >> and for cortical time series >> >> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab >> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 >> --id 13 --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 >> --id 53 --id 54 --id 58 --i >> rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf >> subCorticalTimeSeries.txt >> >> Now I am not sure as how to extract cerebellum ROIs (time series >> as described in Buckner et.al <http://et.al> 2011)? If there are >> any other additional steps I need to perform ? or if I have to >> use some other scripts commands (other than mri_segstats). >> >> >> Cheers, >> Sabin Khadka >> >> On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo >> <ytho...@csail.mit.edu <mailto:ytho...@csail.mit.edu>> wrote: >> >> Hi Sabin, >> >> The structures 601-628 FreeSurferCololLUT.txt correspond to >> anatomical >> substructures of the cerebellum (e.g., Crus I, etc). Is that >> what you >> want? Or are you looking to use the functional parcels defined in >> Buckner 2011? >> >> In addition, I do not know how mri_segstats works, so I >> cannot verify >> how you call the command is correct. Maybe others can provide >> feedback >> here. >> >> However, the Buckner cerebellar parcellations in >> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/ is >> in MNI152 >> space. From your command, I assume your data is in MNI305 >> space. So >> you might need to transform the parcellation from MNI152 to >> MNI305. >> >> Thanks, >> Thomas >> >> On Sat, Jun 18, 2016 at 8:49 AM, Sabin Khadka >> <mr.sabinkha...@gmail.com <mailto:mr.sabinkha...@gmail.com>> >> wrote: >> > Hi all, >> > >> > I am trying to extract mean time series BOLD data using >> FSFAST from Cortical >> > ROIs + sub cortical ROIs and cerebellum. >> > >> > preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh >> -mni305 -fwhm 6 >> > -per-run -stc odd mri_segstats --annot fsaverage lh >> aparc --i >> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz >> --excludeid 1000 >> > --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt >> > mri_segstats --annot fsaverage rh aparc --i >> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz >> --excludeid 2000 >> > --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt >> > >> > and for cortical time series >> > >> > mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab >> > /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id >> 12 --id 13 --id >> > 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 >> --id 54 --id 58 >> > --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf >> > subCorticalTimeSeries.txt >> > >> > But I am not sure on how exactly to extract time series >> from cerebellar >> > regions. So if I want to extract time series from regions >> as described in >> > Buckner et.al <http://et.al> 2011. Could I just use >> mri_segstats for the labels 601-628 in >> > FreeSurferCololLUT.txt? If not could you please direct me >> to processes that >> > I can use. >> > >> > Cheers, >> > Sabin Khadka >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@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. >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
