Freesurfer April 2005

freesurfer@nmr.mgh.harvard.edu

25 participants
35 discussions

parcellation
by Wan Park 06 Apr '05

06 Apr '05

Hi, after doing the parcellation and listing the areas with mris_anatomical_stats I have noticed that in many brains (or hemispheres) there are typically two areas that are frequently missing: S_paracentral S_intracingulate is there any explanation for this? is there any way to avoid this? thanks! wan

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aseg skull strip failed
by Michele Perry 05 Apr '05

05 Apr '05

What is the best way to correct an aseg when non-brain regions (eg the skull) are labelled?

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subject averaging
by orphoebe＠polyu.edu.hk 05 Apr '05

05 Apr '05

Hi, I used the following script in the old post to do the subject averaging of the surfaces. However, the 'T1' and 'orig' sub-directory under 'mri' of the 'average' are empty. Is there any way that I can convert the surface file (e.g. rh.orig) into CORs so that I can view the corresponding brain volume using TkMedit? Thanks, Phoebe. ********************************************************** #!/bin/tcsh -ef set SUBJECTS = (031204_wwk 031204_yts 040115_llk 040219_wly) # set SUBJECTS=($SUBJECTS) set average_subject=average if (-e $SUBJECTS_DIR/${average_subject} == 0) then mksubjdirs $SUBJECTS_DIR/${average_subject} else mkdir -p $SUBJECTS_DIR/${average_subject}/surf endif foreach hemi (lh rh) foreach s (orig white pial inflated) set echo=1 mris_make_average_surface -i 7 -o $s $hemi ${s}_avg sphere.reg ${average_subject} $SUBJECTS unset echo end cd $SUBJECTS_DIR/${average_subject}/surf pwd mris_smooth -n 5 ./${hemi}.white_avg ./$hemi.smoothwm mris_inflate ./${hemi}.smoothwm ./${hemi}.inflated mris_curvature -a 10 -w ./${hemi}.white_avg cp ${hemi}.white_avg.H ${hemi}.curv cp $CSURF_DIR/average/$hemi.sphere.reg . ln -s -f $hemi.sphere.reg $hemi.sphere set echo=1 mris_average_curvature -o $average_subject curv $hemi sphere.reg $SUBJECTS ./${hemi}.curv mris_average_curvature -o $average_subject sulc $hemi sphere.reg $SUBJECTS ./${hemi}.sulc mris_average_curvature -o $average_subject thickness $hemi sphere.reg $SUBJECTS ./${hemi}.thickness end cp $SUBJECTS_DIR/$SUBJECTS[1]/mri/T1/COR-.info $SUBJECTS_DIR/${average_subject}/mri/T1 --- Phoebe Suk-tak Chan, Ph.D. Assistant Professor The Hong Kong Polytechnic University Department of Optometry and Radiography Hunghom, Kowloon Hong Kong SAR Tel: (852) 2766 6095 Fax: (852) 2764 6051

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missing aparc.annot in 'labels' directory
by orphoebe＠polyu.edu.hk 04 Apr '05

04 Apr '05

Hi, I just found out that I forgot to link average7 when I did the 'recon-all' on two subjects' brain data. Will it affect the talairach coordinates? Do I need to do the brain inflation again? Also, I found that the label files, e.g. lh.aparc.annot and rh.aparc.annot, which are expected to be in the 'labels' sub-folder of the subject directory. Is there any way that I can generate these labels files again? Thank you for your help in advance. Phoebe --- Phoebe Suk-tak Chan, Ph.D. Assistant Professor The Hong Kong Polytechnic University Department of Optometry and Radiography Hunghom, Kowloon Hong Kong SAR Tel: (852) 2766 6095 Fax: (852) 2764 6051

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Re: [Freesurfer] missing aparc.annot in 'labels' directory
by orphoebe＠polyu.edu.hk 04 Apr '05

04 Apr '05

Hi Bruce, I would like to read the anatomical labels with the corresponding Tal coordinates on tksurfer. However, the aparc.annot files are missing in the 'labels' sub-directory of each of the subjects. How can I regenerate them again? Thanks, Phoebe ---- Original message ---- >Date: Mon, 4 Apr 2005 14:39:04 -0400 (EDT) >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] missing aparc.annot in 'labels' directory >To: orphoebe(a)polyu.edu.hk >Cc: freesurfer(a)nmr.mgh.harvard.edu > >Hi Phoebe, > >you shouldn't have to redo any of that stuff. Average7 is only used as a >domain for visualizing group data, although you are better off making an >average of the subjects in your study and using it instead (in which case >you shouldn't need average7 at all) > >cheers, >Bruce > > >On Tue, 5 Apr 2005 orphoebe(a)polyu.edu.hk wrote: > >> Hi, >> >> I just found out that I forgot to link average7 when I did >> the 'recon-all' on two subjects' brain data. Will it affect >> the talairach coordinates? Do I need to do the brain >> inflation again? Also, I found that the label files, e.g. >> lh.aparc.annot and rh.aparc.annot, which are expected to be >> in the 'labels' sub-folder of the subject directory. Is >> there any way that I can generate these labels files >> again? >> >> Thank you for your help in advance. >> >> Phoebe >> >> --- >> Phoebe Suk-tak Chan, Ph.D. >> Assistant Professor >> The Hong Kong Polytechnic University >> Department of Optometry and Radiography >> Hunghom, Kowloon >> Hong Kong SAR >> Tel: (852) 2766 6095 >> Fax: (852) 2764 6051 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > --- Phoebe Suk-tak Chan, Ph.D. Assistant Professor The Hong Kong Polytechnic University Department of Optometry and Radiography Hunghom, Kowloon Hong Kong SAR Tel: (852) 2766 6095 Fax: (852) 2764 6051

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Freesurfer April 2005