Mishkin,

This will create what you want:

cd subj/label mri_annotation2label --subject subj \ --hemi lh \ --annotation aparc \ --seg lh.aparc.mgh

replacing subj and lh with appropriate.

then type:

mris_convert -c ./lh.aparc.mgh \ ../surf/lh.white \ lh.aparc.asc

and the output file (lh.aparc.asc) will have lines like this:

71586 -39.60123 -13.37572 -34.24242 1007.00000

which are:

vno X Y Z labelno

where labelno is found in $FREESURFER_HOME/FreeSurferColorLUT.txt, for instance 1007 is ctx-lh-fusiform

Nick

On Tue, 2009-04-07 at 17:00 -0400, Mishkin Derakhshan wrote:

Thanks. After reading up on the wiki it seems that a more general solution I'm loking for would be to somehow get the contents of ?h.aparc.annot into ascii form. I know mris_annotation2label will kind of do this, but it creates one file for every label. What I'm loooking for is a single file with n rows corresponding to the n vertices in ?h.pial, and then next to each one, a number representing what label it belongs to (or what value to look up in the LUT). can this be done somehow, or at the very least can I get the contents of ?h.*.annot into ascii format so I can manipulate things.

thanks, mishkin

On Tue, Apr 7, 2009 at 1:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Mishkin,

yes, the ?h.cortex.label should be created for every subject that labels the cortical regions of the surface.

cheers, Bruce On Tue, 7 Apr 2009, Mishkin Derakhshan wrote:

...

Hello list, I would like to create a mask on fsaverage/surf/?h.pial that masks out the areas where the surface does not follow the cortex, but is just cutting across the mid line or across the brain stem. I know Freesurfer does this to maintain the surface toplogy, and I think it only does this in these two areas. Does a simple txt file with n vertices and a 0 or 1 value at each vertex exist somewhere? Has anyone on the list bothered to label this area manually and would be willing to share? thanks, mishkin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi, I'm not sure whether the --seg option ever got looked into, but for those searching the lists in the future, here is the quick hack I used in perl to accomplish what I wanted: mishkin

#! /usr/bin/perl

if($ARGV <1){ print "\nUsage: $0 <subject_name>\n"; print "Assumes SUBJECTS_DIR is set, and mri_annotation2label is in your path\n"; print "WIll output ?h.annot.asc, which has the names of the parcellations, and\n" print "WIll output ?h.annot.txt, which has the number of the parcellations [1-35]\n" exit(1); }

$name = $ARGV[0]; $DIR = $ENV{'SUBJECTS_DIR'};

@structures = qw(bankssts caudalanteriorcingulate caudalmiddlefrontal corpuscallosum cuneus entorhinal frontalpole fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital lateralorbitofrontal lingual medialorbitofrontal middletemporal paracentral parahippocampal parsopercularis parsorbitalis parstriangularis pericalcarine postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate rostralmiddlefrontal superiorfrontal superiorparietal superiortemporal supramarginal temporalpole transversetemporal unknown);

@sides = qw(lh rh);

foreach $hemi(@sides){ my @master; system("mri_annotation2label --subject ${name} --hemi ${hemi} --outdir ${DIR}/${name}/label/"); $i=0; foreach $reg(@structures){ $i = $i+1; #index number of each label open(FIN,"${DIR}/${name}/label/${hemi}.${reg}.label"); $line = <FIN>; #header $line = <FIN>; #header while($line = <FIN>){ my @array = split(/ /,$line); my $vertex = $array[0]; #get the vertex number $master[${vertex}] = "${reg} $i"; } close(FIN); } open(FASC,"> ${DIR}/${name}/label/${hemi}.annot.asc"); open(FTXT,"> ${DIR}/${name}/label/${hemi}.annot.txt"); foreach $element(@master){ my @array = split(/ /,$element); print FASC "$array[0]\n"; #names print FTXT "$array[1]\n"; #number } close(FASC); close(FTXT); }

On Thu, Nov 5, 2009 at 9:14 PM, Mishkin Derakhshan mishkind@gmail.com wrote:

Hi Nick, I was recently trying to redo something you had helped me out with back in April (see below), but I now get this error: ERROR: Option --seg unknown

The wiki page still says this option exists, but I'm guessing is outdated https://surfer.nmr.mgh.harvard.edu/fswiki/mri_annotation2label#Detailsfor.27...

Was this option deprecated at some point? Could you send me a version where this works, or is there another way, I can get what I'm after:

...

...

to somehow get the contents of ?h.aparc.annot into ascii form. I know mris_annotation2label will kind of do this, but it creates one file for every label. What I'm loooking for is a single file with n rows corresponding to the n vertices in ?h.pial, and then next to each one, a number representing what label it belongs to (or what value to look up in the LUT).

thanks, mishkin

On Wed, Apr 8, 2009 at 4:19 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:

...

Mishkin,

This will create what you want:

cd subj/label mri_annotation2label --subject subj \  --hemi lh \  --annotation aparc \  --seg lh.aparc.mgh

replacing subj and lh with appropriate.

then type:

mris_convert -c ./lh.aparc.mgh \  ../surf/lh.white \  lh.aparc.asc

and the output file (lh.aparc.asc) will have lines like this:

71586 -39.60123 -13.37572 -34.24242 1007.00000

which are:

vno     X       Y       Z       labelno

where labelno is found in $FREESURFER_HOME/FreeSurferColorLUT.txt, for instance 1007 is ctx-lh-fusiform

Nick

On Tue, 2009-04-07 at 17:00 -0400, Mishkin Derakhshan wrote:

...

Thanks. After reading up on the wiki it seems that a more general solution I'm loking for would be to somehow get the contents of ?h.aparc.annot into ascii form. I know mris_annotation2label will kind of do this, but it creates one file for every label. What I'm loooking for is a single file with n rows corresponding to the n vertices in ?h.pial, and then next to each one, a number representing what label it belongs to (or what value to look up in the LUT). can this be done somehow, or at the very least can I get the contents of ?h.*.annot into ascii format so I can manipulate things.

thanks, mishkin

On Tue, Apr 7, 2009 at 1:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Mishkin,

yes, the ?h.cortex.label should be created for every subject that labels the cortical regions of the surface.

cheers, Bruce On Tue, 7 Apr 2009, Mishkin Derakhshan wrote:

...

Hello list, I would like to create a mask on fsaverage/surf/?h.pial that masks out the areas where the surface does not follow the cortex, but is just cutting across the mid line or across the brain stem. I know Freesurfer does this to maintain the surface toplogy, and I think it only does this in these two areas. Does a simple txt file with n vertices and a 0 or 1 value at each vertex exist somewhere? Has anyone on the list bothered to label this area manually and would be willing to share? thanks, mishkin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

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