A list of vertices is made from a path by creating a closed curve from the points along the path and using all the points in the interior of this closed curve.

A label file (.label) is a text file where the first two lines are "header" and each line after that is a vertex. The first line has the form:

#label , from subject YOURSUBJECTNAME

The next line is the number of vertices in your label

The following lines all have 5 columns of the form:

1. verteix number 2. vertex x 3. vertex y 4. vertex z 5. stat

you can just set the stat to 0

See $FREESURFER_HOME/subjects/fsaverage/label/lh.cortex.label for example.

#label , from subject fsaverage 149955 88 -42.261 -81.724 -13.242 0.000000 445 -28.781 -85.827 -16.289 0.000000 446 -39.862 -74.518 -14.432 0.000000 616 -42.856 -74.239 -5.499 0.000000 979 -35.991 -88.051 -14.552 0.000000

Aaron Shmookler wrote:

Can you elaborate on what you mean by making a label "out of the interior?" Also, how would you make a label from my list?

Hi Aaron,

no, they don't really mean anything. They are a side effect of a number of algorithms (tesselation and topology correction). The .asc lists all the vertices, then all the faces:

int MRISwriteAscii(MRI_SURFACE *mris, char *fname) { int vno, fno, n ; VERTEX *v ; FACE *face ; FILE *fp ;

fp = fopen(fname, "w") ; if (!fp) ErrorReturn(ERROR_NOFILE, (ERROR_NOFILE, "MRISwriteAscii: could not open file %s",fname));

fprintf(fp, "#!ascii version of %s\n", mris->fname) ; fprintf(fp, "%d %d\n", mris->nvertices, mris->nfaces) ;

for (vno = 0 ; vno < mris->nvertices ; vno++) { v = &mris->vertices[vno] ; fprintf(fp, "%f %f %f %d\n", v->x, v->y, v->z, v->ripflag) ; } for (fno = 0 ; fno < mris->nfaces ; fno++) { face = &mris->faces[fno] ; for (n = 0 ; n < VERTICES_PER_FACE ; n++) fprintf(fp, "%d ", face->v[n]) ; fprintf(fp, "%d\n", face->ripflag) ; }

fclose(fp) ; return(NO_ERROR) ; }

chers, Bruce

On Wed, 30 Jul 2008, Aaron Shmookler wrote:

Do the vertex numbers mean anything significant or can they be any number?

Also, it appears that there are two different sets of vertices in an mris_convert asc file of ?h.inflated. What are these vertices and what do they mean?

Hi,* * So far I have been able to take my ?h.inflated file and turn it into a label file from my vertices of interest. That is, what I thought are my vertices of interest, namely a closed path around the caudal temporal pole. Given one vertex point I manually choose I want to generate a list of vertices holding 'z' constant and ordered in a clock (-y to +y). While I am getting vertices, the label I am getting is in the occipital lobe. Even after manipulating the numbers and vertices I still cannot manage to put a label on the TP, let alone outside the occipital lobe. Any thoughts and comments you may have would be greatly appreciated. Thanks! ~Aaron

<---begin script here (I am trying to make this work for one subject)--->

#!/bin/tcsh -ef

# acquire all vertices from lh.inflated file (when I execute this script I replace $subj with the actual subject, so this line of code works) mris_convert $subj/surf/lh.inflated ~/Desktop/test.asc

# extract vertices outlining the temporal pole caudal border given constant 'z.' # The constant 'z' I think exists only once; other points along the path have a slightly different 'z'. # Therefore, I give a very small range of 'z' values that I hope are close enough to represent the caudal border # The 'z' coordinate is -61.0105, so search from -62 to -61 # sort the second column, which contains 'y' values cat ~/Desktop/test.asc | awk '{ if($3 > -62 && $3 < -61) print $1, $2, $3, $4}' | sort -n -k2 > ~/Desktop/extract.asc

#echo header 1st line, label information, into label file echo '#! label , from subject $SUBJ/ vox2ras=TkReg coords=white' > ~/Desktop/caudal_border.label

#echo header 2nd line, the number of ROI vertices, into label file cat ~/Desktop/extract.asc | awk 'END{print NR}' >> ~/Desktop/caudal_border.label

#echo ROI vertices into label file with number lines (cat -n) substituting for vertex numbers cat -n ~/Desktop/extract.asc >> ~/Desktop/caudal_border.label

#mris_anatomical_stats the label file -- to be written once appropriate label has been acquired