diff --git a/doc/fdt_surface.html b/doc/fdt_surface.html
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--- a/doc/fdt_surface.html
+++ b/doc/fdt_surface.html
@@ -3,7 +3,7 @@
<HTML><HEAD><meta http-equiv="Content-Type"
content="text/html;charset=utf-8">
<link REL="stylesheet" TYPE="text/css"
-href="../.fsl/fsl.css"><TITLE>FSL</TITLE></HEAD>
+href="../fsl.css"><TITLE>FSL</TITLE></HEAD>
<BODY><IFRAME width="100%" scrolling="no" frameborder="0" src="fdt_top.html">Broken</IFRAME>
<h3>Running probtrackx from freesurfer cortical surfaces</h3>
@@ -76,38 +76,44 @@ flirt -in myroi -ref $SUBJECTS_DIR/john/mri/nifti/brain -out myconformedroi -app
The next thing to do is to project this ROI into a FreeSurfer surface. We recommend using the grey/white interface to seed tractography from the cortex: (assuming the ROI is in the left hemisphere)<br><br>
<code>
printf "john\n1\n1\n1\n1 0 0 0\n0 1 0 0\n0 0 1 0\n0 0 0 1\n" > reg.dat <br>
-mri_vol2surf --src myconformedroi --srcreg reg.dat --projfrac 0.5 --hemi lh --out myroi2surf.mgh <br>
+mri_vol2surf --src myconformedroi.nii.gz --srcreg reg.dat --projfrac 0.5 --hemi lh --out myroi2surf.mgh <br>
mri_binarize --i myroi2surf.mgh --min 0.5 --o myroi2surf.mgh <br>
-mri_cor2label --i myroi2surf.mgh --surf john lh white --id 1 --l myroilabel <br>
+mri_cor2label --i myroi2surf.mgh --surf john lh white --id 1 --l ./myroilabel <br>
</code>
<br>
-This will create a file called <code>myroilabel.label</code> that you can use directly in probtrackx (see following section).
+This will create a file called <code>myroilabel.label</code> that you can use directly in probtrackx (see following section). We recommend checking the label file by loading it onto a freesurfer surface using tksurfer. E.g.:
+<br><br>
+<code>
+tksurfer john lh white
+</code>
+<br><br>Then File->Label->Load labels
+<br><br>
<h4>3. Running probtrackx using surfaces</h4>
All you need to do now, is to run probtrackx specifying four things: (1) the label file as a seed, (2) a description of the whole cortical surface for the corresponding hemisphere [e.g. surf.white.asc], (3) provide a transformation from conformed FreeSurfer space to diffusion space, and (4) a conformed FreeSurfer volume as a reference space:
<br><br>
<code>
-probtrackx -x myroilabel.label --mesh=$SUBJECTS_DIR/john/surf/lh.white.asc --xfm=freesurfer2fa.mat --ref=$SUBJECTS_DIR/john/mri/nifti/brain [+all the other options]
+probtrackx -x myroilabel.label --mesh=$SUBJECTS_DIR/john/surf/lh.white.asc --xfm=freesurfer2fa.mat --seedref=$SUBJECTS_DIR/john/mri/nifti/brain [+all the other options]
</code>
<br><br>
You can also run probtrackx using a nonlinear warpfield to get from freesurfer space to diffusion space (if you had used FNIRT in step 1 above):<br><br>
<code>
-probtrackx -x myroilabel.label --mesh=$SUBJECTS_DIR/john/surf/lh.white.asc --xfm=freesurfer2fa_warp --invxfm=fa2freesurfer_warp --ref=$SUBJECTS_DIR/john/mri/nifti/brain [+all the other options]
+probtrackx -x myroilabel.label --mesh=$SUBJECTS_DIR/john/surf/lh.white.asc --xfm=freesurfer2fa_warp --invxfm=fa2freesurfer_warp --seedref=$SUBJECTS_DIR/john/mri/nifti/brain [+all the other options]
</code>
<br><br>
Note: in this last case, we need both forward and backward transforms fa<-->freesurfer.
<h4>4. Using some of the outputs</h4>
-When using classification targets in probtrackx, together with a surface-based seed, an output is created in the form of a matrix called matrix_seeds_to_all_targets. You can use this file to run find_the_biggest and produce label files for each of the hard-classified clusters. You can also use it to produce overlay files containing connectivity scores to each target.<br><br>
+When using classification targets in probtrackx, together with a surface-based seed, you may use the probtrackx option <code>--seedcountastext</code>, in which case an output is created in the form of a matrix called matrix_seeds_to_all_targets. You can use this file to run find_the_biggest and produce label files for each of the hard-classified clusters. You can also use it to produce overlay files containing connectivity scores to each target.<br><br>
Running find_the_biggest using matrix_seeds_to_all_targets:<br><br>
<code>
find_the_biggest matrix_seeds_to_all_targets myroilabel.label myclusters
</code>
<br><br>
-The output of this command will be a set of files called myclusters<i>.label, i.e. one label file per cluster. You can combine these to produce a single annotation file:
+The output of this command will be a set of files called myclusters<i>.label, i.e. one label file per cluster. You can combine these to produce a single annotation file:
<br><br>
<code>
-mris_label2annot --s john --h lh --ctab $FSLDIR/etc/luts/fsrandlut.txt --a myannot --l myclusters_1.label --l myclusters_2.label [etc.]
+mris_label2annot --s john --h lh --ctab $FSLDIR/etc/luts/fsrandlut.txt --a myannot `ls myclusters_*.label | awk '{print "--l " $1}'`
</code>
<br><br>
Once this is done, you can load the result myannot.annot onto tksurfer. Just type:<br><br>