[Freesurfer] tkmedit --> tksurfer (tkmedit points not being saved)
Although new to Freesurfer, I have in the past been able to save points on tkmedit and bring them up on an inflated tksurfer image. However, now this is not happening. When I click on Save Point or go to Tools>Save Point in tkmedit, no coordinates are brought up in the tkmedit Terminal window. So, when I try to bring up points on tksurfer (goto saved point) no points are shown. Help would be greatly appreciated. Thanks, Aaron ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tkmedit reconstruction to perpendicular axes of ROIs
Is it possible to reconstruct an MRI such that the images in tkmedit are perpendicular to the axis of a particular region such as in my ROI the temporal pole? As I see them the tkmedit MRIs are oblique slices with the dorsal regions appearing caudally on the tksurfer (volumetric) images relative to the ventral regions. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] importing vertices and applying path_new_path_from_marked_vertices
Hello, Here's what I did: 1) mris_convert ?h.inflated file.asc 2) extract vertices of interest into file2.asc Here is what I want to do: I want to import the vertices from file2.asc into tksurfer and apply the *path_new_path_from_marked_vertices *function so that I can then create a label. How might I do this? Thanks, Aaron ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] importing vertices and applying path_new_path_from_marked_vertices
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? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] importing vertices and applying path_new_path_from_marked_vertices
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? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] importing vertices and applying path_new_path_from_marked_vertices
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
___
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