Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30128 discussions

manual parcellation of labels
by Ketwaroo, Gyanprakash Avinash 25 Jan '05

25 Jan '05

Hello, I guess my main question is are the volume tal coordinates in tkmedit equivalent to the vertex Tal in tksurfer. That is, can I ignore drawing the line in tkmedit and converting with csurf, and just trace out the Tal = 0 line in tksurfer? I think this is what you are implying but just want to make sure. Also, the cingulate labels are in RAS coordinates. Is there a quick way to convert the Tal=0 coordinate to a RAS coordinate so that I can just divide the cingulate label by applying a condition (eg RAS < x) rather than tracing it out in tksurfer. Thank you for all your help. Avinash Hi Aviinas, you could draw the label directly on the inflated surfaces, then use mri_label2label to map it from one subject (or the average) to the others. cheers, Bruce

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manual parcellation of labels
by Ketwaroo, Gyanprakash Avinash 25 Jan '05

25 Jan '05

Hi, I want to divide my cingulate labels into anterior and posterior cingulate labels. This divison is based on a line perpendicular to the AC-PC axis, and through the AC. Currently, I am trying to do this by using csurf and clicking and saving points along the Tal = 0 coordinate within the midsagittal plane of the tkmedit view. I then go to the points in the tksurfer view and then draw a line here to create a new label. It seems that there must be an easier way of doing this using the code that csurf employs to link the volume and surface coordinates. If you could suggest a method for automating this, I would greatly appreciate it. Thanks, Avinas

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Functional Overlay
by Ruth Smans 25 Jan '05

25 Jan '05

Hi, I am having problems with functional overlays onto my anatomical. When I go to set functional sessions directory an Alert message appears saying : session:left_down (functional name) scripts subdir not found using /tmp make scripts dir to save session_specific params. What exactly is this refering too? Thanks alot Ruth Smans

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TKSURF ERROR
by Ajay Pillai 20 Jan '05

20 Jan '05

I recently upgraded my fedora to fedora core 3 I am getting the following error when I try to use tksurf /user/freesurfer/bin/Linux/tksurfer: error while loading shared libraries: libtk8.3.so: cannot open shared object file: No such file or directory How do I fix this Ajay

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how to visualize the parcellation
by Wan Park 20 Jan '05

20 Jan '05

hi, after doing: recon-all -stage4b -subjid 40032 -hemi lh recon-all -stage4b -subjid 40032 -hemi rh, i did: parcellate_subject 40032 and it seems to have finished without problems. now, how can i visualize the different areas? thanks, wan

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full surface cuts
by Joongnam Yang 19 Jan '05

19 Jan '05

Hi, I followed the manual instructions on full surface cuts, but not working. Here is what I did. (1) cut five relaxation cuts. (2) right-click. (3) left-click one of regions that are to be kept. (4) select "Fill Uncut Area" button, The image refrehses, but no change is made on the image. The circular midline region is supposed to be cut off. (I looked at the archive; someone had this problem, but she just said later she figured it out and no comment on it was given) Thanks. Nam.

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Re: [Freesurfer] manual editting not implemented
by Joongnam Yang 14 Jan '05

14 Jan '05

Thanks Brian, Does that mean csurf interface is useless for "creating surfaces" to implement the editting of major topological defects? Nam. >>> "Brian T. Quinn" <btquinn(a)nmr.mgh.harvard.edu> 01/14/05 3:22 PM >>> hi Nam- please refrain from using the csurf interface to create surfaces. instead, run through the command line: recon-all -stage2 -subjid <subject_name> this will create a log file($SUBJECTS_DIR/subject_name/scripts/recon-all.log) include this with your email so we can better assist you with your difficulties. thanks, brian On Fri, 14 Jan 2005, Joongnam Yang wrote: > Hi, > > I did manual editting for lateral ventricles, fornix, basal ganglia, optic > nerve, > as illustrated in the cortical reconstruction tutorial, for both left and > right hemispheres, and DID save them in the "wm" volume. > Then I ran "create surface", but nothing is changed. > > What could have been wrong? > > Comments are appreciated. > Nam. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- brian t. quinn

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manual editting not implemented
by Joongnam Yang 14 Jan '05

14 Jan '05

Hi, I did manual editting for lateral ventricles, fornix, basal ganglia, optic nerve, as illustrated in the cortical reconstruction tutorial, for both left and right hemispheres, and DID save them in the "wm" volume. Then I ran "create surface", but nothing is changed. What could have been wrong? Comments are appreciated. Nam.

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Each of the 256 slices?
by Joongnam Yang 13 Jan '05

13 Jan '05

Thanks Evelina, For the manual removal, should we do it for EVER slice of rhe wm volume? Nam. >>> <evelina(a)nmr.mgh.harvard.edu> 01/12/05 11:16 PM >>> Or if all else seems to fail and you have time constraints, you can edit the pons out manually in the wm volume. Use a large radius for the brush size (about a 3 or 4) and use a square brush, then just erase across the pons, where the cutting plane should have been. Coronal is the best view for accomplishing this. Save the wm volume, then rerun the fill and inflation as usual. > did you run the MNI talairaching? Did it work? If not, you need to use > volume scanner coords as input (you can turn them on under > view->information). Make sure it is a point in which the pons appears > disconnected in a horizontal view, and superior to the cerebellar > peduncles. > > Bruce > > > On Wed, 12 Jan 2005, Joongnam > Yang wrote: > > > Hi, > > > > I collected new anatomical data with isometric voxels. > > When I ran "create surface," the pons is not being removed. > > I tried many different coordinates for the pons (either Volume Index or > > Talairach), but the pons is still not being cut out. > > > > Any suggestions? > > > > Thanks > > Nam. > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Parcellation 2
by Wan Park 13 Jan '05

13 Jan '05

Thanks for the previous help! Now I have this problem: setenv CSURF_DIR $FREESURFER_HOME [ash:local/freesurfer_package/freesurfer] wpark% cd subjects [ash:freesurfer_package/freesurfer/subjects] wpark% parcellate_subject 40032 reading atlas from /usr/local/freesurfer_package/freesurfer/average/ lh.atlas2002_simple.gcs... reading color table from GCSA file.... MRISreadVertexPosition(sphere.reg): could not open file /usr/local/freesurfer_package/freesurfer/subjects/40032/su rf/lh.sphere.reg No such file or directory mris_ca_label: could not read annot file sphere.reg for 40032 No such file or directory 40032 is my subject. what could be the problem? thanks, wan

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