Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

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

2 1

parcellation
by Wan Park 13 Jan '05

13 Jan '05

Hi, I am want to parcellate my brains, but when I put "parcellate_subject" alone, I receive the following message; tcsh: CSURF_DIR: Undefined variable What should I do? Second question: Let's say my subject is called bert What's the complete line I should right to do it? Thanks a lot, Wan

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Re: [Freesurfer] two questions
by Joongnam Yang 13 Jan '05

13 Jan '05

Thanks, Bruce, Does MNI talairaching mean more than doing "talairach2" and checking the registration with"tkregister2", which I did? Nam. >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 01/12/05 10:08 PM >>> 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 >

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Re: [Freesurfer] two questions
by evelina＠nmr.mgh.harvard.edu 12 Jan '05

12 Jan '05

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 > > >

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