Freesurfer January 2005

freesurfer@nmr.mgh.harvard.edu

23 participants
50 discussions

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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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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Re: [Freesurfer] two questions
by Joongnam Yang 12 Jan '05

12 Jan '05

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.

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talairach coords on TkMedit
by Joongnam Yang 12 Jan '05

12 Jan '05

Hi, TkMedit doesn't show talairach coordinates. I ran talairach2 -s subjid, and clicked (View->Information->talairach), but still talairach coords row comes out blank in TkMedit, no numbers, just 0,0,0. Would someone suggest anything to make the tal coords available o nTkMedit? Thanks. Nam.

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loading curvature
by Goldman, Aaron (NIH/NIMH) 12 Jan '05

12 Jan '05

Hi, I'm writing a script to make manual editing a bit more convenient, and want to call tksurfer and tkmedit with all the parameters of csurf's "Edit Segmentation" option, and using T1 as the aux volume. Right now, I have: tksurfer $s $h inflated & tkmedit $s wm $h.orig -aux T1 However, I'm not sure how to make the curvature load automatically. Is there a flag I can add for that? Also, is there anything else that should be added/changed? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: <mailto:aarong@mail.nih.gov> aarong(a)mail.nih.gov

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Re: [Freesurfer] normalization failed
by Joongnam Yang 12 Jan '05

12 Jan '05

Hi, I am having trouble removing the pons with recon-all -stage1 -pons-xyz. I've tried five pons coords, unsuccessfully. When you move the mouse location in the sagittal, horizontal, and coronal images, the slice numbers change. When I get the talairach coords for the pons, should the slice numbers be the same or can they be different? Thanks. Nam.

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Preproc-sess failed during smoothing
by Margaret Duff 11 Jan '05

11 Jan '05

Hi, I was trying to preprocess some functional data using the command preproc-sess -fwhm 6 -sf sessid -df sesspar. My subjects study directory is located at /space/troy/1/users/FREESURFER/SM2C2_fsfast/study. The command made it through motion correction, then during smoothing gave me this error: ERROR:: Environment variable FSLOUTPUTTYPE is not set! Please make sure that the appropriate configuration file is sourced by your shell (e.g. by putting it in .profile). e.g. bash or sh users add the line ". ${FSLDIR}/etc/fslconf/fsl.sh" e.g. tcsh or csh users add the line "source ${FSLDIR}/etc/fslconf/fsl.csh" /tmp/ipfsl_23657 /space/lyon/1/home/inverse/freesurfer_alpha/fsl/bin/ip fmc fmcsm .1 -s 2.54237288135593220338 ERROR: ip failed ERROR: ipfsl failed ERROR: spatialsmooth-sess failed I have never received this error before and am not sure if I should just set the env. variable or where the .profile is. What is the recommended course of action and is there any reason I got this error now, and never before? Thanks! Margaret

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Freesurfer January 2005