Freesurfer

freesurfer@nmr.mgh.harvard.edu

13 participants
30061 discussions

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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functional overlay
by ruth.smans＠med.kuleuven.ac.be 11 Jan '05

11 Jan '05

Hi all, I would like to overlay multiple functional datasets onto the same flattened structural image. How do I go about this? Thanks Ruth

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mris_convert patch conversion
by Rutvik Desai 10 Jan '05

10 Jan '05

Converting pathces to ascii using mris_convert with % mris_convert -p rh.temp.patch.flat rh.temp.patch.flat.asc seems to give incorrect topology in the ascii patch (the triangles are "messed up"). I loaded the asc patch into tksurfer, and also converted it back to binary and loaded it in tksurfer. Both have the same problem. The original binary flat patch is fine. I can upload the surfaces if that would be helpful. Runninng Mac OSX 10.3.6. thanks Rutvik

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pons-xyz
by Joongnam Yang 07 Jan '05

07 Jan '05

Thanks Bruce and Brian, When voxel dimensions are less than 1.75, "create surface" went smoothly. Question: The pons is still attached, I want to use -pons-xyz X Y Z TkMedit shows only RAS. (1) How can I have talairach coords shown up on TkMedit (2) RAS and Talairach coords are different, but the manual says use either one. it doesn't matter? Thanks for you answer. Nam.

2 1

MacOSX version of mri_annotation2label available
by Yasunari Tosa 07 Jan '05

07 Jan '05

Hi, We were notified that the current MacOSX version of mri_annotation2label causes bus error. You can get the new version of mri_annotation2label at the usual place: ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158). 220 surfer.nmr.mgh.harvard.edu FTP server (Version wu-2.6.2-15.7x.legacy) ready. Name (surfer.nmr.mgh.harvard.edu:tosa): anonymous 331 Guest login ok, send your complete e-mail address as password. Password: 230 Guest login ok, access restrictions apply. Remote system type is UNIX. Using binary mode to transfer files. ftp> cd pub/dist 250 CWD command successful. ftp> get mri_annotation2label-20050107-Panther.tar.gz ftp> quit -- Yasunari Tosa, Ph.D. Email: tosa(a)nmr.mgh.harvard.edu NMR Ctr, Mass. General Hospital TEL: 617-726-4050 Building 149, 13th Street Charlestown, MA 02129 USA

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recon-all exiting with errors
by Margaret Duff 07 Jan '05

07 Jan '05

Hello, I am trying to run recon-all but it seems to have some problems during nu_correct. I am using the command recon-all -subjid SM2C1tal -stage1, my subjectsdir is /space/troy/1/users/FREESURFER, and I am getting the error, Can't locate MNI/Startup.pm in @INC. then it says all the stuff @INC does contain, the says at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_correct line 38. BEGIN failed--compilation aborted at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_correct line 38. ERROR: nu_correct Does this have to do with the FS software or my settings or usage? Thanks, Margaret

1 0

Re: [Freesurfer] normalization failed
by Joongnam Yang 07 Jan '05

07 Jan '05

Hi, For one subject's data, "process volume" didn't get the skull stripped. The skull was there intact in "brain" volumes. To correct it, I used "expert preferences" and used "don't use watershed analyze", which led to most of the skull removed in "brain" volumes. But still there are pieces of the skull left. (I tried "preflooding" option, no difference). Any suggestions on how to trim the leftovers of the skull? Thanks. Nam.

1 0

Re: [Freesurfer] normalization failed
by Joongnam Yang 06 Jan '05

06 Jan '05

Thanks Bruce, How would I specify the new talairach.xfm in the run of recon-all -stage1. If I copy the new file into the usual /mri/transforms directory, it's overwritten during the recon-all process. Comments are appreciated. Nam. >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 01/06/05 4:55 PM >>> check the talairach transform On Thu, 6 Jan 2005, Joongnam Yang wrote: > Hi, > > During recon-all -stage1 running, I got the following error. > > ....... > MRInormalize: could not find any valid peaks > No such file or directory > mri_normalize: normalization failed > No such file or directory > ERROR: mri_normalize exited with non-zero status > - > Any suggestion would be appreciated. > > Nam. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 1

ascii information file for a label
by Sergey A Solovyev 06 Jan '05

06 Jan '05

Hi, Tksurfer provides a nice tool to display information such as vertex index, spherical coordinates (rho, theta), values of overlaid functionals as a function of the mouse/cursor position. I wonder if there is a way to save all information above (index, spherical coordinates, overlaid functionals values) into an ascii text file for all vertexes located within a certain label (patch)? Something like >mris_convert -p *h.patch.flat *h.patch.flat.asc that in addition to vertex number, provides spherical coordinates, AND values of functional overlay(s) for a patch, or better for a label. Thank you, Serge

3 7

normalization failed
by Joongnam Yang 06 Jan '05

06 Jan '05

Hi, During recon-all -stage1 running, I got the following error. ....... MRInormalize: could not find any valid peaks No such file or directory mri_normalize: normalization failed No such file or directory ERROR: mri_normalize exited with non-zero status - Any suggestion would be appreciated. Nam.

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