Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30128 discussions

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

1 0

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

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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.

2 1

mri_convert
by Joongnam Yang 05 Jan '05

05 Jan '05

Hi, After I ran mri_convert, I saw the "orig" volumes. Are the red crosses in the image significant in that the center cross should be the center of the brain in terms of left and right hemispheres? It is not in the center, much away from the center in my "orig" volumes. If it has to be corrected how would I do it? I tried mri_convert -ic option, to no avaible. Comments are appreciated. Nam.

2 1

3dvolreg motion correction
by Joongnam Yang 05 Jan '05

05 Jan '05

Hi, The man page shows the following for the AFNI motion correction binary. 3dvolreg [options] dataset Registers each 3D sub-brick from the input dataset to the base brick. 'dataset' may contain a sub-brick selector list. Would someone tell me how to specify "dataset"? Is it *.img or COR-* or anything else? Thanks in advance. Nam.

2 1

annotation and labels
by Rutvik Desai 05 Jan '05

05 Jan '05

I parcellated a subject using parcellate_subject, and was trying to see the labels. Doing File->Label->Import annotation and selecting lh.aparc.annot makes tksurfer crash. Trying to convert annotations to labels using mri_annotation2label givies a bus error. What could be the problem? Running Max OSX 10.3.6. thanks, Rutvik ---------- % mri_annotation2label --subject 137 --hemi lh --outdir ./label --table $FREESURFER_HOME/Simple_surface_labels2002.txt subject = 137 annotation = aparc hemi = lh outdir = (null) surface = white Reading surface /usr/local/freesurfer/subjects/137/surf/lh.white Loading annotations from /usr/local/freesurfer/subjects/137/label/lh.aparc.annot reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) reading colortable from annotation file... *** malloc_zone_calloc[22282]: arguments too large: 3221220448,520 CTABreadFrom: could not allocate -1073746848 bin table Cannot allocate memory Bus error %

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