Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

error at autorecon2
by Chacko Cherian 02 Aug '06

02 Aug '06

Hello all, Here's an error I got while doing 'recon-all -autorecon2 -s <subject_name>. Could someone please clarify. Thank you. Chacko Cherian. #@# EM Registration Wed Aug 2 16:35:22 MST 2006 /home/ttest/freesurfer/subjects/case1/case1/case1/mri mri_em_register -mask brainmask.mgz nu.mgz /home/ttest/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/home/ttest/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... Segmentation fault (core dumped) Linux ibmlnx2.samaritan.edu 2.4.20-24.9 #1 Mon Dec 1 11:35:51 EST 2003 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Aug 2 16:35:41 MST 2006 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

2 1

dicom format
by Chacko Cherian 02 Aug '06

02 Aug '06

I got this error while running a single subject in DICOM format.the 'recon-all -autorecon1 -subjid <subject_name> ' stopped at this stage. INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux ibmlnx2.samaritan.edu 2.4.20-24.9 #1 Mon Dec 1 11:35:51 EST 2003 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Aug 2 14:16:22 MST 2006 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

2 1

dicom files
by Chacko Cherian 02 Aug '06

02 Aug '06

Hello all, I have 180 slices of a subject in DICOM format.I am trying to run the 'recon-all' procedure for this subject. Are these slices seen by Freesurfer as individual acquisitions or as a single dicom file? In case they are percieved as individual acquisitions,do I need to manually type all the file names(for each slice) for the recon-all procedure or is there a simpler way. THanks in advance Chacko Cherian. Arizona State University Graduate Research Assistant __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

4 3

mri_watershed question
by Avram Holmes 02 Aug '06

02 Aug '06

All, I am interested in using mri_watershed to remove the skull from an inplane low res structural scan (not an MPRAGE). However, when I try to I get the following message followed by the program crashing. Mode: Atlas analysis ********************************************************* The input file is P1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C changing type of input volume to 8 bits/voxel... MRIchangeType: Building histogram *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=127 y=133 z=24 r=80 first estimation of the main basin volume: 2160181 voxelsSegmentation fault (core dumped) I am sure that I am missing some simple flag. Does anyone know a solution to this before I run off and start using BET. Thanks, Avram

2 1

Would adjusting watershed parameters change pial surface?
by Jake Freimer 02 Aug '06

02 Aug '06

I was wondering if setting the watershed parameters higher and rerunning autorecon2 would expand the pial surface line if the outer rim of the brain is being left out? Or would this not fix the problem? Thanks -- -Jake

2 1

aseg.stats
by Doug Greve 01 Aug '06

01 Aug '06

I have just changed the way that DEV version recon-all creates the aseg.stats file. Previously, it would report everything that it found in FreeSurferColorLUT.txt. This included a lot of stuff that would never be in the subcortical segmentation, and this made the aseg.stats file very messy. The new version only reports on segmentations that are part of the subcortical segmentation process (ie, in mri_ca_label). Note that there may still be some segmentations reported in aseg.stats that are not found in a particular aseg.mgz because that segmentation was not found during labeling (eg, hypointensities). The values in the table (ie, volumes and intensities) should be exactly the same. This change only applies to dev (not to stable) and should be live on Tue. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

5 13

tkmedit problem
by Anthony Steven Dick 01 Aug '06

01 Aug '06

Hello- I have just installed freesurfer. Although tksurfer and tkregister2 seem to work fine, I get the following error message when attempting tkmedit: X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 129 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 15 Current serial number in output stream: 15 ....and I'm not sure if this helps, but when I source the SetUpFreeSurfer.csh script, I get the following: -------- freesurfer-Darwin-tiger-stable-pub-v3.0.3 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast SUBJECTS_DIR /Applications/freesurfer/subjects FUNCTIONALS_DIR /Applications/freesurfer/sessions MINC_BIN_DIR /Applications/freesurfer/mni/bin MINC_LIB_DIR /Applications/freesurfer/mni/lib PERL5LIB /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 GSL_DIR /Applications/freesurfer/lib/gsl TCLLIBPATH /Applications/freesurfer/lib/tcltktixblt/lib MISC_LIB /Applications/freesurfer/lib/misc/lib tcsh: gcc: Command not found. tcsh: gcc: Command not found. FSL_DIR /Applications/freesurfer/fsl Any help at all would be most appreciated. Thanks, Anthony

2 2

need a list of segmented subcorical regions and their intensity values...
by Shahabuddin Ansari 31 Jul '06

31 Jul '06

Hello, I have seen a list of 40 freesurfer-segmented subcortical objects with their respective intensity values somewhere in the documentation, but not able to locate it now. Could somebody help me please. Thanks Shahab __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

2 1

mri_volcluster and neuroanatomical labels
by Paymon Hosseini 31 Jul '06

31 Jul '06

Hello, I was wondering if there is a Freesurfer command for getting neuroanatomical labels for the output clusters of mri_volcluster. thank you very much for your help, paymon

3 3

slice time correction?
by cameo＠nmr.mgh.harvard.edu 31 Jul '06

31 Jul '06

Hi all, I was wondering if fs-fast implements slice time correction at any point during processing? if so does it default to correction for either interleaved or linear acquisition and can this be modified? Thanks, Cameron

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