Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

Linux recon-all error
by krista kelly 16 Nov '13

16 Nov '13

Hello, I'm running freesurfer's recon-all using Linux and the past few subjects I've run, recon-all has exited with errors. I've ran a few subjects so far with no problems, and now all of a sudden there's an issue and I can't figure out why. I have been able to run these "problem' subjects using Linux on other computers with no issues, so it can't be a raw data issue. I have pasted the terminal window text below. If anyone has any idea why this is occurring, I'd love to know! Thanks! -------- freesurfer-Linux-centos4-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni Freesurfer Virtual Machine sudo password: freesurfer fsuser@xubuntu-VirtualBox:~$ recon-all -all -qcache -notal-check -cw256 -subjid BV33 -i ~/Desktop/nii.gzs/BV33.nii.gz WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux xubuntu-VirtualBox 3.2.0-55-generic #85-Ubuntu SMP Wed Oct 2 13:43:27 UTC 2013 i686 i686 i386 GNU/Linux -cw256 option is now persistent (remove with -clean-cw256) /usr/local/freesurfer/subjects/BV33 mri_convert /home/fsuser/Desktop/nii.gzs/BV33.nii.gz /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz mri_convert /home/fsuser/Desktop/nii.gzs/BV33.nii.gz /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/fsuser/Desktop/nii.gzs/BV33.nii.gz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999683, 0.0209404, 0.0139622) j_ras = (-0.0209424, 0.999781, 0) k_ras = (-0.0139591, -0.000292399, 0.999903) writing to /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Nov 14 10:28:28 EST 2013 Found 1 runs /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz /usr/local/freesurfer/subjects/BV33 mri_convert /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz /usr/local/freesurfer/subjects/BV33/mri/orig.mgz --conform --cw256 mri_convert /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz /usr/local/freesurfer/subjects/BV33/mri/orig.mgz --conform --cw256 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999683, 0.0209404, 0.0139622) j_ras = (-0.0209424, 0.999781, 0) k_ras = (-0.0139591, -0.000292399, 0.999903) Original Data has (1, 1, 1) mm size and (176, 230, 175) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/BV33/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/BV33/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/BV33/mri/orig.mgz /usr/local/freesurfer/subjects/BV33/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Nov 14 10:28:40 EST 2013 /usr/local/freesurfer/subjects/BV33/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux xubuntu-VirtualBox 3.2.0-55-generic #85-Ubuntu SMP Wed Oct 2 13:43:27 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s BV33 exited with ERRORS at Thu Nov 14 10:29:51 EST 2013 For more details, see the log file /usr/local/freesurfer/subjects/BV33/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting fsuser@xubuntu-VirtualBox:~$ open /usr/local/freesurfer/subjects/BV33/scripts/recon-all Couldn't get a file descriptor referring to the console fsuser@xubuntu-VirtualBox:~$

3 3

GPU considerations
by Satrajit Ghosh 16 Nov '13

16 Nov '13

Does Freesurfer's GPU bits care about single or double precision? Cheers, satra

1 0

trac-all inquiry
by David Soto 15 Nov '13

15 Nov '13

Hi - trac-all completed in all my Ps except one and I noticed that the dlabel/diff output does not contain all the files I assessed whether it could be do to poor registration, by checking the aparc+aseg file and looks allright I also checked the registration of FA maps to standard space by freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz dtifit_FA.bbr.nii.gz and seems fine also freeview -v brain_anat_orig.nii.gz lowb_brain.nii.gz which also seems fine any ideas pls? thanks! ds On Fri, Aug 16, 2013 at 5:14 PM, Anastasia Yendiki < ayendiki(a)nmr.mgh.harvard.edu> wrote: > > I suspect the current problem is caused by poor registration. Have you > checked the aparc+aseg and/or the registration from diffusion to anatomical > and from anatomical to MNI? > > > On Fri, 16 Aug 2013, David Soto wrote: > -- http://www1.imperial.ac.uk/medicine/people/d.soto/

2 1

Modifying cortical surface for large dysplasia
by Jonathan DuBois 15 Nov '13

15 Nov '13

Hi All, I have run recon-all on a subject with a large cortical dysplasia, and while the segmentation (aseg) seems to be relatively correct, there is a large region of dysplasia not included by the pail surface. The normalized intensity values for the cortex and the excluded region are very similar so it seems that there is a threshold related to the distance from the white matter surface to the pial surface, or perhaps normal gyrification that is constraining the pial surface. Is there a recon-all or expert option for surface reconstruction of abnormally thick cortex? Thanks in advance, Jonathan

2 3

Export T1 volume and a set of points in the same space
by Octavian Lie 15 Nov '13

15 Nov '13

Dear All, I need to export a T1.mgz and N points (Nx3 coordinates .mat file) of the same volume in SPM12b. N are actually intracranial electrodes. For this, I save T1.mgz as .nii prior to import into SPM. Should I use volume index, volume RAS or surface RAS coordinates for N? What other transforms I should apply to the .mat coordinate file so that when read in SPM is in the same space as T1.nii? Please advise, Thank you, Octavian.

2 1

nu_correct not found
by Bernardo jose 15 Nov '13

15 Nov '13

Hello experts, Could you please help me? I have already checked perl is in usr/bin/perl. Sincerely, Bernardo. nu_correct.mni.log is: tmpdir is ./tmp.mri_nu_correct.mni.2629 /Users/bernardomartins/Desktop/manoel/manoel/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2629/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2629/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=4.18, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.2629/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Nov 15 14:23:57 BRST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.2629/nu0.mnc ./tmp.mri_nu_correct.mni.2629/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2629/0/ -iterations 1000 -distance 50 nu_correct: Command not found. ERROR: nu_correct

1 0

Re Freesurfer type
by Anna Jonsson 15 Nov '13

15 Nov '13

Dear list members, I was wondering where in the Freesurfer output the information on which freesurfer version has been used to process scans is located? eg recon-all.log? Thank you, Kind Wishes, Anna

2 1

freesurfer5.3 version In CentOS5
by Rujing Zha 15 Nov '13

15 Nov '13

Dear all, In CentOS5,which freesurfer5.3 version(centos4 or centos6?) can be compatible? Thanks! All the best. 2013-11-15 Rujing Zha

2 1

are there any previous studies on the robustness of freesurfer default parameters as used in cortical thickness computation?
by Mark Alexiuk 15 Nov '13

15 Nov '13

Hi, My interest is in cortical thickness measurements for longitudinal Alzheimer data, namely the ADNI dataset. My understanding is that recon-all can be used to generate cortical thicknesses. I am trying to understand how the default parameter values used in recon-all were arrived at. Are the default parameters optimized in some sense? How robust are the default parameters with respect to the resulting cortical thickness? Will a small change in a parameter value result in a significant difference in some cortical thicknesses? I was able to find the following and would appreciate references to good papers on this topic. Excerpt from abstract: Standard manual tracing and FreeSurfer-based analyses were performed in 77 participants including 67 cognitively normal individuals and 10 individuals with early Alzheimer's disease.... The manual and FreeSurfer approaches yielded nearly identical estimates of amyloid burden (intraclass correlation = 0.98) as assessed by the mean cortical binding potential. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0073377 Thanks for any forthcoming comments. Mark

2 2

list of FreeSurfer 5.3 labels
by Del Re, Elisabetta 15 Nov '13

15 Nov '13

Hi, I am trying to find a list of all the labels available for FreeSurfer 5.3 and am having a hard time finding it. Any suggestions? Thank you, regards, Elisabetta del Re

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