Freesurfer April 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
147 discussions

Which volumes to sum to obtain cereberal and cerebellar GM/WM volumes?
by Jory Hoogendam 19 Apr '10

19 Apr '10

Hello Freesurfer experts, We have generated a list of volumes, using asegstats2table (based on aseg.stats files). We want to compute total grey matter and white matter volumes for right and left hemispheres, separately for the cerebebrum and cerebellum. Which volumes from the list should we sum to generate these grey matter and white matter volumes? And which volumes should be included to calculate CSF for the whole brain? Is it allowed to sum all volumes to obtain intracranial volume? And why does this differ from the last variable of the list (IntraCranialVol)? Thanks in advance, Jory Hoogendam

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Re: [Freesurfer] The error about recon-all -s subjid -autorecon1
by Antoine Leflon 19 Apr '10

19 Apr '10

thanks Can you post these to the list? Nick would be able to help you, or others. On Mon, 19 Apr 2010, Antoine Leflon wrote: [Cacher les citations] Hi Bruce , I use a virtual machine , the Hard Disk simulated is 8GB but there're 1.7GB remaining on it . Is it enough ? Antoine Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> a écrit : Hi Antoine is your partition full? Bruce On Mon, 19 Apr 2010, Antoine Leflon wrote: sorry this error was : ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...40 iterations mghRead: encountered error executing: 'zcat /usr/local/freesurfer/subjects/s2/mri/T1.mgz',frame -1, errno 12 mri_strip_skull: done peeling brain Brain Size = 1657531 voxels, voxel volume = 1.000 mm3 = 1657531 mmm3 = 1657.531 cm3 mri_watershed Error: read failed Linux qq-desktop 2.6.28-15-generic #51-Ubuntu SMP Mon Aug 31 13:33:16 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Wed Sep 9 15:08:15 CST 2009 _______________________________________________ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Re: [Freesurfer] The error about recon-all -s subjid -autorecon1
by Antoine Leflon 19 Apr '10

19 Apr '10

Hi Bruce , I use a virtual machine , the Hard Disk simulated is 8GB but there're 1.7GB remaining on it . Is it enough ? Antoine

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Re: [Freesurfer] The error about recon-all -s subjid -autorecon1
by Antoine Leflon 19 Apr '10

19 Apr '10

sorry this error was : ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...40 iterations mghRead: encountered error executing: 'zcat /usr/local/freesurfer/subjects/s2/mri/T1.mgz',frame -1, errno 12 mri_strip_skull: done peeling brain Brain Size = 1657531 voxels, voxel volume = 1.000 mm3 = 1657531 mmm3 = 1657.531 cm3 mri_watershed Error: read failed Linux qq-desktop 2.6.28-15-generic #51-Ubuntu SMP Mon Aug 31 13:33:16 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Wed Sep 9 15:08:15 CST 2009

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recon-all with nifti
by Christophe Chênes 19 Apr '10

19 Apr '10

For the input,I try using this command: # recon-all -s $MY_SUBJECT -i $SUBJECT_DIR/$MY_SUBJECT/mri/ orig/sujet01.nii.gz -all -notal-check -no-isrunning It returns the following error: # ERROR: /home/christophe/con/dvlp/pipe/FS/subjects/sujet01 exists, delete or re-run with -force ...

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Re: [Freesurfer] The error about recon-all -s subjid -autorecon1
by Antoine Leflon 19 Apr '10

19 Apr '10

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Re: [Freesurfer] The error about recon-all -s subjid -autorecon1
by Antoine Leflon 19 Apr '10

19 Apr '10

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Re: [Freesurfer] The error about recon-all -s subjid -autorecon1
by Antoine Leflon 19 Apr '10

19 Apr '10

Hi , I encountered the same error and I ran the command but the mgh file cannot be opened because it has a width of zero . Did you manage to fix this problem ? thanks , Antoine Leflon

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mri_watershed error
by Antoine Leflon 19 Apr '10

19 Apr '10

Hi , I encountered an error during the watershed and I tried to check the disk space running : zcat /usr/local/freesurfer/subjects/s2/mri/T1.mgz> /usr/local/freesurfer/subjects/s2/mri/T1.mgh An image file appeared but it is impossible to open it because it has a width of zero . what does it mean ? thanks , Antoine Leflon

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EM registration error?
by Wenger, Elisabeth 19 Apr '10

19 Apr '10

Dear freesurfer specialists, in 10 of our subjects the following problem occured: freesurfer exited with error in autorecon2 during EM registration. The protocol looks like this: #------------------------------------- #@# EM Registration Wed Dec 16 21:47:09 CET 2009 /Applications/freesurfer/subjects/1126gv99B/mri \n mri_em_register -mask brainmask.mgz nu.mgz /Applications/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta \n using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/Applications/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros) ************************************************ spacing=8, using 2185 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=13.1 skull bounding box = (60, 23, 28) --> (193, 151, 198) using (104, 66, 113) as brain centroid... mean wm in atlas = 107, using box (88,50,92) --> (120, 81,133) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Darwin LIP-OSX-164-3.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386 recon-all exited with ERRORS at Wed Dec 16 21:48:02 CET 2009 I also attach the whole recon-all.log file. We used a MacPro3,1 and Freesurfer version 4.2.0. Thank you very very much for your help! Best, Elisabeth and Genia

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Freesurfer April 2010