Freesurfer

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30132 discussions

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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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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recon-all error: _FindFacePath
by muet0005＠umn.edu 17 Apr '10

17 Apr '10

Hello, I am getting the following error in the $subjid/scripts/recon-all.log: ERROR: _FindFacePath: could not find path! Linux blade279 2.6.5-7.322-smp #1 SMP Mon Feb 8 09:14:05 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Apr 16 08:23:35 CDT 2010 The recon-all-status.log shows the process ended prematurely here: #@# Fix Topology lh Fri Apr 16 04:28:28 CDT 2010 Linux blade279 2.6.5-7.322-smp #1 SMP Mon Feb 8 09:14:05 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Apr 16 08:23:35 CDT 2010 I've tried running recon-all on this subject two separate times from scratch, getting the same result (thinking perhaps the first time was a random error with our system/software). The image is of good quality --- little motion, good contrast. The brainmask.mgz and aseg.mgz look OK. The inflated surface is very rough (lots of "spikes" coming out of it), but I am not sure if that is just because of how early on in the processing this is. I saw a post related to this from 2008 (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13371.html) but I am not sure if the problem for that user was resolved? Let me know if you have any ideas/suggestions for us to try! Best, Ryan Cut-and-paste the following info into your FreeSurfer problem report: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer/freesurfer-binary-distribution/freesurfer-centos4_x86_64-stable-pub-v4.5.0/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Kernel info: Linux 2.6.5-7.322-smp x86_64 ---------------------------------------------------------------------

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QDEC question about covariates
by Manabu Kubota 17 Apr '10

17 Apr '10

Dear FreeSurfer experts, Hello, I started to use FreeSurfer recently. I want to do group analysis with QDEC in order to compare 2 groups (control group and patient group), regressing out age and gender. When I include 2 discrete factors (diagnosis and gender) and 1 continuous factor (age), and run QDEC, there appear a question of "Does the average thickness, accounting for Gender, differ between Controls and Patients?", but there NOT appear a question of "Does the average thickness, accounting for Gender *AND AGE*, differ between Controls and Patients?". So, it seems that age cannot be regressed out in this way. However, when I include 1 discrete factor (gender only) and 2 continuous factors (age and also diagnosis *dummy parameterized: Controls = 1, Patients = 0*), and run QDEC, there appear a question of "Does the correlation between thickness and Diagnois, accounting for Age and Gender, differ from zero?", and the result seems OK. My question is; 1) Is it right to do the (above-mentioned) latter way to compare difference of thickness between the 2 groups, regressing out age and gender? 2) Why couldn't age regressed out in the former way? 3) In this way, generally is it OK if I enter simple "discrete" factor as a continuous factor in QDEC (for example, gender:male=1, female=0)? This time I want to ask, since I couldn't find an answer in the past archives. Thanks a lot, Manabu Kubota kubotajp(a)kuhp.kyoto-u.ac.jp Graduate School of Medicine, Kyoto University

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Reference for Insula delineation in standard parcellation
by Laluz, Victor 16 Apr '10

16 Apr '10

Hello Freesurfer-ers, I tried to look up a reference for the delineation of the insula label in the standard parcellation and came up empty. Does anyone have a published article, or some form of citation that explains how Freesurfer defines the insula? This is in reference to the insula label starting in version 4.3.0 (I believe). Thanks, Victor

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Multi-echo MPRAGE on GE 3T?
by Kippenhan, Shane (NIH/NIMH) [C] 16 Apr '10

16 Apr '10

Dear FreeSurfers, Does anyone know if a GE implementation of MEMPR (as described in van der Kouwe et all '08) exists anywhere? Thanks, Shane Kippenhan --------------------------------------------------------------- J. Shane Kippenhan, Ph.D. Contractor Imaging Scientist Section on Integrative Neuroimaging CBDB/GCAPP/NIMH/NIH Voice 301 496 9656 Fax 301 496 7437 ----------------------------------------------------------------

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selxavg3-sess error "design is ill-conditioned"
by Ben Letham 15 Apr '10

15 Apr '10

Hello, I'm trying to run selxavg3-sess for an analysis with TER < TR, and it errors with "design is ill-conditioned". I searched the mailing list archive, and the only past problem of this sort that I found was associated with a faulty tpef file, which I am not using. The details: There is only one run. TR is 1.2s, and stimuli were presented at intervals of 1/3 TR (0.4s) (the desired TER). The paradigm file reflects this, it is of the form: 0 0 0.4 1 0.8 0 1.2 2 1.6 1 2 0 I loaded it into matlab and verified that the time points all have a difference of 0.4s. The analysis is, mkanalysis-sess -analysis analysis_name -TR 1.2 -TER 0.4 -paradigm 03TR.par -designtype event-related -nconditions 2 -timewindow 19.2 -prestim 2.4 -mcextreg -funcstem fmcstcsm6 -polyfit 2 -runlistfile runlist_03TR -noautostimdur -force I define two contrasts, mkcontrast_sess -analysis analysis_name -rmprestim -contrast AV-REST -a 1 -c 0 mkcontrast_sess -analysis analysis_name -rmprestim -contrast AVT-REST -a 2 -c 0 And then selxavg3-sess, selxavg3-sess -analysis analysis_name -sf subjectname -df sessdir -overwrite And this errors. Like I said, the only thing I found in the mailing list was a problem with tpef, and so I left it out altogether (as above), and the problem persists. If I change TER to equal TR (1.2), then it works. So the problem has something to do with TER being less than TR. Perhaps something in the par file then? I checked it in matlab, and diff(par(:,1)) = 0.4 for all of the events. Any thoughts would be very appreciated! Ben.

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