Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30066 discussions

Re: [Freesurfer] Problem with latest dev version (crashes correcting errors)
by Tim Jarvis 06 Feb '06

06 Feb '06

For the lh, there is no cerebellum and no skull, looks to be correct. I don't see any rh* files though? brewster 14%> ls /data/brewster2/tjarvis/thesis_data/software/freesurfer/subjects/icbm/surf/ lh.defect_borders lh.defect_chull lh.defect_labels lh.inflated lh.inflated.nofix lh.orig lh.orig.nofix lh.qsphere.nofix lh.smoothwm.nofix On 6 Feb 2006, Bruce Fischl wrote: > yes, mri_ca_register takes a long time. The good news is it works really > well :>. As for the mris_topology_fixing problem, what does the > ?h.orig.nofix surface look like? Does it include cerebellum or skull? Does > it look approximately correct? > > On Mon, 6 Feb 2006, Tim Jarvis wrote: > > > Gave the new dev version a spin with autorecon-all, couple of things... > > > > For the mri_ca_register step, it took a total of 791 minutes! Is this > > normal or could this be a hint as to things going wrong early in the > > pipeline? > > > > Also, the program eventually crashed during the error correction, below are > > the lines that seem like they may have had some effect: > > > > Anyone else experience this problem? > > > > > > > > Thanks > > > > =========================================================================== > > ===== > > > > > > mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz > > > > threshold mask volume at 5 > > writing masked volume to brain.finalsurfs.mgz... > > #-------------------------------------------- > > #@# WM Segmentation Sat Feb 4 03:52:43 CST 2006 > > > > cp wm.mgz wm.seg.mgz > > > > cp: cannot stat `wm.mgz': No such file or directory > > > > mri_segment -keep brain.mgz wm.seg.mgz > > > > preserving editing changes in output volume... > > doing initial intensity segmentation... > > using local statistics to label ambiguous voxels... > > computing class statistics for intensity windows... > > WM: 105.7 +- 6.0 [80.0 --> 125.0] > > GM: 74.1 +- 15.7 [30.0 --> 96.0] > > setting bottom of white matter range to 89.8 > > setting top of gray matter range to 99.7 > > doing initial intensity segmentation... > > using local statistics to label ambiguous voxels... > > using local geometry to label remaining ambiguous voxels... > > > > reclassifying voxels using Gaussian border classifier... > > > > removing voxels with positive offset direction... > > smoothing T1 volume with sigma = 0.250 > > removing 1-dimensional structures... > > 11549 sparsely connected voxels removed... > > thickening thin strands.... > > 20 segments, 3117 filled > > 33169 bright non-wm voxels segmented. > > 4836 diagonally connected voxels added... > > white matter segmentation took 9.5 minutes > > writing output to wm.seg.mgz... > > zcat: > > /data/brewster2/tjarvis/thesis_data/software/freesurfer/subjects/icbm/mri/w > > m.seg.mgz.gz: > > No such file or directory > > mghRead(/data/brewster2/tjarvis/thesis_data/software/freesurfer/subjects/ic > > bm/mri/wm.seg.mgz, > > -1): read error > > mri_segment: could not read file wm.seg.mgz to preserve edits > > > > [.....] > > > > Correction of the Topology > > Finding true center and radius of Spherical Surface...done > > Surface centered at (0,0,0) with radius 100.0 in 9 iterations > > marking ambiguous vertices... > > 19500 ambiguous faces found in tessellation > > segmenting defects... > > 75 defects found, arbitrating ambiguous regions... > > vertex 4982: degenerate normal > > analyzing neighboring defects... > > -merging segment 8 into 1 > > -merging segment 25 into 24 > > -merging segment 40 into 39 > > -merging segment 43 into 41 > > -merging segment 59 into 54 > > 70 defects to be corrected > > 0 vertices coincident > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > > > [.....] > > > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > SVDCMP: No convergence in 20 iterations > > vertex 68123: degenerate normal > > vertex 68123: degenerate normal > > vertex 68123: degenerate normal > > Computing Initial Surface Statistics > > -face loglikelihood: -8.5636 (-4.2818) > > -vertex loglikelihood: -5.4447 (-2.7224) > > -normal dot loglikelihood: -3.5627 (-3.5627) > > -quad curv loglikelihood: -5.1011 (-2.5506) > > Total Loglikelihood : -22.6721 > > > > CORRECTING DEFECT 0 (vertices=336, convex hull=171) > > l_mri = 1.00 l_unmri = 10.00 l_curv = 1.00 l_qcurv = 1.00 > > After retessellation of defect 0, euler #=-64 (187142,557809,370603) : > > difference with theory (-67) = -3 > > > > CORRECTING DEFECT 1 (vertices=1450, convex hull=530) > > After retessellation of defect 1, euler #=-64 (187528,559270,371678) : > > difference with theory (-66) = -2 > > > > CORRECTING DEFECT 2 (vertices=18, convex hull=45) > > After retessellation of defect 2, euler #=-63 (187538,559315,371714) : > > difference with theory (-65) = -2 > > > > CORRECTING DEFECT 3 (vertices=181, convex hull=154) > > After retessellation of defect 3, euler #=-62 (187572,559490,371856) : > > difference with theory (-64) = -2 > > > > CORRECTING DEFECT 4 (vertices=265, convex hull=151) > > After retessellation of defect 4, euler #=-61 (187594,559630,371975) : > > difference with theory (-63) = -2 > > > > CORRECTING DEFECT 5 (vertices=18, convex hull=41) > > After retessellation of defect 5, euler #=-60 (187602,559669,372007) : > > difference with theory (-62) = -2 > > > > CORRECTING DEFECT 6 (vertices=46, convex hull=30) > > After retessellation of defect 6, euler #=-59 (187606,559689,372024) : > > difference with theory (-61) = -2 > > > > CORRECTING DEFECT 7 (vertices=39, convex hull=66) > > After retessellation of defect 7, euler #=-58 (187619,559757,372080) : > > difference with theory (-60) = -2 > > > > CORRECTING DEFECT 8 (vertices=7, convex hull=36) > > After retessellation of defect 8, euler #=-57 (187623,559782,372102) : > > difference with theory (-59) = -2 > > > > CORRECTING DEFECT 9 (vertices=52, convex hull=57) > > After retessellation of defect 9, euler #=-56 (187638,559844,372150) : > > difference with theory (-58) = -2 > > > > CORRECTING DEFECT 10 (vertices=34, convex hull=25) > > normal vector of length zero at vertex 37101 with 0 faces > > vertex 37101 has 0 face > > reading input surface > > /data/brewster2/tjarvis/thesis_data/software/freesurfer/subjects/icbm/surf/ > > lh.qsphere.nofix... > > INFO: Fixing vertex area > > reading brain volume from brain... > > reading wm segmentation from wm... > > Linux brewster 2.4.20-8smp #1 SMP Thu Mar 13 16:43:01 EST 2003 i686 athlon > > i386 GNU/Linux > > > > recon-all exited with ERRORS at Sat Feb 4 05:34:26 CST 2006 > > > > > > > > --------------------------------------- > > Timothy R. Jarvis > > --------------------------------------- > > Graduate Research Assistant > > International Neuroimaging Consortium > > VA Medical Center > > 612-467-2619 > > http://www.neurovia.umn.edu > > --------------------------------------- > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > --------------------------------------- Timothy R. Jarvis --------------------------------------- Graduate Research Assistant International Neuroimaging Consortium VA Medical Center 612-467-2619 http://www.neurovia.umn.edu ---------------------------------------

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Problem with latest dev version (crashes correcting errors)
by Tim Jarvis 06 Feb '06

06 Feb '06

Gave the new dev version a spin with autorecon-all, couple of things... For the mri_ca_register step, it took a total of 791 minutes! Is this normal or could this be a hint as to things going wrong early in the pipeline? Also, the program eventually crashed during the error correction, below are the lines that seem like they may have had some effect: Anyone else experience this problem? Thanks =========================================================================== ===== mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 writing masked volume to brain.finalsurfs.mgz... #-------------------------------------------- #@# WM Segmentation Sat Feb 4 03:52:43 CST 2006 cp wm.mgz wm.seg.mgz cp: cannot stat `wm.mgz': No such file or directory mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM: 105.7 +- 6.0 [80.0 --> 125.0] GM: 74.1 +- 15.7 [30.0 --> 96.0] setting bottom of white matter range to 89.8 setting top of gray matter range to 99.7 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 11549 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3117 filled 33169 bright non-wm voxels segmented. 4836 diagonally connected voxels added... white matter segmentation took 9.5 minutes writing output to wm.seg.mgz... zcat: /data/brewster2/tjarvis/thesis_data/software/freesurfer/subjects/icbm/mri/w m.seg.mgz.gz: No such file or directory mghRead(/data/brewster2/tjarvis/thesis_data/software/freesurfer/subjects/ic bm/mri/wm.seg.mgz, -1): read error mri_segment: could not read file wm.seg.mgz to preserve edits [.....] Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 19500 ambiguous faces found in tessellation segmenting defects... 75 defects found, arbitrating ambiguous regions... vertex 4982: degenerate normal analyzing neighboring defects... -merging segment 8 into 1 -merging segment 25 into 24 -merging segment 40 into 39 -merging segment 43 into 41 -merging segment 59 into 54 70 defects to be corrected 0 vertices coincident SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations [.....] SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations vertex 68123: degenerate normal vertex 68123: degenerate normal vertex 68123: degenerate normal Computing Initial Surface Statistics -face loglikelihood: -8.5636 (-4.2818) -vertex loglikelihood: -5.4447 (-2.7224) -normal dot loglikelihood: -3.5627 (-3.5627) -quad curv loglikelihood: -5.1011 (-2.5506) Total Loglikelihood : -22.6721 CORRECTING DEFECT 0 (vertices=336, convex hull=171) l_mri = 1.00 l_unmri = 10.00 l_curv = 1.00 l_qcurv = 1.00 After retessellation of defect 0, euler #=-64 (187142,557809,370603) : difference with theory (-67) = -3 CORRECTING DEFECT 1 (vertices=1450, convex hull=530) After retessellation of defect 1, euler #=-64 (187528,559270,371678) : difference with theory (-66) = -2 CORRECTING DEFECT 2 (vertices=18, convex hull=45) After retessellation of defect 2, euler #=-63 (187538,559315,371714) : difference with theory (-65) = -2 CORRECTING DEFECT 3 (vertices=181, convex hull=154) After retessellation of defect 3, euler #=-62 (187572,559490,371856) : difference with theory (-64) = -2 CORRECTING DEFECT 4 (vertices=265, convex hull=151) After retessellation of defect 4, euler #=-61 (187594,559630,371975) : difference with theory (-63) = -2 CORRECTING DEFECT 5 (vertices=18, convex hull=41) After retessellation of defect 5, euler #=-60 (187602,559669,372007) : difference with theory (-62) = -2 CORRECTING DEFECT 6 (vertices=46, convex hull=30) After retessellation of defect 6, euler #=-59 (187606,559689,372024) : difference with theory (-61) = -2 CORRECTING DEFECT 7 (vertices=39, convex hull=66) After retessellation of defect 7, euler #=-58 (187619,559757,372080) : difference with theory (-60) = -2 CORRECTING DEFECT 8 (vertices=7, convex hull=36) After retessellation of defect 8, euler #=-57 (187623,559782,372102) : difference with theory (-59) = -2 CORRECTING DEFECT 9 (vertices=52, convex hull=57) After retessellation of defect 9, euler #=-56 (187638,559844,372150) : difference with theory (-58) = -2 CORRECTING DEFECT 10 (vertices=34, convex hull=25) normal vector of length zero at vertex 37101 with 0 faces vertex 37101 has 0 face reading input surface /data/brewster2/tjarvis/thesis_data/software/freesurfer/subjects/icbm/surf/ lh.qsphere.nofix... INFO: Fixing vertex area reading brain volume from brain... reading wm segmentation from wm... Linux brewster 2.4.20-8smp #1 SMP Thu Mar 13 16:43:01 EST 2003 i686 athlon i386 GNU/Linux recon-all exited with ERRORS at Sat Feb 4 05:34:26 CST 2006 --------------------------------------- Timothy R. Jarvis --------------------------------------- Graduate Research Assistant International Neuroimaging Consortium VA Medical Center 612-467-2619 http://www.neurovia.umn.edu ---------------------------------------

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PACE motion correction
by Ed Vul 06 Feb '06

06 Feb '06

I used PACE online motion correction on Bay 3, and now I am trying to figure out how to retrieve the motion data: how much motion was there? Any and all help is much appreciated. Thanks Ed

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segmentation fault (core dumped) error during autorecon2 step
by Renat Yakupov 03 Feb '06

03 Feb '06

Hi everybody, I am running freesurfer-Linux-rh9-dev20051003 version of FreeSurfer on Fedora Core 3. I installed it without a problem and I can successfully run autorecon1 step, However, when I attempt autorecon2 step, it exits with an error after about 8 hours of processing. Please see attached a text file of complete autorecon2 step output and please see below the last lines about the error: Editing WM with SubCort Seg Fri Feb 3 08:30:54 HST 2006 mri_edit_wm_with_aseg wm.mgz aseg.mgz wm.mgz Segmentation fault (core dumped) ERROR: mri_edit_wm_with_aseg with non-zero status Linux extra 2.6.9-1.667 #1 Tue Nov 2 14:41:25 EST 2004 i686 i686 i386 GNU/Linux recon-all exited with errors at Fri Feb 3 08:31:08 HST 2006 I ran it on two different subjects' data with the same outcome. The weird thing is that these two subjects' dataset were processed on another computer with the same version of FreeSurfer and Fedora Core, and there were no problems. The computer I am having problems on is a Dell OptiPlex GX620. Has anybody encountered anything like that? Any ideas what might cause it? Thank you. Regards, Renat.

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uncorrected vs. corrected comparisions ???
by trinity＠nmr.mgh.harvard.edu 02 Feb '06

02 Feb '06

Hi - I have a question about the fixed effects and random effects analysis. Are the values from the averaged maps corrected or uncorrected? Also, which is better to use for a group comparision? Are there certain instances when one is better to use than the other? Thank you! Trinity

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cluster thresholding
by Sasha Wolosin 02 Feb '06

02 Feb '06

Dear all, Has the January dev release incorporated the new corrections for multiple comparisons in group analysis, e.g. cluster thresholding? Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin(a)kennedykrieger.org Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Problem with setting segmentation threshold values
by Goradia, Dhruman D 01 Feb '06

01 Feb '06

Hi, I am interested in changing the white matter low limit for the segmentation step. For this I typed the following in the command prompt: recon-all -subjid <subjectname> -autorecon2 -seg-wlo <low limit value> this gave me an error stating that it could not recognize -seg-wlo flag. I was wondering if there is a mistake in writing the command? I would also like to know if there is any default lower limit for gray matter threshold used my mri_segment? If so what is it and can it be changed? Thank you. Dhruman Dhruman D. Goradia Research Specialist Western Psychiatric Institute and Clinic 3811 O'Hara St Suit 431 Pittsburgh PA 15213.

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newest dev question
by Sasha Wolosin 31 Jan '06

31 Jan '06

Dear all, Is the latest January dev release compatible with the previous one (Oct 2005) with regards to surface-based measures? Are there any differences in the segmentation algorithms or in the implementation of these algorithms which might cause differences in the surface files? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Display of thickness measurement
by Antao Du 31 Jan '06

31 Jan '06

Hi, I am interested in measuring the cortical thickness in entorhinal cortex. I can display the thickness measurement by " tkmedit AD1232 brain.mgz lh.white " to look at the measurement in entorhinal region, but I don't know the boundary of entorhinal cortex by this way. Is there any way that I can only display the measurement of cortical thckness in the entorhinal cortex? Thanks, Antao

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feat2surf
by Strien, N van 31 Jan '06

31 Jan '06

Hi, I am having several problems with the feat2surf script when using this on my own data. For privacy purposes I renamed my subject to bert, however this refers not to the sample dataset: The problems that I face with the feat2surf script are as follows: 1) If I do not edit the script manually it stops when not finding a data file (zstat1.img) in analyze format. If I edit the feat2surf script so it only finds a zstat1.nii file it continues. 2) Results are not stored under 4 new subdirectories in the .feat main directory (as suggested in the tutorial). They are stored (and overwritten) in the /root directory. (I know it’s a bad habit of mine to work under the root account, but I expect the outputdir will only change to /home/$username/ if I change user. Ẃhen the script only looks for .nii files (and finds them) it exits nicely (after commenting away some of the images the feat2surf script looks for such as cluster* and rendered*). 3) When opening for example the rh volume in tksurfer, I get an error message that the .mgh volume is incorrect. This is the output when I run the feat2surf script without editing it. Mon Jan 30 13:32:00 CET 2006 /media/userdata/experiments/stereo_mtl/pilot/bert/results/fwhm5_hp50/1st_lev el mri_vol2surf --src mblok1+.feat/stats/*.img --srcreg mblok1+.feat/reg/freesurfer/anat2exf.register.dat --trgsubject bert2 --hemi lh --out /*.mgh --surf white --out_type mgh srcvol = mblok1+.feat/stats/*.img srcreg = mblok1+.feat/reg/freesurfer/anat2exf.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = bert2 surfreg = sphere.reg interp = nearest float2int = round INFO: float2int code = 0 ERROR: analyzeRead(): cannot find any files for mblok1+.feat/stats/*.img ERROR: could not read mblok1+.feat/stats/*.img as type 16 ERROR: with mri_vol2surf --src mblok1+.feat/stats/*.img --srcreg mblok1+.feat/reg/freesurfer/anat2exf.register.dat --trgsubject bert2 --hemi lh --out /*.mgh --surf white --out_type mgh When I ran mri_vol2surf manually (see command line below; $out1 = the output dir I created manually to store the results in), the computer runs forever displaying a vol2surf_linear message. I left it running overnight and it didn't finish. Any suggestions in what I could alter to get it right? The functional overlay works fine with tkmedit. Thanks in advance, Niels van Strien mri_vol2surf --src $datalocation/mblok1+.feat/stats/zstat1.nii --srcreg $datalocation/mblok1+.feat/reg/freesurfer/anat2exf.register.dat --trgsubject bert2 --hemi lh --out $out1/zstat1.nii.mgh --surf white --out_type mg srcvol = /media/userdata/experiments/stereo_mtl/pilot/bert/results/fwhm5_hp50/1st_lev el/mblok1+.feat/stats/zstat1.nii srcreg = /media/userdata/experiments/stereo_mtl/pilot/bert/results/fwhm5_hp50/1st_lev el/mblok1+.feat/reg/freesurfer/anat2exf.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = bert2 surfreg = sphere.reg interp = nearest float2int = round INFO: float2int code = 0 WARNING: missing NIfTI-1 orientation (qform_code = 0) WARNING: your volume will probably be incorrectly oriented Done loading volume Reading surface /media/userdata/subjects/bert2/surf/lh.white INFO: NOT fixing vertex area Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 vol2surf_linear: nhits = 74277/126030 2 0 0 0 vol2surf_linear: nhits = 74277/126030 3 0 0 0 vol2surf_linear: nhits = 74277/126030 4 0 0 0 vol2surf_linear: nhits = 74277/126030 5 0 0 0 vol2surf_linear: nhits = 74277/126030 6 0 0 0 vol2surf_linear: nhits = 74277/126030 7 0 0 0 vol2surf_linear: nhits = 74277/126030 8 0 0 0

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