Freesurfer February 2006

freesurfer@nmr.mgh.harvard.edu

40 participants
52 discussions

Newest stream
by Clifford A. Smith, PhD 08 Feb '06

08 Feb '06

With the most recent release, does the skullstripping take place with brainmask.auto.mgz and brainmask.mgz? After completing recon-all autorecon-all I checked brain.mgz. I had some frontal areas missing, so ran recon-all -skullstrip -wsthresh 30. Brainmask.mgz looks good. I believe that I know the answer, but to be safe, after running autorecon2 brain.mgz will reflect these edits? Thanks, Cliff ------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893

3 3

output problems
by Durastanti, Valentina (NIH/NINDS) [F] 07 Feb '06

07 Feb '06

-----Original Message----- Dear All: after launching the command: "mris_anatomical..." I have an output where all the results are written but the mean cortical thickness (where I get 0.0000+0.00) and surface area (where I get 0 as well). Thoughts? Thanks you! Valentina

2 1

Importing .8 and .5 scans into freesurfer
by Faden, Eric (NIH/NIMH) [F] 07 Feb '06

07 Feb '06

I have scans that are at .8 and .5 resolution as dicoms. Currently I am using to3d to rotate the images to the proper orientation. After that I have tried using 3drefit -xdel 1.0 -ydel 1.0 -zdel 1.0 to "resize" the image so that mri_convert doesn't resample the image, but this is also messing up the statistics for obvious reasons. Is it reasonable to just multiply the statistics by .512 (.8 ^ 3) and .125 (.5 ^ 3)? or how else can I prevent freesurfer from resampling my images to 1.0 resolution? -Eric

2 2

already skullstriped
by wuhappy＠seu.edu.cn 07 Feb '06

07 Feb '06

Hi, I already have the skullstriped brains data on the original image space. The skullstriped data is good. I want to know whether I can use the skullstripped data directly instead of starting from the original T1 images in FreeSurfer. Thank you very much! -Steven -- Ph.D. Laboratory of Image Science & Technology (LIST), Department of Biomedical Engineering, Southeast University, Nanjing, Jiangsu Province, P.R. of China,210096 Phone: +86-25-3794249 Fax: +86-26-3792698

2 1

RE: [Freesurfer] Problem with latest dev version (crashes correctingerrors)
by Durastanti, Valentina (NIH/NINDS) [F] 06 Feb '06

06 Feb '06

Dear all, I'm running freesurfer and I have a problem at the step one with a patient (recon-all -stage1 -subjid ...): before ending the step I found: MOTION CORRECTING/tmp/cor 2 mmc Minctracc: command not found ERROR mritoself failed ERROR mri_motion_correct Non-zero status Coul you help me? Thanks valentina

2 1

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 ---------------------------------------

1 0

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 ---------------------------------------

2 1

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

2 1

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.

2 1

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

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer February 2006