Freesurfer February 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
236 discussions

trying to download Yeo_2011 atlases
by Sudhin A. Shah 28 Feb '13

28 Feb '13

Hello, Is there a link to the http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011? Its not apparent on the page and the link doesn't seem to be working.. Thanks, S

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Re: [Freesurfer] Cortical thickness asymmetries ?
by Douglas N Greve 28 Feb '13

28 Feb '13

Hi Sophie, check out this wiki page http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi doug On 02/28/2013 10:18 AM, Sophie Maingault wrote: > > Dear experts, > > I would like to study cortical thickness asymmetries. According to old > messages it seems impossible so I would like to know if it is always > the case or not ? Maybe, there is a command to subtract the values for > each vertex in the left hemisphere minus the values for each vertex in > the right hemisphere and then use this new variable in qdec ? > > Thank you for your answer ! > > Sophie > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Help -- asegstats2table error, Please Help
by Ashley Hannah 28 Feb '13

28 Feb '13

Hello, I am trying to make a table of cortical volumes, however when I run the command: asegstats2table -subjects Sub1 Sub2 Sub3 --segno 17 53 --tablefile=aseg.vol.table I receive the following error message: ERROR: The stats file Sub1/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files I have tried running this multiple ways (such as one subject at a time, selecting different regions) with no avail. If I use '--skip' then it skips every subject. The stats files are present and the volumes within them are normal, I do not understand this error message. Does anyone know a way around this? Ashley Hannah * *

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downloading freesurfer
by Avram, Alexandru (NIH/NICHD) [F] 28 Feb '13

28 Feb '13

I am unable to download freesurfer from the ftp server. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Linux… Looks like the server is down again. Thanks, Alexandru ------------------------------------------------------------------------ Alexandru V. Avram, Ph.D. National Institutes of Health (NIH) National Institute of Child Health and Human Development (NICHD) 13 South Dr, Rm 3W16 Bethesda, MD 20892 (301) 402-6786 (O) (301) 480-0163 (F) alexandru.avram(a)nih.gov<mailto:alexandru.avram@nih.gov> ------------------------------------------------------------------------

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GM and WM volume for each lobe...
by Gonzalo Rojas Costa 28 Feb '13

28 Feb '13

Hi: I need to compute the GM and WM volume for each lobe... I know that for GM, I must use: mri_annotation2label --subject bert --hemi rh --lobesStrict lobesfile mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.lobesfile.stats -b -a ../label/lh.lobesfile.annot bert lh white And, for WM I know that I must use the commands: mri_aparc2aseg and mri_segstats, but I don't know the options of each command that I must use... Could you please send me the complete commands for WM?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Head motion question
by Allison Gruber 28 Feb '13

28 Feb '13

Dear Freesurfer, I was wondering if there is any output from Tracula that quantifies head motion (or the head motion correction performed). If so, is there any standard in the field about an acceptable level or a cut-off point? Thank you for your help, Allison Gruber

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labels to lobes
by Sudhin A. Shah 28 Feb '13

28 Feb '13

Hello, Is there a lookup table I can use to convert free surfer labels to lobes? Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I have 86 labels and want an easy way to differentiate them into the corresponding lobes. Thanks, S

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Re: [Freesurfer] FreeSurfer recon-all two sets of error
by Bruce Fischl 28 Feb '13

28 Feb '13

Hi Blessy what format is this? If you don't send it with an extension there is no way to know.... Bruce On Tue, 26 Feb 2013, Blessy M wrote: > Forgot the image. please find attached. > > > On Tue, Feb 26, 2013 at 2:45 PM, Blessy M <blessam(a)gmail.com> wrote: > I ran this command, and got the attached image > tkmedit ./ brainmask.mgz lh.inflated.nofix > > For some reason tksurfer is not looking good/complete > tksurfer ./ lh inflated > > > On Tue, Feb 26, 2013 at 11:53 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > you can save a tif of it and post it to the list > On Tue, 26 Feb 2013, Blessy M wrote: > > Yes it is still at defect 32. > > The tail of the recon-all.log is as follows: > > CORRECTING DEFECT 30 (vertices=18, convex hull=22) > After retessellation of defect 30, euler #=-7 (59491,172395,112897) : difference with theory > (-28) = -21 > > CORRECTING DEFECT 31 (vertices=244, convex hull=142) > After retessellation of defect 31, euler #=-6 (59502,172495,112987) : difference with theory > (-27) = -21 > > CORRECTING DEFECT 32 (vertices=44865, convex hull=8969) > > > Should I attach the lh.inflated.nofix in a separate email to you, Bruce? > > > > On Tue, Feb 26, 2013 at 10:08 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > is it still on defect 32? What does the tail of the recon-all.log say? And can you > send us an image of the > lh.inflated.nofix (if it is the lh that is running)? > > On Tue, 26 Feb 2013, Blessy M wrote: > > I verified lh.orig.nofix, and it looks fine. But, there has been no new files > created since Saturday > (2/23/2013). > > I am considering stopping the process. > > I was thinking, I had created a skull stripped image, and was giving that as > input to recon-all in the > command below: > recon-all -subjid . -noskullstrip -autorecon1 -notal-check -autorecon2 > -autorecon3 > > Should -noskullstrip flag be after autorecon1? > > > > On Mon, Feb 25, 2013 at 3:35 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > try looking at the lh.inflated.nofix or lh.orig.nofix (or rh, whichever > one is running) and see if > something is > dramatically wrong (like skull attached to brain, or hemis connected, > etc....) > On Mon, 25 Feb 2013, Blessy M wrote: > > Recon is still running. I started the process on 2/21/2013. Its been > 4 days. > > I ran this command, and viewed the aseg file, and that looks > reasonable > tkmedit ./ brainmask.mgz -aux T1.mgz -surfs -aseg > > Currently it is at this stage: > > Correction of the Topology > Finding true center and radius of Spherical Surface...done > Surface centered at (0,0,0) with radius 100.0 in 13 iterations > marking ambiguous vertices... > 124766 ambiguous faces found in tessellation > segmenting defects... > ...... > > 61 defects to be corrected > 0 vertices coincident > ...... > ...... > CORRECTING DEFECT 31 (vertices=244, convex hull=142) > After retessellation of defect 31, euler #=-6 (59502,172495,112987) > : difference with theory > (-27) = -21 > > CORRECTING DEFECT 32 (vertices=44865, convex hull=8969) > > > > > > > > > On Fri, Feb 22, 2013 at 5:33 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: > I don't think either one of these are errors, just warnings > that occur pretty > frequently and I > don't think should > impact the results. Does the recon finish? Do the results look > ok? > > On Fri, 22 Feb 2013, Blessy M wrote: > > > I am getting the bottom two sets of errors while doing a > simple recon-all. > > More specifically while running this command: > recon-all -subjid . -noskullstrip -autorecon1 > -notal-check -autorecon2 > -autorecon3 > > Has someone encountered this kind of errors? Is there a > fix? > > 1) > Computing MAP estimate using 2772 samples... > ******************************************** > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF > ROUTINE MCSRCH ERROR > RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION > OR GRADIENT ARE > INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: > 011: -log(p) = > 7296.5 tol 0.000010 > ... > ... > > 2) > unfolding failed - restoring original position > -------------------- > 0146: dt=13.779160, rms=0.814 (0.000%), neg=0, > invalid=766 > blurring input image with Gaussian with sigma=0.500... > 0000: dt=0.000, rms=0.814, neg=0, invalid=766 > gcamFindOptimalTimeStep: Complete in 101542.133 ms > iter 0, gcam->neg = 801 > > ...................... > > unfolding failed - restoring original position > -------------------- > 0158: dt=13.828393, rms=0.814 (-0.069%), neg=0, > invalid=766 > blurring input image with Gaussian with sigma=0.500... > 0000: dt=0.000, rms=0.814, neg=0, invalid=766 > gcamFindOptimalTimeStep: Complete in 100610.148 ms > > > > > > 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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stuck at CORRECTING DEFECT 41
by Eli Fredman 28 Feb '13

28 Feb '13

Hi all, I have been trying to run freesurfer on a case for awhile now. After receiving multiple errors when using the skull stripped nifti (nii.gz) file, I tried to use the original dicoms as the input. While I haven't run into any errors, the process seems to have frozen at "CORRECTING DEFECT 41 (vertices=89913, convex hull=4452)". Any help would be greatly appreciated. Thanks, Eli ========== INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-380 (nv=211494, nf=423748, ne=635622, g=191) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 12 iterations marking ambiguous vertices... 188325 ambiguous faces found in tessellation segmenting defects... 55 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 11 into 10 -merging segment 15 into 13 -merging segment 18 into 14 -merging segment 24 into 17 -merging segment 36 into 23 -merging segment 38 into 23 -merging segment 31 into 29 -merging segment 39 into 33 -merging segment 46 into 45 -merging segment 0 into 51 45 defects to be corrected 0 vertices coincident reading input surface /projects/schiz/ra/eli/freesurfer5.1/subjects/002dicoms/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.0381 (-4.5191) -vertex loglikelihood: -5.9029 (-2.9514) -normal dot loglikelihood: -3.5586 (-3.5586) -quad curv loglikelihood: -5.9424 (-2.9712) Total Loglikelihood : -24.4420 CORRECTING DEFECT 0 (vertices=82, convex hull=99) After retessellation of defect 0, euler #=-22 (115136,340924,225766) : difference with theory (-42) = -20 CORRECTING DEFECT 1 (vertices=33, convex hull=78) After retessellation of defect 1, euler #=-21 (115149,340994,225824) : difference with theory (-41) = -20 CORRECTING DEFECT 2 (vertices=33, convex hull=68) After retessellation of defect 2, euler #=-20 (115168,341086,225898) : difference with theory (-40) = -20 CORRECTING DEFECT 3 (vertices=101, convex hull=114) After retessellation of defect 3, euler #=-19 (115213,341271,226039) : difference with theory (-39) = -20 CORRECTING DEFECT 4 (vertices=128, convex hull=124) After retessellation of defect 4, euler #=-18 (115250,341441,226173) : difference with theory (-38) = -20 CORRECTING DEFECT 5 (vertices=24, convex hull=54) After retessellation of defect 5, euler #=-17 (115262,341498,226219) : difference with theory (-37) = -20 CORRECTING DEFECT 6 (vertices=26, convex hull=57) After retessellation of defect 6, euler #=-16 (115271,341549,226262) : difference with theory (-36) = -20 CORRECTING DEFECT 7 (vertices=571, convex hull=248) After retessellation of defect 7, euler #=-15 (115423,342130,226692) : difference with theory (-35) = -20 CORRECTING DEFECT 8 (vertices=380, convex hull=194) After retessellation of defect 8, euler #=-14 (115506,342478,226958) : difference with theory (-34) = -20 CORRECTING DEFECT 9 (vertices=993, convex hull=488) After retessellation of defect 9, euler #=-15 (115632,343151,227504) : difference with theory (-33) = -18 CORRECTING DEFECT 10 (vertices=92, convex hull=56) After retessellation of defect 10, euler #=-14 (115642,343197,227541) : difference with theory (-32) = -18 CORRECTING DEFECT 11 (vertices=245, convex hull=137) After retessellation of defect 11, euler #=-12 (115687,343396,227697) : difference with theory (-31) = -19 CORRECTING DEFECT 12 (vertices=42, convex hull=87) After retessellation of defect 12, euler #=-10 (115704,343479,227765) : difference with theory (-30) = -20 CORRECTING DEFECT 13 (vertices=105, convex hull=48) After retessellation of defect 13, euler #=-10 (115716,343539,227813) : difference with theory (-29) = -19 CORRECTING DEFECT 14 (vertices=172, convex hull=170) After retessellation of defect 14, euler #=-8 (115780,343817,228029) : difference with theory (-28) = -20 CORRECTING DEFECT 15 (vertices=5, convex hull=31) After retessellation of defect 15, euler #=-7 (115781,343828,228040) : difference with theory (-27) = -20 CORRECTING DEFECT 16 (vertices=9, convex hull=28) After retessellation of defect 16, euler #=-6 (115784,343843,228053) : difference with theory (-26) = -20 CORRECTING DEFECT 17 (vertices=33, convex hull=61) After retessellation of defect 17, euler #=-5 (115799,343912,228108) : difference with theory (-25) = -20 CORRECTING DEFECT 18 (vertices=19, convex hull=36) Warning - incorrect dp selected!!!!(-97.779794 >= -97.779795 ) After retessellation of defect 18, euler #=-4 (115800,343927,228123) : difference with theory (-24) = -20 CORRECTING DEFECT 19 (vertices=2147, convex hull=849) After retessellation of defect 19, euler #=-3 (116319,345967,229645) : difference with theory (-23) = -20 CORRECTING DEFECT 20 (vertices=6, convex hull=25) After retessellation of defect 20, euler #=-2 (116320,345976,229654) : difference with theory (-22) = -20 CORRECTING DEFECT 21 (vertices=40, convex hull=54) After retessellation of defect 21, euler #=-1 (116337,346050,229712) : difference with theory (-21) = -20 CORRECTING DEFECT 22 (vertices=5, convex hull=28) Warning - incorrect dp selected!!!!(-60.449796 >= -60.449800 ) After retessellation of defect 22, euler #=0 (116339,346063,229724) : difference with theory (-20) = -20 CORRECTING DEFECT 23 (vertices=28, convex hull=68) After retessellation of defect 23, euler #=1 (116348,346118,229771) : difference with theory (-19) = -20 CORRECTING DEFECT 24 (vertices=55, convex hull=89) After retessellation of defect 24, euler #=3 (116361,346191,229833) : difference with theory (-18) = -21 CORRECTING DEFECT 25 (vertices=7, convex hull=24) After retessellation of defect 25, euler #=4 (116364,346206,229846) : difference with theory (-17) = -21 CORRECTING DEFECT 26 (vertices=34, convex hull=61) After retessellation of defect 26, euler #=5 (116377,346272,229900) : difference with theory (-16) = -21 CORRECTING DEFECT 27 (vertices=220, convex hull=226) After retessellation of defect 27, euler #=6 (116428,346544,230122) : difference with theory (-15) = -21 CORRECTING DEFECT 28 (vertices=116, convex hull=73) After retessellation of defect 28, euler #=6 (116438,346608,230176) : difference with theory (-14) = -20 CORRECTING DEFECT 29 (vertices=87, convex hull=115) After retessellation of defect 29, euler #=7 (116474,346762,230295) : difference with theory (-13) = -20 CORRECTING DEFECT 30 (vertices=5, convex hull=36) Warning - incorrect dp selected!!!!(-57.697888 >= -57.697893 ) After retessellation of defect 30, euler #=8 (116476,346776,230308) : difference with theory (-12) = -20 CORRECTING DEFECT 31 (vertices=6, convex hull=22) After retessellation of defect 31, euler #=9 (116478,346787,230318) : difference with theory (-11) = -20 CORRECTING DEFECT 32 (vertices=34, convex hull=26) After retessellation of defect 32, euler #=10 (116483,346809,230336) : difference with theory (-10) = -20 CORRECTING DEFECT 33 (vertices=292, convex hull=113) After retessellation of defect 33, euler #=11 (116504,346932,230439) : difference with theory (-9) = -20 CORRECTING DEFECT 34 (vertices=22, convex hull=70) After retessellation of defect 34, euler #=12 (116515,346990,230487) : difference with theory (-8) = -20 CORRECTING DEFECT 35 (vertices=6, convex hull=19) After retessellation of defect 35, euler #=13 (116517,347003,230499) : difference with theory (-7) = -20 CORRECTING DEFECT 36 (vertices=10, convex hull=48) After retessellation of defect 36, euler #=15 (116521,347034,230528) : difference with theory (-6) = -21 CORRECTING DEFECT 37 (vertices=5, convex hull=28) After retessellation of defect 37, euler #=16 (116522,347046,230540) : difference with theory (-5) = -21 CORRECTING DEFECT 38 (vertices=39, convex hull=93) After retessellation of defect 38, euler #=17 (116545,347155,230627) : difference with theory (-4) = -21 CORRECTING DEFECT 39 (vertices=20, convex hull=30) After retessellation of defect 39, euler #=18 (116549,347178,230647) : difference with theory (-3) = -21 CORRECTING DEFECT 40 (vertices=26, convex hull=52) After retessellation of defect 40, euler #=19 (116560,347231,230690) : difference with theory (-2) = -21 CORRECTING DEFECT 41 (vertices=89913, convex hull=4452) -- Eli Fredman, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6118 Cell: (314) 952-8098 Fax: (617) 525-6150

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Cortical thickness asymmetries ?
by Sophie Maingault 28 Feb '13

28 Feb '13

Dear experts, I would like to study cortical thickness asymmetries. According to old messages it seems impossible so I would like to know if it is always the case or not ? Maybe, there is a command to subtract the values for each vertex in the left hemisphere minus the values for each vertex in the right hemisphere and then use this new variable in qdec ? Thank you for your answer ! Sophie

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Freesurfer February 2013