Freesurfer January 2010

freesurfer@nmr.mgh.harvard.edu

78 participants
123 discussions

Vol index to Talairach
by Oya, Hiroyuki 19 Jan '10

19 Jan '10

Dear experts, I like to find Tarairach and MNI coordinate from volume index (data has been already processed with recon-all) off line using Matlab. Which transform should I use to find it ? Thank you. Hiroyuki

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brainmask
by Satrajit Ghosh 19 Jan '10

19 Jan '10

if one wants to get at the brain only (similar to bet), is brainmask.mgz the best file to use? on some of our data, we are noticing a lot of eyeball. i presume one can use aseg as an alternative. is this more recommended than brainmask.mgz? also, is the total brain volume computation based on aseg or some other file? cheers, satra

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Paired Analysis, Smoothing Step
by Stidd, Reva (NIH/NIMH) [F] 19 Jan '10

19 Jan '10

Hi there, I've got a sample of subjects with T1 and T2 scans that I'm trying to compare. I did the entire longitudinal stream protocol, and am now doing the paired analysis protocol. I'm stuck on the Spatial Smoothing step: I've only gotten either a ">" or a message reading, "ERROR: Option -sval unknown." Is there any reason why? Thanks, -Reva ---------------------------- CHP-MP6:subjects revastidd$ ls (all *.long.* files, base files and timepoint scans are listed plus the following files/folders:) 12SIB FSGD README Random Output V1_average bert fsaverage lh.paired-diff.thickness.mgh mris_preproc.surface.lh.log mris_preproc.surface.rh.log random rh.paired-diff.thickness.mgh sample-001.mgz sample-002.mgz wmparc.vol.table CHP-MP6:subjects revastidd$ mri_surf2surf --s fsaverage --hemi lh --fwhm 5 \ --sval lh.paired-diff.thickness.mgh \ --tval lh.paired-diff.thickness.sm05mgh ERROR: Option --sval unknown CHP-MP6:subjects revastidd$ mri_surf2surf --s faverage --hemi lh --fwhm 5 \ --sval lh.paired-diff.thickness.mgh \ --tval lh.paired-diff.thickness.sm05.mgh \ FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 Kernel info: Darwin 9.8.0 i386 Current Working Directory: /Applications/freesurfer/subjects Which freesurfer: /Applications/freesurfer/bin/freesurfer I've also attached a screenshot of the current files in my subject directory. Please let me know if you need anything else. Thank you for your help! -Reva

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number of vertices per hemisphere using mri_glmfit
by Stefan Brauns 19 Jan '10

19 Jan '10

Hi there, I am running surface based analysis of cortical thickness using FreeSurfer. Sometimes I constrain the analysis to certain regions of the brain, e.g. only frontal lobes. I would like to find out how many vertices per hemisphere are analysed with the mri_glmfit I am running. Is there a possibility to get these values from any of the log-files? What is the usual number of vertices per hemisphere? Many thanks, Stefan

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a question about rebuild_gca_atlas.csh
by Guang Zeng 19 Jan '10

19 Jan '10

Hi, there, In rebuild_gca_atlas.csh, I read something like: # A talairach registration should be generated for this first subject as well, # in order to align the final atlas to the Talairach space. Is this talairach registration file the same as the talairach.xfm under each subject's /mri/transforms/ direcotry? Thanks! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/196390709/direct/01/

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fs-fast sfa-sess retinotopy error
by Jason Connolly 19 Jan '10

19 Jan '10

Dear freesurfer experts: I am new to fs-fast and I am currently running sfa-sess on some retinotopy data and I think the main error is "cannot determine format of 005/f" I read in a previous post related to retinotopy that you need to add the full path to the .nii files and then it will work. My question is: where do you add the full path? Many thanks, Jason. Error message: sfa-sess -analysis rtopy -s jason-functional -------------------------------------------------------------- sfa-sess logfile is /usr/local/freesurfer/subjects/jason/brainmapper/log/sfa-sess-bold-rtopy-1001181608.log -------------------------------------------------------------- ------------------------------------------- /usr/local/freesurfer/subjects/jason/brainmapper/jason-functional Mon Jan 18 16:08:48 GMT 2010 INFO (jason-functional): RunList = 005 007 012 013 -------------------------------------------------- /usr/local/freesurfer/subjects/jason/brainmapper/jason-functional/bold selfreqavg -TR 1.5 -o rtopy/polar/h -i 005/f -i 007/f -i 012/f -cfg /usr/local/freesurfer/subjects/jason/brainmapper/rtopy/analysis.cfg -parname rtopy.par -------------------------------------------------- --- Parsing Config File: /usr/local/freesurfer/subjects/jason/brainmapper/rtopy/analysis.cfg ---- -ncycles 15 -delay 0 -nskip 0 -fwhm 0 DirectionList: +1 -1 +1 Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2009 The MathWorks, Inc. Version 7.8.0.347 (R2009a) 64-bit (glnxa64) February 12, 2009 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Extension format = >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> nii >> >> >> >> >> >> >> hanrad = 0 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ERROR: cannot determine >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> format of 005/f >> ??? Attempt to reference field of non-structure array. >> ??? Attempt to reference field of non-structure array. >> ??? Attempt to reference field of non-structure array. >> >> ??? Attempt to reference field of non-structure array. >> >> ??? Undefined function or variable 'lastslice'. >> ??? Attempt to reference field of non-structure array. >> >> >> ??? Attempt to reference field of non-structure array. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ??? Index exceeds matrix dimensions. >> >> >> >> >> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >> >> >> >> >> >> >> >> >> >> >> >> >> Slice >> ??? Undefined function or variable 'lastslice'. >> >> >> >> ??? Attempt to reference field of non-structure array. Error in ==> MRIwrite at 94 hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3) mri.nframes]; >> >> >> ??? Attempt to reference field of non-structure array. Error in ==> MRIwrite at 94 hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3) mri.nframes]; >> >> >> ??? Attempt to reference field of non-structure array. Error in ==> MRIwrite at 94 hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3) mri.nframes]; >> >> >> >> Saving header to rtopy/polar/h >> >> >> selfreqavg COMPLETED mri_convert rtopy/polar/h.nii -o rtopy/polar/h-offset.nii --frame 10 mri_convert rtopy/polar/h.nii -o rtopy/polar/h-offset.nii --frame 10 niiRead(): error opening file rtopy/polar/h.nii $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from rtopy/polar/h.nii...

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mri_glmfit-sim and longitudinal analysis
by Thomas, Adam (NIH/NIMH) [E] 18 Jan '10

18 Jan '10

I have a small group of subjects where each subject has been scanned once a week for five weeks while learning a task. I'd like to look for changes in cortical thickness across the scans. I've already looked at grey matter density in FSL using randomise (http://www.fmrib.ox.ac.uk/fsl/randomise/index.html) for clusterwise multiple comparison correction and would like to do something similar for cortical thickness. It doesn't look like mri_glmfit-sim allows you to specify exchangeability blocks so that scans are only swapped with scans of the same subject in the simulation. Or can it do this and I'm just not seeing it? Any other recommendation on how to approach this analysis in FS? Thanks, -Adam --- Adam Thomas adamt(a)nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room 1D80 Bethesda MD. 20892-1148 Phone: 301-402-6351

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gm segmentation problem
by johanna feiler 18 Jan '10

18 Jan '10

Dear freesurfer experts, After running the autorecon2 process the pial surface fails to catch up pieces of gm in the insula region. I gained little improvement with setting control points, but the problem still occurs, lasting about five slices. As an illustration, I attached a screenshot. How can I solve this problem? Thanks for your help! Johanna Feiler ______________________________________________________ GRATIS für alle WEB.DE-Nutzer: Die maxdome Movie-FLAT! Jetzt freischalten unter http://movieflat.web.de

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recon-all now taking too long
by Rodrigo Zepeda 18 Jan '10

18 Jan '10

Hi, I have noticed that recently recon-all is taking a lot longer than usual to finish. It used to take around 30 to 48 hours, but the last couple that I have done are taking a whole week. It seems to get stuck in a repetitive step and it numbers each iteration like this: not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/stable4/average/RB_all_2008-03-26.gca'... freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.30 (predicted orig area = 6.2) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.04 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.759, neg=0, invalid=766 0001: dt=252.406048, rms=0.710 (6.426%), neg=0, invalid=766 0002: dt=157.425287, rms=0.695 (2.149%), neg=0, invalid=766 0003: dt=199.529412, rms=0.687 (1.109%), neg=0, invalid=766 0004: dt=115.649123, rms=0.684 (0.433%), neg=0, invalid=766 0005: dt=517.888000, rms=0.677 (1.076%), neg=0, invalid=766 0006: dt=74.457516, rms=0.675 (0.226%), neg=0, invalid=766 0007: dt=74.457516, rms=0.675 (0.073%), neg=0, invalid=766 0008: dt=74.457516, rms=0.674 (0.143%), neg=0, invalid=766 0009: dt=74.457516, rms=0.672 (0.227%), neg=0, invalid=766 0010: dt=74.457516, rms=0.670 (0.292%), neg=0, invalid=766 0011: dt=74.457516, rms=0.668 (0.289%), neg=0, invalid=766 0012: dt=74.457516, rms=0.667 (0.258%), neg=0, invalid=766 0013: dt=74.457516, rms=0.665 (0.229%), neg=0, invalid=766 0014: dt=74.457516, rms=0.664 (0.195%), neg=0, invalid=766 0015: dt=74.457516, rms=0.663 (0.191%), neg=0, invalid=766 0016: dt=74.457516, rms=0.661 (0.213%), neg=0, invalid=766 0017: dt=74.457516, rms=0.660 (0.192%), neg=0, invalid=766 0018: dt=74.457516, rms=0.659 (0.154%), neg=0, invalid=766 0019: dt=74.457516, rms=0.658 (0.132%), neg=0, invalid=766 0020: dt=74.457516, rms=0.657 (0.119%), neg=0, invalid=766 0021: dt=74.457516, rms=0.656 (0.140%), neg=0, invalid=766 0022: dt=74.457516, rms=0.655 (0.162%), neg=0, invalid=766 0023: dt=74.457516, rms=0.654 (0.162%), neg=0, invalid=766 0024: dt=74.457516, rms=0.653 (0.138%), neg=0, invalid=766 0025: dt=74.457516, rms=0.652 (0.114%), neg=0, invalid=766 0026: dt=74.457516, rms=0.652 (0.117%), neg=0, invalid=766 0027: dt=74.457516, rms=0.651 (0.130%), neg=0, invalid=766 0028: dt=74.457516, rms=0.650 (0.138%), neg=0, invalid=766 0029: dt=74.457516, rms=0.649 (0.124%), neg=0, invalid=766 0030: dt=74.457516, rms=0.649 (0.104%), neg=0, invalid=766 0031: dt=32.368000, rms=0.649 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.649, neg=0, invalid=766 0032: dt=129.472000, rms=0.647 (0.306%), neg=0, invalid=766 0033: dt=517.888000, rms=0.645 (0.194%), neg=0, invalid=766 0034: dt=517.888000, rms=0.645 (0.016%), neg=0, invalid=766 0035: dt=517.888000, rms=0.645 (-0.929%), neg=0, invalid=766 setting smoothness coefficient to 0.15 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.651, neg=0, invalid=766 0036: dt=51.963303, rms=0.646 (0.707%), neg=0, invalid=766 0037: dt=216.338028, rms=0.634 (1.907%), neg=0, invalid=766 0038: dt=39.422680, rms=0.630 (0.681%), neg=0, invalid=766 0039: dt=145.152000, rms=0.627 (0.498%), neg=0, invalid=766 0040: dt=73.437288, rms=0.622 (0.677%), neg=0, invalid=766 0041: dt=75.051233, rms=0.619 (0.604%), neg=0, invalid=766 0042: dt=23.040000, rms=0.618 (0.092%), neg=0, invalid=766 0043: dt=23.040000, rms=0.618 (0.058%), neg=0, invalid=766 0044: dt=23.040000, rms=0.617 (0.112%), neg=0, invalid=766 It continues to do that for days. I have run it in 2 different computers and it makes no difference. Any ideas why this is now taking so long and how to make a bit faster? Thanks! Rodrigo

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error in autorecon1
by Cindy Eckart 18 Jan '10

18 Jan '10

Dear Freesurfers, when I try to run the recon-all flow, it exits at the skull stripping stage in some subjects, giving out error messages like this: register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (52, 9, 21) --> (208, 255, 220) using (104, 91, 121) as brain centroid... mean wm in atlas = 126, using box (85,61,96) --> (123, 121,145) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf When I checked all prior steps, I realized that the nu.mgz was particularly dark and tried to improve it by manually setting control points in the white matter... however, without success, even under inclusion of some control points the skull strip could not be finished.... Then I found a similar problem in the mailing list archive (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-April/007603.ht…) tried the solution proposed there and altered my 001.mgz with a scaling factor of 3 (cp 001.mgz 001_orig.mgz / mri_convert --scale 3 001_orig.mgz 001.mgz / rerun recon-all) again without any success..... Finally, I have no idea how to find another solution! Has anyone an idea?? Every suggestions is highly appreciated! Thanks and greetings Cindy ___________________________________________________________ Preisknaller: WEB.DE DSL Flatrate für nur 16,99 Euro/mtl.! http://produkte.web.de/go/02/

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Freesurfer January 2010