Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

does mkcontrast-sess correct for multiple comparisons?
by Rosa Lafer-Sousa 12 Mar '13

12 Mar '13

Hi freesurfers! I am curious about corrections for multiple comparisons. I use mkcontrast to generate my statistical maps and am curious if the function provides any internal corrections for multiple comparisons Does mkcontrast-sess correct for multiple comparisons? If so, how? thank you, Rosa -- Rosa Lafer-Sousa Lab Manager, Conway Lab Wellesley College - Neuroscience 106 Central Street Wellesley, MA Harvard Medical School -Neurobiology 220 Longwood Ave WAB Rm 215 Boston, MA 02115 210-325-3185 rlaferso(a)wellesley.edu

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Talairach Transform error. Good registration.
by Adam Martersteck 12 Mar '13

12 Mar '13

Dear FreeSurfers, I am currently having trouble with 1 subject during the initial recon-all during the talairach transform stage. I have attached a pdf of the registeration found in tkregister and the copy of the recon-all.log. Here are the last lines of the recon-all.log: “#@# Talairach Failure Detection Tue Jan 29 14:09:29 CST 2013 /SA140b/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0528, pval=0.0034 < threshold=0.0050)” I have tried re-running the subject from scratch and re-running from the same directory as suggested in the fswiki/FSTutorial/Talairach (if the registration is fixed). In both cases -- the same error results. Should I be using the -notal-check if the registration is good? Notes: I am using FreeSurfer version 5.1.0 recon’ing on a linux. I am using expert options [mri_normalize -b 20 -n 5] and the –mprage flag when running the recon-all. Thanks for any help! Adam Martersteck Cognitive Neurology and Alzheimer’s Disease Center Northwestern University, Feinberg School of Medicine

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R: Re: Question on tracula and dwi-T1 overlap
by stdp82＠virgilio.it 12 Mar '13

12 Mar '13

Thank you Anastasia. What do you think about the issue in the file attacked (I'm noting that same subjects are lacking of same tracts or same tracts are incomplete) Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 12-mar-2013 17.02 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's in the dlabel/diff/ directory has been mapped to the same space as the DWI, so those are the volumes that can be compared directly to dwi.nii.gz. a.y On Tue, 12 Mar 2013, stdp82(a)virgilio.it wrote: > Hi list, > > I have two questions, please. > > I'm using version 5.1 to complete my analysis. > > 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of the same > subject (figure 1 and 3). You can note the dwi do not overlap to the aseg. > How can I resolve this issue? > > 2-After TRACULA analysis, I'm noting that same subjects are lacking of same > tracts or same tracts are incomplete (figure 3). > > Could it depends from the issue in question 1? I'm thinking to rerun all > using version 5.2 but before starting new analyses, I'd like to ask you > which is the possible error. > > > Stefano > >_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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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Question on tracula and dwi-T1 overlap
by stdp82＠virgilio.it 12 Mar '13

12 Mar '13

Hi list, I have two questions, please. I'm using version 5.1 to complete my analysis. 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of the same subject (figure 1 and 3). You can note the dwi do not overlap to the aseg.How can I resolve this issue? 2-After TRACULA analysis, I'm noting that same subjects are lacking of same tracts or same tracts are incomplete (figure 3). Could it depends from the issue in question 1? I'm thinking to rerun all using version 5.2 but before starting new analyses, I'd like to ask you which is the possible error. Stefano

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Neuroimaging Data Manager Position
by Emily Lindemer 12 Mar '13

12 Mar '13

A Neuroimaging Data Manager position is available in the VA Boston Healthcare System (VABHS) Neuroimaging Research for Veterans (NeRVe) Center. The candidate will be responsible for effective management and maintenance of neuroimaging data within the NeRVe Center infrastructure. Responsibilities include provisioning, management of neuroimaging software, and operation, and maintenance monitoring of neuroimaging systems including individual and group file permission management. The individual will also contribute to the innovative development of the neuroimaging Center infrastructure. The individual will ensure that neuroimaging hardware, operating systems, software, and related procedures adhere to internal research standards. This individual will assist project teams with technical issues in neuroimaging data analysis and data management including backups and archiving. These activities include Linux shell scripting and more advanced coding, determining neuroimaging needs and strategies, and necessary testing of imaging systems. The individual should be trained in Linux, Windows and Macintosh operating systems. Applicants should have a minimum of a Bachelor’s degree, with a technical major, such as engineering or computer science. Certification in Linux/Unix, Macintosh, and/or Microsoft would be beneficial, as would prior data management or neuroimaging experience. Interested candidates should email a cover letter, CV, and degree transcripts to Emily Lindemer at emily.lindemer(a)va.gov . * *

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Neuroimaging Research Technician Position
by Emily Lindemer 12 Mar '13

12 Mar '13

A Neuroimaging Research Technician position is available in the VA Boston Healthcare System (VABHS) Neuroimaging Research for Veterans (NeRVe) Center. The Neuroimaging Research Technician will provide technical support for image preprocessing and analysis (using programs such as FSL and FreeSurfer), maintenance and development of in-house custom processing codes (script writing in unix/linux, matlab, etc), and assist staff members in the conduct of neuroimaging research as well as administrative tasks related to the Center. This includes developing expertise and training other investigators with the operation of current MRI hardware (scanner console, goggles, headphones, BioPac system, etc) and software for data processing and analysis. Additional responsibilities will include management of online documentation and center resources. Technical skills and familiarity with Linix/Unix, Matlab, and imaging software packages such as FSL and FreeSurfer is beneficial. Applicants should have a minimum of a Bachelor’s degree, with a background in Neuroscience, Computer Science, Engineering, Math or Physics. A two year commitment is required. Interested candidates should email a cover letter, resume, and contact information for two professional references to Emily Lindemer at emily.lindemer(a)va.gov . * *

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Rejoindre mon réseau sur LinkedIn
by prerona mukherjee via LinkedIn 12 Mar '13

12 Mar '13

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Re: [Freesurfer] preproc-sess
by Meryem Ayse Yucel 12 Mar '13

12 Mar '13

> Hi Doug, > > This is the terminal output. The output volumes don't seem to be smoothed. > > preproc-sess -s 8003 -fsd bold -stc up -fwhm 5 -per-run > -------------------------------------------------------------- > preproc-sess logfile is log/preproc-sess.8003.log > -------------------------------------------------------------- > $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ > mayucel > setenv FREESURFER_HOME /usr/local/freesurfer/stable5_2_0 > setenv SUBJECTS_DIR > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/ > Linux wiggum 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 > x86_64 x86_64 x86_64 GNU/Linux > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT > /usr/local/freesurfer/stable5_2_0/fsfast/bin/preproc-sess > -s 8003 -fsd bold -stc up -fwhm 5 -per-run > Tue Mar 12 11:01:41 EDT 2013 > instem f > mc 1 f fmcpr > stc 1 fmcpr fmcpr.up > sm 0 > mask 1 brain > 8003 Template ----------------------------- > mktemplate-sess -s 8003 -d > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT -fsd > bold -update > > Session: > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003 > ---------------- > Tue Mar 12 11:01:41 EDT 2013 > Detected input format at nii > 8003 Update not needed > Run: 001 ---------------- > Tue Mar 12 11:01:42 EDT 2013 > 8003 001 Update not needed > Run: 002 ---------------- > Tue Mar 12 11:01:42 EDT 2013 > 8003 002 Update not needed > Run: 003 ---------------- > Tue Mar 12 11:01:42 EDT 2013 > 8003 003 Update not needed > Run: 004 ---------------- > Tue Mar 12 11:01:42 EDT 2013 > 8003 004 Update not needed > Run: 005 ---------------- > Tue Mar 12 11:01:42 EDT 2013 > 8003 005 Update not needed > Tue Mar 12 11:01:42 EDT 2013 > mktemplate-sess completed > 8003 Mask ------------------------ > mkbrainmask-sess -maskstem brain -fsd bold -s 8003 -d > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT > -update > ------------------------------------------------ > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003 > Tue Mar 12 11:01:42 EDT 2013 > 8003 Update not needed for session-level mask > 8003 Update not needed for run 001 mask > 8003 Update not needed for run 001 meanval > 8003 Update not needed for run 002 mask > 8003 Update not needed for run 002 meanval > 8003 Update not needed for run 003 mask > 8003 Update not needed for run 003 meanval > 8003 Update not needed for run 004 mask > 8003 Update not needed for run 004 meanval > 8003 Update not needed for run 005 mask > 8003 Update not needed for run 005 meanval > Tue Mar 12 11:01:43 EDT 2013 > mkbrainmask-sess done > 8003 Registration ----------------------------- > register-sess -s 8003 -d > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT -fsd > bold -dof 6 -per-run -update > -------------------------------------------------------------- > register-sess logfile is > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/log/register-sess.8003.log > -------------------------------------------------------------- > Tue Mar 12 11:01:44 EDT 2013 > > setenv SUBJECTS_DIR > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/ > cd /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT > /usr/local/freesurfer/stable5_2_0/fsfast/bin/register-sess -s 8003 -d > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT -fsd > bold -dof 6 -per-run -update > > freesurfer-Linux-centos6_x86_64-stable-v5.2.0-20130302 > Linux wiggum 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 > x86_64 x86_64 x86_64 GNU/Linux > > Session: > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003 > ---------------- > Tue Mar 12 11:01:44 EDT 2013 > Run: 001 ---------------- > Tue Mar 12 11:01:44 EDT 2013 > Update not needed > Run: 002 ---------------- > Tue Mar 12 11:01:44 EDT 2013 > Update not needed > Run: 003 ---------------- > Tue Mar 12 11:01:44 EDT 2013 > Update not needed > Run: 004 ---------------- > Tue Mar 12 11:01:44 EDT 2013 > Update not needed > Run: 005 ---------------- > Tue Mar 12 11:01:44 EDT 2013 > Update not needed > Tue Mar 12 11:01:44 EDT 2013 > register-sess completed > 8003 MC ----------------------------- > mc-sess -fstem f -fmcstem fmcpr -s 8003 -d > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT -fsd > bold -per-run -update > Logfile is > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/log/mc-8003-bold.log > ------------------------------------------- > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003 > RunList: 001 002 003 004 005 > ------- ************************** ----------- > ------- Motion Correcting Run 001 ----------- > ------- ************************** ----------- > sess = 8003 > Tue Mar 12 11:01:45 EDT 2013 > mc-afni2 --i 001/f.nii --t 001/template.nii.gz --o 001/fmcpr.nii.gz > --mcdat 001/fmcpr.mcdat > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold > mri_info --nframes --o /tmp/mriinfo.45950 001/template.nii.gz > log file is 001/fmcpr.nii.gz.mclog > mcdat file is 001/fmcpr.mcdat > tmp dir is 001/tmp.mc-afni2.45950 > #@# -------------------------------- > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold > mri_convert 001/template.nii.gz 001/tmp.mc-afni2.45950/tempvol.nii.gz > --nskip 0 --ndrop 0 -odt float > mri_convert 001/template.nii.gz 001/tmp.mc-afni2.45950/tempvol.nii.gz > --nskip 0 --ndrop 0 -odt float > nskip = 0 > ndrop = 0 > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from 001/template.nii.gz... > TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.99985, 0.00684944, -0.0159016) > j_ras = (-0.00597876, -0.998514, -0.0541706) > k_ras = (-0.016249, -0.0540675, 0.998405) > changing data type from short to float (noscale = 0)... > writing to 001/tmp.mc-afni2.45950/tempvol.nii.gz... > #@# -------------------------------- > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold > mri_convert 001/f.nii 001/tmp.mc-afni2.45950/invol.nii.gz -odt float > mri_convert 001/f.nii 001/tmp.mc-afni2.45950/invol.nii.gz -odt float > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from 001/f.nii... > TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.99985, 0.00684944, -0.0159016) > j_ras = (-0.00597876, -0.998514, -0.0541706) > k_ras = (-0.016249, -0.0540675, 0.998405) > changing data type from short to float (noscale = 0)... > writing to 001/tmp.mc-afni2.45950/invol.nii.gz... > #@# -------------------------------- > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold > 3dvolreg.afni -verbose -dfile 001/fmcpr.mcdat -1Dmatrix_save 001/fmcpr.mat > -base 001/tmp.mc-afni2.45950/tempvol.nii.gz -prefix > 001/tmp.mc-afni2.45950/outvol.nii.gz 001/tmp.mc-afni2.45950/invol.nii.gz > ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit] > ++ Authored by: RW Cox > *+ WARNING: If you are performing spatial transformations on an oblique > dset, > such as 001/tmp.mc-afni2.45950/tempvol.nii.gz, > or viewing/combining it with volumes of differing obliquity, > you should consider running: > 3dWarp -deoblique > on this and other oblique datasets in the same session. > See 3dWarp -help for details. > ++ Oblique dataset:001/tmp.mc-afni2.45950/tempvol.nii.gz is 3.236461 > degrees from plumb. > ++ Reading in base dataset 001/tmp.mc-afni2.45950/tempvol.nii.gz > ++ Oblique dataset:001/tmp.mc-afni2.45950/invol.nii.gz is 3.236461 degrees > from plumb. > ++ Reading input dataset 001/tmp.mc-afni2.45950/invol.nii.gz > ++ Edging: x=3 y=3 z=0 > ++ Creating mask for -maxdisp > + Automask has 4078 voxels > + 2056 voxels left in -maxdisp mask after erosion > ++ Initializing alignment base > ++ Starting final pass on 121 sub-bricks: > 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120.. > ++ CPU time for realignment=0 s [=0 s/sub-brick] > ++ Min : roll=-0.197 pitch=-0.042 yaw=-0.035 dS=-0.011 dL=-0.802 > dP=-0.691 > ++ Mean: roll=+0.065 pitch=+0.003 yaw=-0.003 dS=+0.125 dL=-0.043 > dP=+0.070 > ++ Max : roll=+0.483 pitch=+0.219 yaw=+0.022 dS=+0.308 dL=+0.762 > dP=+0.524 > ++ Max displacements (mm) for each sub-brick: > 0.98 1.10 0.87 0.85 0.85 1.05 0.98 0.91 0.88 0.87 0.76 0.89 0.83 0.81 > 0.81 0.72 0.71 0.79 0.80 0.74 0.67 0.63 0.63 0.66 0.71 0.75 0.56 0.57 > 0.54 0.52 0.62 0.66 0.53 0.44 0.46 0.48 0.55 0.59 0.58 0.33 0.33 0.39 > 0.46 0.56 0.47 0.47 0.49 0.26 0.50 0.52 0.42 0.32 0.28 0.37 0.38 0.39 > 0.23 0.22 0.12 0.09 0.00 0.03 0.31 0.27 0.18 0.15 0.14 0.17 0.37 0.49 > 0.41 0.27 0.13 0.06 0.52 0.49 0.31 0.27 0.25 0.26 0.30 0.38 0.38 0.26 > 0.34 0.36 0.73 0.87 0.82 0.84 0.68 0.70 0.78 0.91 0.78 0.76 0.77 1.01 > 0.89 0.98 0.86 0.76 0.74 0.96 1.04 0.93 0.88 0.75 0.98 0.97 1.15 1.21 > 1.21 1.23 1.20 1.37 1.14 1.09 0.98 0.90 0.98 > ++ Max displacement in automask = 1.37 (mm) at sub-brick 115 > ++ Wrote dataset to disk in 001/tmp.mc-afni2.45950/outvol.nii.gz > #@# -------------------------------- > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold > mri_convert 001/tmp.mc-afni2.45950/outvol.nii.gz 001/fmcpr.nii.gz > --in_like 001/template.nii.gz > mri_convert 001/tmp.mc-afni2.45950/outvol.nii.gz 001/fmcpr.nii.gz > --in_like 001/template.nii.gz > reading info from 001/template.nii.gz... > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from 001/tmp.mc-afni2.45950/outvol.nii.gz... > TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 > INFO: frames are not the same > i_ras = (-0.99985, 0.00684944, -0.0159016) > j_ras = (-0.00597876, -0.998514, -0.0541706) > k_ras = (-0.016249, -0.0540675, 0.998405) > writing to 001/fmcpr.nii.gz... > ... cleaning up .... > Tue Mar 12 11:01:55 EDT 2013 > mc-afni2 done > INFO: Making external regressor from mc params > mcdat2mcextreg --i 001/fmcpr.mcdat --o 001/mcprextreg > Tue Mar 12 11:01:56 EDT 2013 > > setenv SUBJECTS_DIR > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/ > cd > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold > /usr/local/freesurfer/stable5_2_0/fsfast/bin/mcdat2mcextreg --i > 001/fmcpr.mcdat --o 001/mcprextreg > > freesurfer-Linux-centos6_x86_64-stable-v5.2.0-20130302 > Linux wiggum 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 > x86_64 x86_64 x86_64 GNU/Linux > mri_glmfit --table > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmpdir.mcdat2extreg.46048/table.dat > --glmdir > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmpdir.mcdat2extreg.46048/glm > --osgm --y-out > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmpdir.mcdat2extreg.46048/y.out.nii > --pca > > $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > cwd > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold > cmdline mri_glmfit --table > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmpdir.mcdat2extreg.46048/table.dat > --glmdir > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmpdir.mcdat2extreg.46048/glm > --osgm --y-out > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmpdir.mcdat2extreg.46048/y.out.nii > --pca > sysname Linux > hostname wiggum > machine x86_64 > user mayucel > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > OneSampleGroupMean 1 > y > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmpdir.mcdat2extreg.46048/table.dat > logyflag 0 > usedti 0 > glmdir > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmpdir.mcdat2extreg.46048/glm > IllCondOK 0 > ReScaleX 1 > DoFFx 0 > Creating output directory > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmpdir.mcdat2extreg.46048/glm > Loading y from > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmpdir.mcdat2extreg.46048/table.dat > Found 6 data colums > Found 121 data rows > Saving design matrix to > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmpdir.mcdat2extreg.46048/glm/Xg.dat > Normalized matrix condition is 1 > Matrix condition is 1 > search space = 6.000000 > DOF = 120 > Starting fit and test > Fit completed in 0 minutes > Writing results > osgm > maxvox sig=40.7364 F=429.568 at index 3 0 0 seed=1363108614 > Measure:MC osgm > Tx 4.793 > Ty 0.672 > Tz -2.203 > Rx 40.736 > Ry -0.488 > Rz 5.441 > Computing PCA (121) > mri_glmfit done > ninputs = 1 > Checking inputs > nframestot = 121 > Allocing output > Done allocing > nframes = 121 > Computing PCA > Writing to > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmpdir.mcdat2extreg.46048/pca.nii > mcdat2mcextreg done > 8003 002 Update not needed > 8003 003 Update not needed > 8003 004 Update not needed > 8003 005 Update not needed > > > Tue Mar 12 11:02:02 EDT 2013 > mc-sess completed SUCCESSFULLY > 8003 STC ----------------------------- > stc-sess -i fmcpr -o fmcpr.up -so up -s 8003 -d > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT -fsd > bold -update > Tue Mar 12 11:02:02 EDT 2013 > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT > /usr/local/freesurfer/stable5_2_0/fsfast/bin/stc-sess > -i fmcpr -o fmcpr.up -so up -s 8003 -d > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT -fsd > bold -update > $Id: stc-sess,v 1.10 2011/02/24 20:19:03 greve Exp $ > wiggum > 8003 ----------------- > Tue Mar 12 11:02:02 EDT 2013 > --------------------------------------------- > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT > stc.fsl --i > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/fmcpr.nii.gz > --o > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/fmcpr.up.nii.gz > --up > Tue Mar 12 11:02:02 EDT 2013 > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT > /usr/local/freesurfer/stable5_2_0/fsfast/bin/stc.fsl > --i > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/fmcpr.nii.gz > --o > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/fmcpr.up.nii.gz > --up > $Id: stc.fsl,v 1.7.4.1 2011/03/28 20:38:31 greve Exp $ > wiggum > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT > mri_info --nslices --o > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmp.46180/nslices.dat > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/fmcpr.nii.gz > nslices = 6 > ---------- Slice Sequence --------------- > 1 > 2 > 3 > 4 > 5 > 6 > ----------------------------------------- > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT > mri_convert > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/fmcpr.nii.gz > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmp.46180/in.nii > mri_convert > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/fmcpr.nii.gz > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmp.46180/in.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/fmcpr.nii.gz... > TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.99985, 0.00684944, -0.0159016) > j_ras = (-0.00597876, -0.998514, -0.0541706) > k_ras = (-0.016249, -0.0540675, 0.998405) > writing to > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmp.46180/in.nii... > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT > slicetimer.fsl -i > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmp.46180/in.nii > -o > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmp.46180/out.nii > --ocustom=/autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmp.46180/saof.dat > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT > mri_convert > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmp.46180/out.nii > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/fmcpr.up.nii.gz > mri_convert > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmp.46180/out.nii > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/fmcpr.up.nii.gz > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/tmp.46180/out.nii... > TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.99985, 0.00684944, -0.0159016) > j_ras = (-0.00597876, -0.998514, -0.0541706) > k_ras = (-0.016249, -0.0540675, 0.998405) > writing to > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/001/fmcpr.up.nii.gz... > stc.fsl Done > -rw-rw-r-- 1 mayucel mayucel 10896975 Mar 5 10:11 > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/002/fmcpr.up.nii.gz > -rw-rw-r-- 1 mayucel mayucel 10684000 Mar 5 10:10 > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/002/fmcpr.nii.gz > Update not needed > -rw-rw-r-- 1 mayucel mayucel 10897860 Mar 5 10:11 > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/003/fmcpr.up.nii.gz > -rw-rw-r-- 1 mayucel mayucel 10682045 Mar 5 10:10 > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/003/fmcpr.nii.gz > Update not needed > -rw-rw-r-- 1 mayucel mayucel 10890231 Mar 5 10:11 > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/004/fmcpr.up.nii.gz > -rw-rw-r-- 1 mayucel mayucel 10641066 Mar 5 10:10 > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/004/fmcpr.nii.gz > Update not needed > -rw-rw-r-- 1 mayucel mayucel 18130123 Mar 5 10:12 > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/005/fmcpr.up.nii.gz > -rw-rw-r-- 1 mayucel mayucel 17829350 Mar 5 10:10 > /autofs/cluster/bartman/1/users/mayucel/DATA-HYPERCAPNIA-2012/PROJECT/8003/bold/005/fmcpr.nii.gz > Update not needed > Started at Tue Mar 12 11:02:02 EDT 2013 > Ended at Tue Mar 12 11:02:10 EDT 2013 > stc-sess Done > ---------------------------------------- > Started at Tue Mar 12 11:01:41 EDT 2013 > Ended at Tue Mar 12 11:02:10 EDT 2013 > preproc-sess done > > >

1 0

mri_ca_train fails in rebuild_gca_atlas
by alexandra.cristobal＠urjc.es 12 Mar '13

12 Mar '13

Hi everybody, I'm trying to create my own atlas with the rebuild_gca_atlas script. I obtain the "Input TR, TE, FlipAngle for each subjects must match" error in the # TRAIN FROM SEGMENTED_SUBJECTS USING M3D_ONE step (using mri_ca_train for all subjects). TR, TE and FlipAngle are the same for all patients. What can be the problem? The log is: mri_ca_train -prior_spacing 2 -node_spacing 4 -mask brain.mgz -parc_dir seg_edited.mgz -xform talairach_one.m3z -T1 norm.mgz -check 4163 4168 /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca reading input 0: /Applications/freesurfer/subjects/4163/mri/norm.mgz spacing priors every 2.0 mm spacing nodes every 4.0 mm using MR volume brain.mgz to mask input volume... reading segmentation from subject's mri/seg_edited.mgz directory reading xform from talairach_one.m3z reading T1 data from subject's mri/norm.mgz directory will conduct sanity-check of labels... training on 2 subject and writing results to /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4 *************************************************************************** processing subject 4163, 1 of 2... reading volume /Applications/freesurfer/subjects/4163/mri/brain.mgz for masking... gunzip -c /Applications/freesurfer/subjects/4163/mri/transforms/talairach_one.m3z checking labels in subject 4163... max_xtal_l_hippo = -12.6 max_xtal_l_caudate = -5.8 max_xtal_l_amygdala = -17.1 max_xtal_l_putamen = -12.7 max_xtal_l_pallidum = -11.4 min_xtal_r_hippo = 15.2 min_xtal_r_caudate = 6.4 min_xtal_r_amygdala = 16.4 min_xtal_r_putamen = 13.9 min_xtal_r_pallidum = 13.1 Input TR, TE, FlipAngle for each subjects must match. 23 prior holes filled *************************************************************************** processing subject 4168, 2 of 2... nn Thank you in advance.

2 9

qdec question
by Kristina Nalbandian 12 Mar '13

12 Mar '13

Hello! I am running qdec group analysis on my patient data and have one very important question. I am studying the differences between two Epilepsy subtypes. Each one of my patients has a hemisphere of onset, either Left or Right, that I would like to use in looking for differences between ipsilateral and contralateral hemispheres. However, ipsilateral patients need to be grouped together, but qdec only allows me to visualize left or right hemispheres separately. Is there a way to combine left hemispheres with right hemispheres in an attempt to study grey matter thickness in hemispheres ipsilateral to seizure onset? [Because the ipsilateral hemisphere is the right hemisphere for some patients and left hemisphere for others]. For example, is it possible to somehow flip the right hemisphere such that ipsilateral hemispheres align together? Thank you in advance for your help, Kristina Nalbandian

2 1

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Freesurfer March 2013