Freesurfer

freesurfer@nmr.mgh.harvard.edu

8 participants
30091 discussions

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

2 1

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 . * *

1 0

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 . * *

1 0

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

12 Mar '13

LinkedIn ------------ prerona mukherjee souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de prerona mukherjee http://www.linkedin.com/e/-qq80um-he77izat-3g/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de prerona mukherjee http://www.linkedin.com/e/-qq80um-he77izat-3g/rso/235545018/_HAj/name/66471… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-he77izat-3g/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

1 0

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

Binary volume to surface _ mri_vol2surf
by Christopher 12 Mar '13

12 Mar '13

Dear Freesurfer community, I have processed a subject (name:P061_pre, 3D MPRAGE T1) with Freesurfer 5.1. A resection area has been defiened on this volume and exists as a binary volume (1:voxels of interest, 0:others) lesionMask.mgz. I now would like to project this volume on the surface of the subject, e.g. lh.white. I have tried using mri_vol2surf : mri_vol2surf --src lesionMask.mgz --out lesionMask_surf.mgh --out_type mgh --hemi lh --regheader P061_pre The command seems to work: srcvol = lesionMask.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /root/data/FS51/freesurfer/subjects/P061_pre/mri/orig.mgz as target reference. Reading surface /root/data/FS51/freesurfer/subjects/P061_pre/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 79054 Writing to ./lesionMask_surf.mgh Dim: 128233 1 1 But when trying to open the surface with freeview, it returns an error message : freeview -f lesionMask_surf.mgh ERROR: MRISread: cannot read surface data from file /home/epilepsy/sorted/P061/preMR/lesionMask_surf.mgh! Segmentation fault What did I miss ? Thanks for your help, -- Christopher Coello, Ph.D. Preclinical PET/CT unit Institute of Basic Medical Sciences Faculty of Medicine, University of Oslo, Norway tel. +4745154516

3 5

qdec question
by Kristina Nalbandian 11 Mar '13

11 Mar '13

1 0

Extract pial surface
by Valtina Pouegue 11 Mar '13

11 Mar '13

Hi Freesurfers, I would like to extract the whole pial surface of a brain volume. I already done the segmentation and i have ( rh.pial and lh.pial surfaces). Does it exist a way to get the whole pial surface without separation? Thanks. VP

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer