Freesurfer March 2005

freesurfer@nmr.mgh.harvard.edu

28 participants
35 discussions

Surface crossing
by Keyma Prince 22 Mar '05

22 Mar '05

Hello, In the attached image the pial surface and the wm mater surface are crossing. Can you let me know if this should be fixed or if it will have an effect on the parcellation steps? The whole volume is located at /space/engram/10/users/rk_fmri_struc/Y15_102304_STRUC. -Keyma Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139

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FW: [Freesurfer] thickness measures
by Kirk, Gregory 21 Mar '05

21 Mar '05

-----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Kirk, Gregory Sent: Tuesday, March 15, 2005 1:49 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] thickness measures Hi I would like to know if anyone has much experience doing pediatrics with freesurfer. I was able to get what look like good results from a 2 year old and a 16 year old, the surfaces look good with only automated topology fixing. An 8 year old needs a lot of manual work. The +- on the cortical thickness was .8 and .9, I don't know if that is larger than usual or not, for averge of a hemisphere. Greg. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Parcellation II
by Wan Park 21 Mar '05

21 Mar '05

cheers! i did exactly the same thing with another brain but this time i obtained this which looks much better: (i am sending this again in a smaller size to avoid the mediator) i guess this is correct. now, how can i use this areas to calculate the gray matter volume of these "standard areas"? thanks! wan

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Parcellation
by Wan Park 21 Mar '05

21 Mar '05

Hello, I need to parcellate the brain in "standard areas" (eg. prefrontal, occipital, temporal, etc.). I have a MAC and I did the parcellation with the new binaries that Kevin Teich sent me. What I have is a multicolor brain painted in tiny pieces. Is this correct? What I am interested is to calculate the gray matter volume (with mris_anatimical_stats) of some "standard areas". How can I do this? Thank you very much! Wan

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recon-all -stage1 sharpen_volume
by Michele Perry 18 Mar '05

18 Mar '05

When I run recon-all -stage1 -subjid <subjectID>, it exits after the following: --------------------------------------------- Nu Intensity Correction Fri Mar 18 17:19:49 PST 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, -0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [mperry@ip06:<SUBJECTS_DIR>/<subjectID>/mri/] [2005-03-18 17:19:59] running: /usr/pubsw/packages/mni/1.2/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_31180/ nu0.mnc nu1.imp Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at /usr/pubsw/packages/mni/1.2/bin/sharpen_volume line 33. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/1.2/bin/sharpen_volume line 33. nu_estimate_np_and_em: crashed while running sharpen_volume (termination status=512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) ERROR: nu_correct ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on 693727244 310617732 347870136 48% ------------------------------------------ recon-all exited with errors at Fri Mar 18 17:19:59 PST 2005 vi /usr/pubsw/packages/mni/1.2/bin/sharpen_volume line 33 is: use MNI::Startup qw(nocputimes); That's the first line after all the initial comments. Any advice? Michele

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nu_correct problem
by Michele Perry 16 Mar '05

16 Mar '05

I'm having problems with recon-all. It used to work but recently, every time I've used it, I get a nu_correct error. I don't think we have had any freesurfer upgrades since the last time recon-all worked. Here's the log. Anyone know what's wrong? ip07:mperry[12] setenv SUBJECTS_DIR <path/to/subjects/dirs> ip07:mperry[13] setenv FUNCTIONALS_DIR <path/to/subjects/dirs> ip07:mperry[14] recon-all -stage1 -subjid subject_ID ######################################## program versions used $Id: recon-all-nmr,v 1.50 2004/08/31 18:05:08 tosa Exp $ $Id: mri_motion_correct2,v 1.8 2004/10/04 22:52:12 greve Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.12 2 003/11/14 16:52:24 stever Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.5.2.1 2003/07/05 01:58:08 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.12 2003/09/18 15:01:33 bert Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6. 4 2001/04/24 13:38:42 neelin Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.11.2.1 2003/11/17 06:01:15 stever Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### INFO: SUBJECTS_DIR is <path/to/subjects/dirs> --------------------------------------------- MotionCor Tue Mar 15 16:03:21 PST 2005 <path/to/subjects/dirs>/<subject_ID>/mri/orig mri_motion_correct2 -o . -i 001 -i 002 tmpdir is ./tmp-mri_motion_correct2-23141 -------------------------------------------------------------- mri_motion_correct2 logfile is ./mri_motion_correct2.log -------------------------------------------------------------- ----------------------------------------- Converting 001 Tue Mar 15 16:03:21 PST 2005 mri_convert 001 <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_mo tion_correct2-23141/cor-1.mnc reading from 001... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, -0) writing to <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion_ correct2-23141/cor-1.mnc... ----------------------------------------- Converting 002 Tue Mar 15 16:03:29 PST 2005 mri_convert 002 <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_mo tion_correct2-23141/cor-2.mnc reading from 002... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, -0) writing to <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion_ correct2-23141/cor-2.mnc... ----------------------------------------- Motion Correcting <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_ motion_correct2-23141/cor-2.mnc Tue Mar 15 16:03:36 PST 2005 COG of v1: 2.191772 14.916920 -47.842663 COG of v2: 2.203371 14.932534 -47.776924 [trans] = 0.011599 0.015615 0.065739 Initial objective function val = 0.01807109 Final objective function value = 0.00892547 ----------------------------------------- Resampling <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion_ correct2-23141/cor-2.mnc Tue Mar 15 16:04:30 PST 2005 Transforming slices:............................................................ ................................................................................ ................................................................................ ....................................Done ----------------------------------------- Averaging Tue Mar 15 16:04:37 PST 2005 Processing:..................................................................... ................................................................................ ................................................................................ ...........................Done ----------------------------------------- Converting Average to output Tue Mar 15 16:04:41 PST 2005 mri_convert <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion _correct2-23141/avgvol.mnc . -tr 2730 -te 3.31 -TI 1000 -flip_angle 0.122173 reading from <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motio n_correct2-23141/avgvol.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, -0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to .... Started at: Tue Mar 15 16:03:21 PST 2005 Ended at: Tue Mar 15 16:04:46 PST 2005 mri_motion_correct2: done --------------------------------------------- Nu Intensity Correction Tue Mar 15 16:04:46 PST 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, -0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [mperry@ip07:<path/to/subjects/dirs>/<subject_ID>/mri/] [2005-03-15 16:0 4:54] running: /usr/pubsw/packages/mni/1.2/bin/nu_estimate_np_and_em -parzen -log -sharpen 0. 15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -d istance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_2326 4/ nu0.mnc nu1.imp spawn: exec of sharpen_volume failed: No such file or directory nu_estimate_np_and_em: crashed while running sharpen_volume (termination status= 65280) nu_correct: crashed while running nu_estimate_np_and_em (termination status=6528 0) ERROR: nu_correct ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on 693727248 307742336 350745536 47% /space/aliens/1 ------------------------------------------ recon-all exited with errors at Tue Mar 15 16:04:55 PST 2005

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RE: [Freesurfer] thickness measures
by Kirk, Gregory 15 Mar '05

15 Mar '05

Hi I would like to know if anyone has much experience doing pediatrics with freesurfer. I was able to get what look like good results from a 2 year old and a 16 year old, the surfaces look good with only automated topology fixing. An 8 year old needs a lot of manual work. The +- on the cortical thickness was .8 and .9, I don't know if that is larger than usual or not, for averge of a hemisphere. Greg.

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mkbrainmask failed
by Jia Liu 14 Mar '05

14 Mar '05

Dear group- When I tried mkbrainmask-sess with my data, I encountered an error (see below), and the program aborted. Could any one tell me how to fix this problem? I am using the newest version available from FreeSurfer download site. Thanks, jia zion:/nfs/home/jliu/data/test/mystudy> mkbrainmask-sess -sf sessid_re001_2 -df sesspar ---------------------------------------------------------------------------- -------------------- /nfs/home/jliu/data/test/20040527rd Sun Mar 13 16:49:50 CST 2005 -------------------------------------------------- /nfs/home/jliu/data/test/20040527rd/bold mkbrainmask -i 005/f -o masks/brain -thresh 0.1 -umask 2 -------------------------------------------------- Scratch Dir is /tmp/mkbrainmask_22219 # ---------- Converting bvolume to .img ------------------ # mri_convert 005/f_000.bshort /tmp/mkbrainmask_22219/f.img Reading 005/f_000.bshort ... Reading 005/f_001.bshort ... Reading 005/f_002.bshort ... Reading 005/f_003.bshort ... Reading 005/f_004.bshort ... Reading 005/f_005.bshort ... Reading 005/f_006.bshort ... Reading 005/f_007.bshort ... Reading 005/f_008.bshort ... Reading 005/f_009.bshort ... Reading 005/f_010.bshort ... Reading 005/f_011.bshort ... Reading 005/f_012.bshort ... Reading 005/f_013.bshort ... Reading 005/f_014.bshort ... Reading 005/f_015.bshort ... Reading 005/f_016.bshort ... Reading 005/f_017.bshort ... Reading 005/f_018.bshort ... Reading 005/f_019.bshort ... Reading 005/f_020.bshort ... reading from 005/f_000.bshort... INFO: bvolumeRead: min = 0, max = 1480 TR=1.50, TE=32.00, TI=32.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -0.990268, 0.139173) k_ras = (-0, 0.139173, 0.990268) writing to /tmp/mkbrainmask_22219/f.img... Analyze Output Matrix -3.125 0.000 -0.000 104.375; 0.000 -3.095 0.668 146.084; 0.000 0.435 4.753 -44.536; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to 3 # ---------- Using FSL's BET to Extract Brain------------------ # This program has not been compiled for this data type /nfs/home/jliu/data/test/20040527rd/bold bet /tmp/mkbrainmask_22219/f /tmp/mkbrainmask_22219/brain -m -f 0.1 ERROR: bet failed ERROR: mkbrainmask failed Exit 1

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Transformations
by Lars Tjelta Westlye 14 Mar '05

14 Mar '05

Hi, I'm having some problems using the talairach command on scewed T1 volumes (the subject has been scewedly scanned). The talairach coordinates (mni Talairach) does not seem to transform the volume properly, resulting in scewed segmentations when I manually insert the mni Talairach coordinates into the mri_filled command. (that is, mni Talairach coordinates for lh, rh, c.callossum and pons). Are there any alternative transformation commands which may solve this issue? Best wishes, Lars Tjelta Westlye

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FreeSurfer/FSL course
by Bruce Fischl 12 Mar '05

12 Mar '05

--------------------------------------------------------------------- Announcing: FSL & FreeSurfer Course 18-22 July 2005 - Boston, USA Organised by FMRIB Centre, University of Oxford and Martinos Center for Biomedical Imaging, MGH/MIT/HMS http://www.fmrib.ox.ac.uk/fslcourse/2005 --------------------------------------------------------------------- We are pleased to announce the 2005 FSL & FreeSurfer course in Waltham, Boston, USA. The intensive course covers both the theory and practice of functional and structural brain image analysis. Background concepts and the practicalities of analyses are taught in detailed lectures; these are interleaved with hands-on practical sessions where attendees learn how to carry out analysis for themselves on real data, with at most two attendees per computer. By the end of the course, attendees should be able to fully analyse their own FMRI and MRI data sets. The course is aimed at both new and existing users of these packages and will cover both basic and advanced features. The methods covered include * Functional MRI analysis: - GLM-based analysis of FMRI data including Bayesian multi-subject statistics (FSL - FEAT) - Model-free (ICA) analysis of FMRI data (FSL - MELODIC) * Cortical-flattening of images and its applications (FreeSurfer): - Cortical flattening for improved FMRI analysis, including inter-subject averaging - Group studies of cortical morphometry; thickness, folding, surface area, volume * Structural MRI analysis: - Image registration and unwarping (FSL - FLIRT/FUGUE) - Brain extraction and tissue-type segmentation (FSL - BET/FAST) - Structural spatial statistical analysis e.g. atrophy (FSL - SIENA/SIENAX) * Analysis of diffusion-weighted imaging data, including tractography and related applications (FSL - FDT) * Paradigm optimisation (Optseq) --------------------------------------------------------------------- For more information and to regsiter, visit: http://www.fmrib.ox.ac.uk/fslcourse/2005/ ---------------------------------------------------------------------

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Freesurfer March 2005