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30076 discussions

Qdec question
by Xiangchuan Chen 05 Nov '07

05 Nov '07

Hi all, I am using Qdec to examine the anatomical differences between two groups of subjects. The surface-based measures I can select are thickness, area, area.pial, sulc, curv, and jacobian_white. Could anybody tell me what anatomical features the later three (sulc, curv, and jacobian_white) actually measure? Thanks in advance, Xiangchuan Chen

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Re: [Freesurfer] COR-files
by Xiangchuan Chen 05 Nov '07

05 Nov '07

Hi Chris, I guess you might click on "Save Main Volume As...", and then "OK". In this case, 257 COR- files would be created in the /mri folder. I happened to do it once, and redid the whole edit work. Xiangchuan ======== Start Of Original Message ======== Date: 2007-11-05 Time: 10:05:47 From: Chris Watson (Christopher.Watson(a)childrens.harvard.edu) To: freesurfer(a)nmr.mgh.harvard.edu (freesurfer(a)nmr.mgh.harvard.edu) Subject: [Freesurfer] COR-files >Hello, this is my first time using Freesurfer. > >I was making some edits to the brainmask.mgz and T1.mgz volumes, and >saved them and left Friday evening. I would like to continue making >edits today. How do I open these volumes so that they include the edits >I made? When I saved, 256 COR-files were created in the >SUBJECTS_DIR/<subject>/mri directory. Do I use mri_convert? If so, what >is the syntax? > >mri_convert --in_type cor COR-001 --out_type spm ??? > >Thanks, >Chris >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ========= End Of Original Message =========

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COR-files
by Chris Watson 05 Nov '07

05 Nov '07

Hello, this is my first time using Freesurfer. I was making some edits to the brainmask.mgz and T1.mgz volumes, and saved them and left Friday evening. I would like to continue making edits today. How do I open these volumes so that they include the edits I made? When I saved, 256 COR-files were created in the SUBJECTS_DIR/<subject>/mri directory. Do I use mri_convert? If so, what is the syntax? mri_convert --in_type cor COR-001 --out_type spm ??? Thanks, Chris

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recon-all error
by Anil Roy 04 Nov '07

04 Nov '07

Hi All, I got the following error while running recon-all on a set of dicoms. It seems to be a problem with the intensity correction stage but I can't get it to work. Any help is appreciated. Thanks, Anil. [root@wonglinux1 freesurfer]# recon-all -i /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702-0002-0001-0001.dcm -s O-07-002 -autorecon-all INFO: SUBJECTS_DIR is /mnt/win/MRI_data/MWIN4/Freesurfer Actual FREESURFER_HOME /usr/local/freesurfer Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386 GNU/Linux WM removal version /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002 mri_convert /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702- 0002-0001-0001.dcm/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz mri_convert /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702- 0002-0001-0001.dcm/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz reading from /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702- 0002-0001-0001.dcm... Getting Series No INFO: Found 162 files in /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom INFO: Scanning for Series Number 2 Scanning Directory INFO: found 160 files in series INFO: loading series header info. RunNo = 1 INFO: sorting. INFO: (192 256 160), nframes = 1, ismosaic=0 FileName /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702-0002-0001-0001.dcm Identification NumarisVer syngo MR 2006T 4VB12T ScannerModel TrioTim PatientName 9702 Date and time StudyDate 20070328 StudyTime 113239.765000 SeriesTime 114403.109000 AcqTime 113640.352512 Acquisition parameters PulseSeq tfl3d1 Protocol MPRAGE AXIAL PhEncDir ROW EchoNo 0 FlipAngle 9 EchoTime 3.36 InversionTime 900 RepetitionTime 2300 PhEncFOV 192 ReadoutFOV 256 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 256 NImageCols 192 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 101.4164 183.6733 -63.6460 VolRes 1.0000 1.0000 1.0000 VolDim 192 256 160 Vc -0.9991 0.0030 -0.0434 Vr -0.0000 -0.9977 -0.0681 Vs -0.0435 -0.0680 0.9967 VolCenter 2.0258 50.8135 3.2105 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2300.00, TE=3.36, TI=900.00, flip angle=9.00 i_ras = (-0.999053, 0.00296272, -0.0434174) j_ras = (-2.12178e-10, -0.99768, -0.0680798) k_ras = (-0.0435184, -0.0680153, 0.996735) writing to /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Nov 4 16:38:15 CST 2007 Found 1 runs /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/rawavg.mgz /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002 mri_convert /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/rawavg.mgz /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz --conform mri_convert /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/rawavg.mgz /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz --conform reading from /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/rawavg.mgz... TR=2300.00, TE=3.36, TI=900.00, flip angle=9.00 i_ras = (-0.999053, 0.00296272, -0.0434174) j_ras = (-2.12178e-10, -0.99768, -0.0680798) k_ras = (-0.0435184, -0.0680153, 0.996735) Original Data has (1, 1, 1) mm size and (192, 256, 160) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 4 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz... mri_add_xform_to_header -c /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/transforms/talairach.xfm /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Sun Nov 4 16:38:45 CST 2007 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri /usr/local/freesurfer/bin//mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $ Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386 GNU/Linux Sun Nov 4 16:38:45 CST 2007 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 tmpdir is ./tmp.mri_nu_correct.mni.7437 /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7437/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7437/nu0.mnc Can't find the talairach xform '/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/transforms/talairach.xfm TR=2300.00, TE=3.36, TI=900.00, flip angle=9.00 i_ras = (-1, -1.52311e-10, -6.04436e-10) j_ras = (5.26148e-10, 2.33896e-09, -1) k_ras = (1.65039e-10, 1, 5.09647e-09) writing to ./tmp.mri_nu_correct.mni.7437/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Sun Nov 4 16:39:03 CST 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.7437/nu0.mnc ./tmp.mri_nu_correct.mni.7437/nu1.mnc [root@wonglinux1:/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/] [2007-11-04 16:39:03] running: /usr/local/freesurfer/mni/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_7482/ ./tmp.mri_nu_correct.mni.7437/nu0.mnc ./tmp.mri_nu_correct.mni.7437/nu1.imp Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Sun Nov 4 16:39:07 CST 2007

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ReconAllDevTable
by Michael Harms 02 Nov '07

02 Nov '07

Hello, Just a couple miscellaneous items/suggestions regarding the very helpful ReconAllDevTable: 1) The entry for -inflate2 currently indicates that ?h.white is the input file. This should be ?h.smoothwm instead. 2) It might be helpful to add a line to the -skullstrip stage indicating the 'mri_em_register' command that preceeds 'mri_watershed' so as to indicate where the "talairach_with_skull.lta" file comes from that is used as part of 'mri_watershed' in v4.0.1 3) Do you have "archived" versions of the ReconAll table that are appropriate for previous stable releases? If so, it would be great if the wiki contained links to those. If not, it might be helpful to create such "snapshots" of the ReconAll flow table so that there is a convenient place to access the process flow that is most accurate for previous (non-developmental) releases. cheers, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Correcting surfaces - is this really bad?
by Dr. Claudia Wheeler-Kingshott 02 Nov '07

02 Nov '07

Hello, we have a few cases of what we think is a bad surface and would like your opinion on whether it is really bad (considering that we are interested in the temporal lobes). Should we correct the wm map to include the bits of wm that do not seem to be included? I attach shots of the "bad" inflated surface, the corresponding brainmask + pials and wm. The cross is in the same position as the blue dot on the surface. Thanks Claudia Inflated surface, zoomed on spikes brainmask with pials. Crossing point corresponding to blue dot on the surface. Corresponding white matter map -- ----------------------------------------- Claudia Wheeler-Kingshott, PhD Senior Lecturer Department of Inflammation Institute of Neurology, UCL Queen Square London WC1N 3BG tel. 0207 8373711 x4301 email: c.wheeler-kingshott(a)ion.ucl.ac.uk

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Freesurfer FAQ
by Pedro Paulo Oliveira Jr 02 Nov '07

02 Nov '07

Hi, I started the Wiki Page on FreeSurfer FAQ: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions_2fFAQ Any corrections and suggestions are welcome! I think we can avoid some questions to the list if we increase the FAQ. Regards Pedro Paulo Oliveira Jr.

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Volume of sub-cortical structures
by Dan Dillon 01 Nov '07

01 Nov '07

Dear FreeSurfers, Hopefully a very easy question . . . I want to compare the volume of subcortical structures in two groups of subjects. All I need to do that is the volume information contained in aseg.stats, right? Just want to double-check before I get started. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: dillon(a)wjh.harvard.edu

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topology defect
by Michael Harms 01 Nov '07

01 Nov '07

Hello, We have a case where -autorecon2 completed successfully, yet the right surface appears to have a topological defect. We discovered this because we got the following message upon trying to run 'mris_volume' on the pial surface: --- mris_volume: surface rh.pial has an incorrect topology (eno=1) --- Here is the output of mris_euler_number on that surface: --- euler # = v-e+f = 2g-2: 133519 - 400551 + 267033 = 1 --> 1 holes F =2V-4: 267033 != 267038-4 (1) 2E=3F: 801102 != 801099 (3) total defect index = 4 --- Below I've appended the final lines from the log file of the Fix Topology stage (FS v3.0.5). I've also attached two jpgs of the likely problem -- note the small black spot on the inflated surface, and the break of the orig and white surfaces in the medial temporal region of the tkmedit snapshot. (There is a small break in the pial surface as well, but it is hard to see in the jpg). Should we just try running the Topology Fixer again? What should we try in order to get a correct topology for this surface? thanks, Mike H. ------------------------ CORRECTING DEFECT 35 (vertices=61, convex hull=108) After retessellation of defect 35, euler #=-4 (133456,400244,266784) : difference with theory (-2) = 2 CORRECTING DEFECT 36 (vertices=86, convex hull=119) After retessellation of defect 36, euler #=-2 (133489,400394,266903) : difference with theory (-1) = 1 CORRECTING DEFECT 37 (vertices=9, convex hull=34) After retessellation of defect 37, euler #=-1 (133494,400421,266926) : difference with theory (0) = 1 CORRECTING DEFECT 38 (vertices=136, convex hull=61) After retessellation of defect 38, euler #=0 (133507,400486,266979) : difference with theory (1) = 1 CORRECTING DEFECT 39 (vertices=32, convex hull=74) After retessellation of defect 39, euler #=1 (133519,400551,267033) : difference with theory (2) = 1 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.04-->6.15) (max @ vno 133750 --> 134053) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.04-->6.15) (max @ vno 133750 --> 134053) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 120 mutations (34.1%), 232 crossovers (65.9%), 195 vertices were eliminated building final representation... 3035 vertices and 0 faces have been removed from triangulation after topology correction, eno=1 (nv=133519, nf=267033, ne=400551, g=0) writing corrected surface to /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/011228_12436/surf/rh.orig... edge (34451<-->132983) has one single face 264775 ! edge (34451<-->132972) has one single face 264857 ! edge (132972<-->34451) has one single face 264857 ! edge (132972<-->132983) has one single face 264959 ! edge (132983<-->34451) has one single face 264775 ! edge (132983<-->132972) has one single face 264959 ! 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 59.9 minutes reading input surface /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/011228_12436/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... edge 34451 <--> 133998 has 1 face(s)! (264775) 133827 34451 133998 !!! edge 34451 <--> 133986 has 1 face(s)! (264857) 133909 133986 34451 !!! edge 133986 <--> 133998 has 1 face(s)! (264959) 133986 133992 133998 !!! 3 defective edges removing intersecting faces 000: 269 intersecting 001: 48 intersecting 002: 24 intersecting 003: 20 intersecting 004: 24 intersecting 005: 14 intersecting 006: 3 intersecting /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/011228_12436/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.02 hours removing intersecting faces 000: 202 intersecting 001: 43 intersecting 002: 20 intersecting expanding nbhd size to 2 003: 20 intersecting 004: 18 intersecting 005: 12 intersecting 006: 3 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated

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Qdec covariates
by Alexander Fornito 31 Oct '07

31 Oct '07

Hi all, If i run a model in qdec that inludes 1 discrete and 1 continuous factor, does the output for the group contrast covary for the continuous variable? For example, if I want to compare two groups, and include group as my discrete factor and age as a continuous factor, will the output for the group contrast (Does the average thickness differ between grp1 and grp2?) covary for age? I've notice that running it without continuous factors leads to different results, so I just wanted to confirm this is the case. Also, just wanted to check that group contrasts are run as level_1 - level_2, so that positive values (i.e., red-yellow) indicate level_1 > level_2. Thanks for your help, Alex

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