Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Why surface values differ
by Simo Vanni 19 Aug '08

19 Aug '08

Dear Experts, I am going to average data from multiple subjects' surfaces to average surface of my study, obtained by mris_make_average_surface. The problem is that when I am testing this with simply one subject as input: #1 Create surface data for subject 1 mri_vol2surf --src ./DATA.img --src_type analyze --reg ./register.dat --hemi rh --o ./DATA.w --out_type w #2 Turn w to curv mri_surf2surf --srcsubject Subject1 --sval ./DATA.w --sfmt w --trgsubject Subject1 --tval rh.DATA.curv --tfmt curv --hemi rh #3 average the one subject to group brain mris_average_curvature -o AverageSurface DATA.curv rh sphere.reg Subject1 DATA_on_AverageSurface.curv I get a different result (kind of smoothed result, much more close-to-zero data points around the higher values), compared to when I simply #2 Turn w to curv , but now directly to AverageSurface mri_surf2surf --srcsubject Subject1 --sval ./DATA.w --sfmt w --trgsubject AverageSurface --tval rh.DATA.curv --tfmt curv --hemi rh Why? If there is automatic smoothing in mris_average_curvature, can this be turned off? best regards, Simo Vanni -- ************************************************************ Simo Vanni, MD PhD, Academy Research Fellow Vision Systems Physiology Brain Research Unit/AMI centre Low Temperature Laboratory Helsinki University of Technology PO BOX 3000, 02015-TKK, Espoo Finland tel: +358-9-451 6159 fax: +358-9-451 2969 e-mail: vanni(a)neuro.hut.fi https://ltl.tkk.fi/wiki/BRU/Vision_Systems_Physiology ************************************************************

1 0

mkanalysis
by Elif SIKOGLU 18 Aug '08

18 Aug '08

Hello. In the tutorial, for configuring the analysis, it says - ' you will specify the model of task-related signal in the "Event Related/Block Design" panel.' I have a block design, so l left it checked. However when I was looking through the analysis.info file located bold/analysis, I realized that the analysis is specified as event-related. How do I make the distinction between event related and block design? Does it FSFast figure it out by looking into the paradigm files? Thanks,

2 1

about aseg.stats
by 李日 18 Aug '08

18 Aug '08

Hello: I have run the recon-all command and it finished without errors. The FreeSurfer has generated a stats file $SUBJECTS_DIR/<subjid>/stats/aseg.stats, there are some information in this file as follows that I can't understand well: ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 2 335490 335490.0 Left-Cerebral-White-Matter 109.0668 9.6489 43.0000 183.0000 140.0000 which number corresponding with Volume_mm3? what does normMean normStdDev mean? what does Index SegId mean? thanks in advance Tim

2 1

talairach transform error
by Michelle W. Voss 18 Aug '08

18 Aug '08

Hello, This is my first time trying to use freesurfer on our data. We collect siemens dicom images, so I first manually reconstructed to .mgz format and tried running the recon-all script. I've posted the log below. Any ideas for fix? thanks, Michelle mri_convert -it siemens_dicom -ot mgz ONR1_021508.MR.ONR_BASIC.23.1.2008.02.15.11.06.59.890625.162672170.IMA 001.mgz bash-3.2$ recon-all -s sub01 -autorecon-all INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin cronos.vp.uiuc.edu 9.4.0 Darwin Kernel Version 9.4.0: Mon Jun 9 19:30:53 PDT 2008; root:xnu-1228.5.20~1/RELEASE_I386 i386 #-------------------------------------------- #@# MotionCor Mon Aug 18 08:43:20 CDT 2008 Found 1 runs /Applications/freesurfer/subjects/sub01/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. \n cp /Applications/freesurfer/subjects/sub01/mri/orig/001.mgz /Applications/freesurfer/subjects/sub01/mri/rawavg.mgz \n /Applications/freesurfer/subjects/sub01 \n mri_convert /Applications/freesurfer/subjects/sub01/mri/rawavg.mgz /Applications/freesurfer/subjects/sub01/mri/orig.mgz --conform \n mri_convert /Applications/freesurfer/subjects/sub01/mri/rawavg.mgz /Applications/freesurfer/subjects/sub01/mri/orig.mgz --conform $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /Applications/freesurfer/subjects/sub01/mri/rawavg.mgz... TR=1800.00, TE=3.87, TI=900.00, flip angle=8.00 i_ras = (-1, 2.02171e-10, 3.45578e-11) j_ras = (-2.05103e-10, -0.985703, -0.168489) k_ras = (-0, -0.168489, 0.985703) Original Data has (1.33333, 1.33333, 1.3) mm size and (160, 192, 144) 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 /Applications/freesurfer/subjects/sub01/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/sub01/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/sub01/mri/orig.mgz /Applications/freesurfer/subjects/sub01/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Mon Aug 18 08:43:33 CDT 2008 \n mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 \n /Applications/freesurfer/subjects/sub01/mri /Applications/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.7 2007/01/06 00:01:14 nicks Exp $ Darwin cronos.vp.uiuc.edu 9.4.0 Darwin Kernel Version 9.4.0: Mon Jun 9 19:30:53 PDT 2008; root:xnu-1228.5.20~1/RELEASE_I386 i386 Mon Aug 18 08:43:33 CDT 2008 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nschmans(a)W0084482(i686-apple-darwin8.8.1) on 2006-10-03 at 21:43:56 tmpdir is ./tmp.mri_nu_correct.mni.14318 /Applications/freesurfer/subjects/sub01/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14318/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14318/nu0.mnc $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from orig.mgz... TR=1800.00, TE=3.87, TI=900.00, flip angle=8.00 i_ras = (-1, 1.38778e-17, 3.46945e-18) j_ras = (-3.46945e-18, 1.49012e-08, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.14318/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Aug 18 08:43:39 CDT 2008 nu_correct -clobber ./tmp.mri_nu_correct.mni.14318/nu0.mnc ./tmp.mri_nu_correct.mni.14318/nu1.mnc [michellevoss@cronos.vp.uiuc.edu:/Applications/freesurfer/subjects/sub01/mri/] [2008-08-18 08:43:39] running: /Applications/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 /var/folders/VA/VAuuEIaYHGGfD8BbrnpkQE+++TI/-Tmp-/nu_correct_14368/ ./tmp.mri_nu_correct.mni.14318/nu0.mnc ./tmp.mri_nu_correct.mni.14318/nu1.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 50 CV of field change: 0.00125843 [michellevoss@cronos.vp.uiuc.edu:/Applications/freesurfer/subjects/sub01/mri/] [2008-08-18 08:44:07] running: /Applications/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.14318/nu0.mnc /var/folders/VA/VAuuEIaYHGGfD8BbrnpkQE+++TI/-Tmp-/nu_correct_14368//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Mon Aug 18 08:44:10 CDT 2008 nu_correct -clobber ./tmp.mri_nu_correct.mni.14318/nu1.mnc ./tmp.mri_nu_correct.mni.14318/nu2.mnc [michellevoss@cronos.vp.uiuc.edu:/Applications/freesurfer/subjects/sub01/mri/] [2008-08-18 08:44:10] running: /Applications/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 /var/folders/VA/VAuuEIaYHGGfD8BbrnpkQE+++TI/-Tmp-/nu_correct_15024/ ./tmp.mri_nu_correct.mni.14318/nu1.mnc ./tmp.mri_nu_correct.mni.14318/nu2.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 2 CV of field change: 0.000811469 [michellevoss@cronos.vp.uiuc.edu:/Applications/freesurfer/subjects/sub01/mri/] [2008-08-18 08:44:12] running: /Applications/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.14318/nu1.mnc /var/folders/VA/VAuuEIaYHGGfD8BbrnpkQE+++TI/-Tmp-/nu_correct_15024//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done mri_convert ./tmp.mri_nu_correct.mni.14318/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.14318/nu2.mnc nu.mgz --like orig.mgz WARNING: --like does not work on multi-frame data $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from ./tmp.mri_nu_correct.mni.14318/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.38778e-17, 3.46945e-18) j_ras = (-3.46945e-18, 1.49012e-08, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... Mon Aug 18 08:44:24 CDT 2008 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Mon Aug 18 08:44:24 CDT 2008 /Applications/freesurfer/subjects/sub01/mri \n talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm \n /Applications/freesurfer/subjects/sub01/mri /Applications/freesurfer/bin/talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $ Darwin cronos.vp.uiuc.edu 9.4.0 Darwin Kernel Version 9.4.0: Mon Jun 9 19:30:53 PDT 2008; root:xnu-1228.5.20~1/RELEASE_I386 i386 Mon Aug 18 08:44:24 CDT 2008 -------------------------------------------- mri_convert nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from nu.mgz... TR=1800.00, TE=3.87, TI=900.00, flip angle=8.00 i_ras = (-1, 1.38778e-17, 3.46945e-18) j_ras = (-3.46945e-18, 1.49012e-08, -1) k_ras = (0, 1, 0) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 129.000; 0.000 0.000 1.000 -131.394; 0.000 -1.000 0.000 136.405; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 -------------------------------------------- mpr2mni305 talsrcimg Mon Aug 18 08:44:27 CDT 2008 /Applications/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.3 2007/08/04 02:23:35 nicks Exp $ target=711-2C_as_mni_average_305 --------------------------------------------------------------------- analyzeto4dfp talsrcimg -O0 -y --------------------------------------------------------------------- $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Mon Aug 18 08:44:28 2008 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- dyld: Library not loaded: /usr/local/lib/libg2c.0.dylib Referenced from: /Applications/freesurfer/bin/gauss_4dfp Reason: image not found Trace/BPT trap ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133 ERROR: mpr2mni305 execution aborted ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin cronos.vp.uiuc.edu 9.4.0 Darwin Kernel Version 9.4.0: Mon Jun 9 19:30:53 PDT 2008; root:xnu-1228.5.20~1/RELEASE_I386 i386 recon-all exited with ERRORS at Mon Aug 18 08:44:29 CDT 2008

2 1

edit white matter
by 李日 15 Aug '08

15 Aug '08

Hi I have run the recon-all -autorecon2 command and I checked the inflate surface, it seems like something like a needle on the surface, Is this normal? I paste some pictures in the accessory, and by the way, I checked the white matter surface and pial surface and they seems all right.Can somebody tell why there is a needle on the surface? Thanks in advance.

4 5

subcortical volume analysis & qdec
by MRI CDPI 14 Aug '08

14 Aug '08

Dear List, I am testing within qdec an analysis of the subcortical volumes and using for this the subjects of the buckner_data.( First of all i am not sure it this is already implemented within freesurfer - in the Design card it says something like 'Volume-Based not yet implemented' ) Well, i created with asegstats2table a table including all subjects and also the gender and age information. With this i saved a qdec.table.dat. Feeding this table into qdec is doing fine, but when in try to run the analysis with morphometry/ volume the program stops because it can´t find the lh.volume.fwhm10.fsaverage.mgh. My question is, how can i create this file within the recon-all .... -qcache? Perhaps this morphometry volume analysis is just for volume measurements of the surface? I would apreciate if somebody could help me out with my doubts! Thanks, Thomas

2 1

aseg.stats file
by irene 14 Aug '08

14 Aug '08

Hi all, I need data which are in the aseg.stats file (which is in the stats file). Some patients haven't the aseg.stats file in the stats file, so does somebody know where I can find the aseg.stats file? Thanks Irene Mattisi Multiple Sclerosis Centre of Padova, Italy

2 1

downloadable manual
by Eliezer Kanal 14 Aug '08

14 Aug '08

Hello folks - I recently downloaded freesurfer and am slowly becoming more familiar with it. However, having to search through the myriad of pages on the wiki every time I have a question is very cumbersome, and more often than not, fruitless. Is there a downloadable manual available anywhere? Thanks - Eliezer Kanal Graduate Student, Bioengineering Center for Clinical Neurophysiology University of Pittsburgh

8 11

Compute First Level Analysis
by Balaji Goparaju 14 Aug '08

14 Aug '08

Hi Doug and all, When i run selxavg3-sess -analysis LD-analysis -s LD-functional i seem to get errors in some other files, The output is as follows: [balaji-goparajus-computer:~/Desktop/subjectdata] balajigo% selxavg3-sess -analysis LD-analysis -s LD-functional -------------------------------------------------------------- selxavg3-sess logfile is /Users/balajigoparaju/Desktop/subjectdata/log/selxavg3-sess-bold-LD-analysis-080728180123.log -------------------------------------------------------------- ------------------------------------------- /Users/balajigoparaju/Desktop/subjectdata/LD-functional Mon Jul 28 18:01:23 EDT 2008 anadir = /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/LD-analysis ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2008 The MathWorks, Inc. Version 7.6.0.324 (R2008a) February 10, 2008 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2.2 2007/11/27 18:42:09 greve Exp $ outtop = /Users/balajigoparaju/Desktop/subjectdata Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 LD-contrast.mat Loaded /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/emotion.par as a par2 file. ERROR: empty nonpar matrix for mcextreg ??? Attempt to reference field of non-structure array. Error in ==> flac_taskregind at 37 nev = length(flac.ev); Error in ==> flac_customize at 267 flacnew.indtask = flac_taskregind(flacnew); Error in ==> fast_selxavg3 at 97 flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Thank you for the help you have been providing!

2 1

Processing after edits.
by Matt Clarkson 14 Aug '08

14 Aug '08

Hi there, If you run recon-all, and then do some edits, for example control points, then the tutorial says you do: recon-all -autorecon2-cp -autorecon3 -subjid subject4_before Similarly for white matter: recon-all -autorecon2-wm -autorecon3 -subjid 111_manual_edits_before and similarly for brain mask: recon-all -autorecon2-pial -autorecon3 -subjid subject3_before So, if I have done all 3 types of edits, would it be better to do: recon-all -autorecon2-cp -autorecon3 -subjid subject3_before recon-all -autorecon2-wm -autorecon3 -subjid subject3_before recon-all -autorecon2-pial -autorecon3 -subjid subject3_before or would I do: recon-all -autorecon2-cp -autorecon2-wm -autorecon2-pial -autorecon3 -subjid subject3_before While the second option is more than likely quicker, will it make any difference to the results? Many thanks in advance. -- Matt Clarkson Senior Research Associate Dementia Research Centre UCL Institute Of Neurology Queen Square London WC1N 3BG m.clarkson(a)ucl.ac.uk Tel: 08451 555 000 ext. 723653 Fax: 020 7676 2066

2 1

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