Freesurfer July 2011

freesurfer@nmr.mgh.harvard.edu

129 participants
195 discussions

Re: [Freesurfer] how can do ''mri_convert''quickly when there are too many subjects
by Peter J. Molfese 16 Jul '11

16 Jul '11

A script is definitely the easiest way to process quite a few subjects. You can save some headache by using a recon-all command with an input for your image files. For example: "recon-all -s sleep_001 -i sleep_001.nii -all" will create a subject folder in the correct location named sleep_001 and begin the entire freesurfer pipeline taking the NIFTI image sleep_001.nii as the input. You can modify it to just import the files by dropping the "-all". I've included a bash script below for simplifying this. This script takes the NIFTI files you want to process as arguments and then automatically sets the Subject ID and begins processing. Once it completes a single subject, it will start the next subject. You can track the progress of subjects by seeing which folders have been created in the SUBJECTS_DIR. If you have a multiprocessor system, you can run the script with different subjects in multiple terminal windows. To execute the script: 1. Save the script as fs_subject.sh 2. chmod +x fs_subject.sh 3. place the script in a folder with all of your NIFTI files (not required but may make your life easier) 4. execute the script with ./fs_subject.sh sleep_001.nii sleep_002.nii sleep_003.nii (don't forget to replace sleep_* with your NIFTI file names) 4a. If your subjects meet a standard naming convention you could do something like: ./fs_subject.sh sleep_*.nii (this would submit all subjects fitting the pattern of having "sleep_" at the beginning of the name. #!/bin/bash # ./fs_subject.sh # takes nifti files as arguments for submitting into freesurfer pipeline #setup Freesurfer if not currently loaded on path export FREESURFER_HOME=/usr/local/freesurfer #source $FREESURFER_HOME/SetUpFreeSurfer.sh . $FREESURFER_HOME/SetUpFreeSurfer.sh for FS in $* do subjectID=$(/bin/echo $FS | /usr/bin/sed 's/.nii//') recon-all -s $subjectID -i $FS -all done Hope this helps! Ultimately if you have a lot of computers and a lot of subjects, using Sun Grid Engine (SGE) or Apple's xgrid (if you have Macs) can really expedite the processing of subjects. Best, Peter > Date: Fri, 15 Jul 2011 12:22:38 -0500 > From: Freesurfer Local Archive <freesurfer(a)jonca.org> > Subject: Re: [Freesurfer] how can do ''mri_convert''quickly when there > are too many subjects > To: ??? <wgh0805(a)126.com> > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CABphhh-ZcMapCqq+0x66d0EXqQgdt-vPVojXt30O0P63kzoLAw(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > I suspect that your subject directory/file names will match some > pattern. You can use combination of a loop and shell "ls" command to > cycle through all the subjects matching provided pattern. For example > if you have data in directories you would do something line this: > > #!/bin/tcsh > > cd /path/to/native/files > > for x in `ls -dA1 name_pattern_*`; > do > mkdir -p $SUBJECTS_DIR/${x}/mri/orig > $FREESURFER_HOME/bin/mri_convert ${x}.nii.gz $SUBJECTS_DIR/${x}/mri/orig/001.mgz > done > > If all files are in the same directory substitute '-dA1' for "-A1" and > it should work. Note this assumes that you have nifti files, for DICOM > you will need to modify it further. > > Cheers, > > Jacek > > 2011/7/15 ??? <wgh0805(a)126.com>: >> ??Hi Bruce, >> >> ?????In our research,if there are?100 subjects,how?can I ?process these data >> easily.For example?when I want to compare their thickness's difference?at >> first?I should do >> " mri_convert? bert.nii bert.nii.gz",but when there are too many subjects,is >> there a way to do all of these 100 subjects at the same time? >> >> ?Many thanks, >> ?Wang >> >> >> >> _______________________________________________ >> 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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Book with FreeSurfer chapter
by Pedro Paulo de Magalhães Oliveira Junior 15 Jul '11

15 Jul '11

Just for information: *Handbook of Imaging the Alzheimer Brain* * Editors: J.W. Ashford, A. Rosen, M. Adamson, P. Bayley, O. Sabri, A. Furst, S.E. Black and M. Weiner July 2011, 824 pp., hardcover ISBN 978-1-60750-792-5 (print) ** The chapter that describes the usage of FreeSurfer in AD is "Automated Volumetric Methods to Detect Alzheimer's Disease" / Pedro Paulo de Magalhães Oliveira Jr. et al. *

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how can do ''mri_convert''quickly when there are too many subjects
by 汪贵宏 15 Jul '11

15 Jul '11

Hi Bruce, In our research,if there are 100 subjects,how can I process these data easily.For example，when I want to compare their thickness's difference，at first，I should do " mri_convert bert.nii bert.nii.gz",but when there are too many subjects,is there a way to do all of these 100 subjects at the same time? Many thanks, Wang

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help on MAC ".licence" file
by 119829640 15 Jul '11

15 Jul '11

Hi: To register the freesurfer, I use the command "gedit .licence" and paste my registration information to it in ubuntu. It does works. However, I got a trouble when using MAC laptop. I don't know how to create the .licence file. I have got the registration information for MAC. I will be very appreciated if you can give me some clues and answers. Thank u very much.

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Re: [Freesurfer] DOF and smoothing in mri_glmfit
by Agnieszka Burzynska 15 Jul '11

15 Jul '11

Dear Doug, I wanted to follow up on our discussion: I have re-run the analysis with the smoothing during the 1st level analysis and indeed the activation pattern looks more as we expect from the 3D analysis in FSL, although the regions that are "active" are the same. Thank you for your advice! Best, Aga On 7/7/11 5:14 PM, "Agnieszka Burzynska" <burzynska(a)mpib-berlin.mpg.de> wrote: > Thank you! I think I will just try it out: now run it as it is but also run > the 1st level with smoothing, as I need to add some contrasts anyway. Then I > should also know the difference between volume and surface smoothing. > Cheers, > Aga > > On 7/7/11 5:07 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > >> The problem with doing the smoothing at the first level in FEAT is that >> it will be volume-based, not surface-based. I'm not sure what to tell >> you about using the varcopes. They will certainly be very noisy without >> smoothing, so probably smoothing is a good idea, even if it's volume-based. >> >> doug >> >> Agnieszka Burzynska wrote: >>> Dear Doug, >>> Thank you so much. I completely see you point, but I have re-run the 1st >>> level feat without smoothing just because it has been recommended not to >>> smooth in the volume and then transfer it onto the surface, but rather first >>> smooth on the surface >>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer) >>> >>> What I plan to do in the end is to include the cortical thickness as the >>> vertex-wise covariate in the functional group analysis. >>> >>> So the final analysis will be on the group level, where, as you say, the >>> varcopes should not matter that much. >>> >>> However, I was also thinking of analyzing varcopes in addition to copes >>> (group analysis) to relate the variance of BOLD signal to the thickness. >>> >>> Would you then recommend going back and taking the initial 1st level >>> analysis with regular smoothing? >>> >>> Thank you! >>> Aga >>> >>> On 7/7/11 4:43 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: >>> >>> >>>> Hi Aga, your commands look right. For the DOF, it should be the sum of >>>> the DOFs from all the runs (probably won't make much of a difference). >>>> Smoothing is a bit of an issue when you want to look at individual >>>> results. Technically, you should smooth before you do the first level >>>> analysis (ie, before your compute the varcope), but this would require >>>> doing the FEAT analysis directly on surface data. Smoothing after >>>> computing the varcope means that the varcope will not be accurate (it >>>> will be too large). The penalty is that you will see less activation >>>> than you should. At the group level, this is not such a big deal because >>>> you're either not using the varcope or you are using it as a weight. >>>> doug >>>> >>>> Agnieszka Burzynska wrote: >>>> >>>>> Dear all, >>>>> I am combining 3 runs of a subject using fixed effects GLM and I wanted to >>>>> make sure I am doing the right thing. >>>>> >>>>> For each subject I use: >>>>> mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof >>>>> 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label >>>>> $SUBJECTS_DIR/fsaverage/label/lh.cortex.label --fwhm 5 >>>>> >>>>> , while lh.cope1.mgh contains the concatenated cope1 images of the same >>>>> subject in fsaverage space (the same for varcope1). >>>>> >>>>> 1) Is it the right way? >>>>> 2) I took DOF from subjectX.feat/stats/dof of one of the runs. Is it >>>>> correct? >>>>> 3) The functional data has not been smoothed in the 1st level analysis in >>>>> FSL (as recommended), and also not smoothed during sampling the copes to a >>>>> common space. Therefore I want to smooth it here for the first time, but >>>>> only with 5mm. Does it sound right? >>>>> >>>>> Cheers, >>>>> Aga >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>>> >>> >>> >>>

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Re: [Freesurfer] retinotopy manual?
by Douglas Greve 14 Jul '11

14 Jul '11

I think you can load overlays into freeview. After that it is a matter of setting the thresholds right. I think we have a fix for the "sliver" problem. doug On 7/14/11 10:26 PM, Babak wrote: > Thanks Doug, > I fixed that problem and completed the analysis process, but tksurfer > doesn't work on my system. It seems to be the Sliver problem, and I used the > freeview to look at my surfaces and volumes. I'm not sure however if I can > use freeview for retinotopic mapping. Could you kindly give me some insight > on that? > > Thanks Again, > Babak > > -----Original Message----- > From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Friday, July 08, 2011 3:57 PM > To: Babak > Subject: Re: [Freesurfer] retinotopy manual? > > does > /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/fmcpr.sm5.haluk.lh.n > ii.gz > exist? If not, then you need to run the preprocessing (or exclude > -no-preproc) > > Babak wrote: >> Hi Doug, >> >> Another freeSurfer newbie question . I followed your steps for >> retinotopic mapping in freesurfer >> > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg16562.html) >> and got as far as selxavg3. I have attached the error and log file >> that I got, if you could kindly have a look. >> >> Thanks a lot, >> >> Babak >> >> ---------------------------------------------------- Log File >> --------------------------------------------- >> >> [bnooryme@Vision-1 data-parent]$ selxavg3-sess -a rtopy.haluk.lh -sf >> /data/fMRIdata/1/users/babak/data-parent/haluk/subjectname -d >> /data/fMRIdata/1/users/babak/data-parent -no-preproc >> >> Surface data haluk lh >> >> -------------------------------------------------------------- >> >> selxavg3-sess logfile is >> > /data/fMRIdata/1/users/babak/data-parent/log/selxavg3-sess-bold-rtopy.haluk. > lh-110708131238.log >> -------------------------------------------------------------- >> >> ------------------------------------------- >> >> /data/fMRIdata/1/users/babak/data-parent/haluk >> >> Fri Jul 8 13:12:38 CDT 2011 >> >> anadir = >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/rtopy.haluk.lh >> >> DoGLMFit = 1 >> >> DoContrasts = 1 >> >> UpdateNeeded = 1 >> >> ------------------------------------------ >> >> ------- 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 1984-2009 The MathWorks, Inc. >> >> Version 7.9.0.529 (R2009b) 64-bit (glnxa64) >> >> August 12, 2009 >> >> To get started, type one of these: helpwin, helpdesk, or demo. >> >> For product information, visit www.mathworks.com. >> >> /home/programs/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> #@# haluk ############################### >> >> /data/fMRIdata/1/users/babak/data-parent/haluk >> >> ------------------------- >> >> $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ >> >> /home/programs/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> /home/programs/freesurfer/fsfast/toolbox/fast_ldanaflac.m >> >> /home/programs/freesurfer/matlab/MRIread.m >> >> ------------------------- >> >> outtop = /data/fMRIdata/1/users/babak/data-parent >> >> Extension format = nii.gz >> >> ??? Error using ==> MRIread at 76 >> >> ERROR: cannot determine format of >> >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/fmcpr.sm5.haluk.lh >> >> (MRIread) >> >> Error in ==> flac_customize at 87 >> >> mri = MRIread(fstem,1); >> >> Error in ==> fast_selxavg3 at 65 >> >> flac0 = flac_customize(flac0); >> >>>> ------------------------------------------ >> ERROR: fast_selxavg3() failed\n >> >> [bnooryme@Vision-1 data-parent]$ >> >> ---------------------------------------------------- Log File >> --------------------------------------------- >> >> selxavg3-sess log file >> >> /home/programs/freesurfer/fsfast/bin/selxavg3-sess >> >> -a rtopy.haluk.lh -sf >> /data/fMRIdata/1/users/babak/data-parent/haluk/subjectname -d >> /data/fMRIdata/1/users/babak/data-parent/ >> >> $Id: selxavg3-sess,v 1.57 2010/08/25 19:07:25 greve Exp $ >> >> uid=18368(bnooryme) gid=9999(xdem) groups=9999(xdem),13700(ogmen) >> context=user_u:system_r:unconfined_t >> >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003 >> >> Linux Vision-1.EE.UH.EDU 2.6.18-238.12.1.el5 #1 SMP Sat May 7 20:18:50 >> EDT 2011 x86_64 x86_64 x86_64 GNU/Linux >> >> Thu Jul 7 15:28:23 CDT 2011 >> >> preproc-sess -s haluk -d /data/fMRIdata/1/users/babak/data-parent -a >> rtopy.haluk.lh -nolog >> >> -------------------------------------------------------------- >> >> preproc-sess logfile is /dev/null >> >> -------------------------------------------------------------- >> >> $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $ >> >> bnooryme >> >> setenv FREESURFER_HOME /home/programs/freesurfer >> >> setenv SUBJECTS_DIR /home/programs/freesurfer/subjects >> >> Linux Vision-1.EE.UH.EDU 2.6.18-238.12.1.el5 #1 SMP Sat May 7 20:18:50 >> EDT 2011 x86_64 x86_64 x86_64 GNU/Linux >> >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003 >> >> /home/programs/freesurfer/fsfast/bin/preproc-sess >> >> -s haluk -d /data/fMRIdata/1/users/babak/data-parent -a rtopy.haluk.lh >> -nolog >> >> Thu Jul 7 15:28:23 CDT 2011 >> >> instem f >> >> mc 1 f fmcpr >> >> stc 0 fmcpr >> >> sm 0 >> >> mask 1 brain >> >> haluk Template ----------------------------- >> >> mktemplate-sess -s haluk -d /data/fMRIdata/1/users/babak/data-parent >> -fsd bold -nolog -update >> >> Session: /data/fMRIdata/1/users/babak/data-parent/haluk ---------------- >> >> Thu Jul 7 15:28:24 CDT 2011 >> >> Detected input format at nii >> >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003 >> >> mri_convert >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/template.nii.gz >> --frame 0 >> >> mri_convert >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/template.nii.gz >> --frame 0 >> >> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >> >> reading from >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii... >> >> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 >> >> i_ras = (-1, -0, 0) >> >> j_ras = (-0, -1, 0) >> >> k_ras = (-0, -0, 1) >> >> keeping frame 0 >> >> writing to >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/template.nii.gz... >> >> Run: 003 ---------------- >> >> Thu Jul 7 15:28:26 CDT 2011 >> >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003 >> >> mri_convert >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/template.nii.gz >> --mid-frame >> >> mri_convert >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/template.nii.gz >> --mid-frame >> >> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >> >> reading from >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii... >> >> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 >> >> i_ras = (-1, -0, 0) >> >> j_ras = (-0, -1, 0) >> >> k_ras = (-0, -0, 1) >> >> keeping frame 147 >> >> writing to >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/template.nii.gz... >> >> Thu Jul 7 15:28:28 CDT 2011 >> >> mktemplate-sess completed >> >> haluk Mask ------------------------ >> >> mkbrainmask-sess -maskstem brain -fsd bold -s haluk -d >> /data/fMRIdata/1/users/babak/data-parent -nolog -update >> >> ------------------------------------------------ >> >> /data/fMRIdata/1/users/babak/data-parent/haluk >> >> Thu Jul 7 15:28:28 CDT 2011 >> >> mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil >> 1 -nerode 0 >> >> FSLMATHS fslmaths.fsl >> >> Scratch Dir is /tmp/mkbrainmask_25550 >> >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold >> >> mri_convert template.nii.gz /tmp/mkbrainmask_25550/in.nii >> >> mri_convert template.nii.gz /tmp/mkbrainmask_25550/in.nii >> >> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >> >> reading from template.nii.gz... >> >> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 >> >> i_ras = (-1, -0, 0) >> >> j_ras = (-0, -1, 0) >> >> k_ras = (-0, -0, 1) >> >> writing to /tmp/mkbrainmask_25550/in.nii... >> >> # ---------- Using FSL's BET to Extract Brain------------------ # >> >> /data/fMRIdata/1/users/babak/data-parent/haluk/bold >> >> bet.fsl /tmp/mkbrainmask_25550/in.nii /tmp/mkbrainmask_25550/brain -m >> -f 0.1 >> >> /home/programs/freesurfer/bin/bet.fsl: line 150: /bin/remove_ext: No >> such file or directory >> >> /home/programs/freesurfer/bin/bet.fsl: line 151: /bin/remove_ext: No >> such file or directory >> >> /home/programs/freesurfer/bin/bet.fsl: line 153: /bin/imtest: No such >> file or directory >> >> /home/programs/freesurfer/bin/bet.fsl: line 153: [: =: unary operator >> expected >> >> /home/programs/freesurfer/bin/bet.fsl: line 231: /bin/bet2: No such >> file or directory >> >> mri_binarize --i /tmp/mkbrainmask_25550/brain_mask.nii --min .01 --o >> /tmp/mkbrainmask_25550/brain_mask.nii >> >> niiRead(): error opening file /tmp/mkbrainmask_25550/brain_mask.nii >> >> $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ >> >> cwd /data/fMRIdata/1/users/babak/data-parent/haluk/bold >> >> cmdline mri_binarize --i /tmp/mkbrainmask_25550/brain_mask.nii --min >> .01 --o /tmp/mkbrainmask_25550/brain_mask.nii >> >> sysname Linux >> >> hostname Vision-1.EE.UH.EDU >> >> machine x86_64 >> >> user bnooryme >> >> input /tmp/mkbrainmask_25550/brain_mask.nii >> >> frame 0 >> >> nErode3d 0 >> >> nErode2d 0 >> >> output /tmp/mkbrainmask_25550/brain_mask.nii >> >> Binarizing based on threshold >> >> min 0.01 >> >> max +infinity >> >> binval 1 >> >> binvalnot 0 >>

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tracula pub
by GREGORY R KIRK 14 Jul '11

14 Jul '11

i thought at one time i saw a paper on the tracula methods, maybe it was the better tractography allignment paper. is there a paper specifically about the global tractography method and related, or an mit tech. report or anything thanks greg

4 4

Tracula - error in pre-proc
by phoebe＠nmr.mgh.harvard.edu 14 Jul '11

14 Jul '11

Hi, I do the pre-processing with the following command: trac-all -prep -c ./scripts/dmrirc_single_subject THe process exits with error when it comes to fslroi (attached pls find the log file). I try to re-run the fslroi command as follow: fslroi /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi.nii. gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz 0 25 It works and the lowb.nii.gz looks normal. In case if I have the same problem with another dataset, how can I incorporate the number of frames (25) in the trac-all command for the fslroi? Can I continue the remaining procedures of trac-all from this point? Thank you. Phoebe. -- ___________________________________ Phoebe Suk-tak Chan, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Bldg. 149, 13th St., mailcode 149-2301 Charlestown, MA 02129 phoebe(a)nmr.mgh.harvard.edu

3 3

Saving all the edits
by Antonella Kis 14 Jul '11

14 Jul '11

Hi Bruce, I promise this is my last question for today. I finished all the wm edits and I understood from the tutorial that I have to save this work. I understood that by default tkmedit will edit on the main volume loaded, if the wm volume is loaded as your aux volume (which is my case), I also needed to select Aux volume as the Target (and I did) but how I am saving my edits before I start to recreate the final surfaces with the command: recon-all -autorecon2-wm -subjid wm1_edits_before Many thanks and have a great day! Antonella

2 1

Choice of input surface for mris_make_face_parcellation
by Michael Waskom 14 Jul '11

14 Jul '11

Hi Bruce, I'm playing around with mris_make_face_parcellation, and I'm looking for guidance on choosing the "input surface". In the usage message, the example that is given says: "example: mris_make_face_parcellation lh.inflated $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot" The choice of the inflated surface seems weird to me, as isn't it really just used for visualization? Seems like you'd either want to use a surface that's representative of the actual brain geometry (e.g. white, or "graymid") or the sphere. But I'm a little confused in general about what's going on behind the scenes here so I don't trust my intuition. Cheers, Michael

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Freesurfer July 2011