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:gr...@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 >> _______________________________________________ Freesurfer mailing list Freesurfer@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. 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