Freesurfer

freesurfer@nmr.mgh.harvard.edu

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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 >>

2 1

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

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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

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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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Re: [Freesurfer] Attachement for the Corrections with white matter
by Bruce Fischl 14 Jul '11

14 Jul '11

Hi Antonella, the surfaces look fine. As for the cerebellum, I don't think the watershed did that - it's too even. What does the orig.mgz look like? cheers Bruce On Thu, 14 Jul 2011, Antonella Kis wrote: > > > > Good morning Bruce, > > Looking back to the Slice No.82 I am attaching now the brainmask for this slide. While switching between brainmask and wm.mgz my opinion is that I shouldn't add any > vertex on the wm.mgz on the right hemisphere. > Is this correct? I am not sure about the bottom part. It looks like part of the cerebellum had been removed. Should I adjust the watershed threshold by passing the > -wsthresh flag to recon-all? > > > Thank you very much for your help. > Antonella > > > ____________________________________________________________________________________________________________________________________________________________________________ > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Wednesday, July 13, 2011 4:51 PM > Subject: Re: Corrections with white matter > > yes, the brainmask would be fine. The wm.mgz is to diagnose what went > wrong, but the brainmask tells you whether it is right or not > On Wed, 13 Jul > 2011, Antonella Kis wrote: > > > > > Hi Bruce, > > > > Thanks again for helping so much. But how about the example in the tutorial > > * FsTutorial/WhiteMatterEdits. > > I was following the example in how to fill the cutting into for yellow line. There is mentioned only to open the brainmask and wm.mgz and switching/checking between the > two > > volumes. Will be this OK? > > > > Many thanks, > > Antonella > > > >___________________________________________________________________________________________________________________________________________________________________________ > _ > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > To: Antonella Kis <atorok9(a)yahoo.com> > > Sent: Wed, July 13, 2011 4:36:21 PM > > Subject: Re: Corrections with white matter > > > > Hi Antonella, > > > > you can't tell whether it is correct from overlaying it on the wm.mgz. You need to look at it over the MRI itself (either the norm.mgz or the orig.mgz) and see if you > would > > have drawn it in the same place. The place where the yellow line doesn't follow the voxel surface is where a topological defect was corrected. It will be topologically > > correct, but possibly not geometrically so. > > > > Bruce > > > > > > On Wed, 13 Jul 2011, Antonella Kis wrote: > > > > > hi Bruce, > > > > > > Sorry they are tiff. I attached them again. > > > > > > Thank you very much. > > > Antonella > > > > >>__________________________________________________________________________________________________________________________________________________________________________ > _ > > _ > > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > > To: Antonella Kis <atorok9(a)yahoo.com> > > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > > Sent: Wed, July 13, 2011 3:47:15 PM > > > Subject: Re: Corrections with white matter > > > > > > Hi Antonella, > > > > > > what format are the attachments in? They don't have an extension > > > Bruce > > > On Wed, 13 > > > Jul 2011, Antonella Kis wrote: > > > > > > > > > > > Hi Bruce, > > > > > > > > Sorry to bother you again. I am doing my corrections for the white matter and I have few slides where I am not sure what should I do. On the slice no. 82 do I need to > > > > fill/edit voxels on the right hemisphere area where the white surface (yellow line) does not follow the surface of the brain, but in fact cuts into it 9the black > > area). > > > Is > > > > this a geometric inaccuracy caused by a lesion where white matter has been marked as non-white matter? I also attached the next slice no. 81 to see how things will > > > change. > > > > > > > > Thank you very much for your help! > > > > Antonella > > > > > > > > > > > > > > > > > > > > > > > > > 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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Re: [Freesurfer] Corrections with white matter
by Antonella Kis 14 Jul '11

14 Jul '11

Hi Bruce, Thanks again for helping so much. But how about the example in the tutorial * FsTutorial/WhiteMatterEdits.I was following the example in how to fill the cutting into for yellow line. There is mentioned only to open the brainmask and wm.mgz and switching/checking between the two volumes. Will be this OK? Many thanks, Antonella ________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Sent: Wed, July 13, 2011 4:36:21 PM Subject: Re: Corrections with white matter Hi Antonella, you can't tell whether it is correct from overlaying it on the wm.mgz. You need to look at it over the MRI itself (either the norm.mgz or the orig.mgz) and see if you would have drawn it in the same place. The place where the yellow line doesn't follow the voxel surface is where a topological defect was corrected. It will be topologically correct, but possibly not geometrically so. Bruce On Wed, 13 Jul 2011, Antonella Kis wrote: > hi Bruce, > > Sorry they are tiff. I attached them again. > > Thank you very much. > Antonella > >____________________________________________________________________________________________________________________________________________________________________________ >_ > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Wed, July 13, 2011 3:47:15 PM > Subject: Re: Corrections with white matter > > Hi Antonella, > > what format are the attachments in? They don't have an extension > Bruce > On Wed, 13 > Jul 2011, Antonella Kis wrote: > > > > > Hi Bruce, > > > > Sorry to bother you again. I am doing my corrections for the white matter and >I have few slides where I am not sure what should I do. On the slice no. 82 do I >need to > > fill/edit voxels on the right hemisphere area where the white surface >(yellow line) does not follow the surface of the brain, but in fact cuts into it >9the black area). > Is > > this a geometric inaccuracy caused by a lesion where white matter has been >marked as non-white matter? I also attached the next slice no. 81 to see how >things will > change. > > > > Thank you very much for your help! > > Antonella > > > > > > > > > > > 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. > >

2 2

QC Montages error
by Chindhuri Selvadurai 14 Jul '11

14 Jul '11

I am getting an error when using a script that combines these 3 actions: preproc.sh std_map_qc_montages.bash put_tpef.bash Freesurfer version 4 SUBJECTS_DIR: /cluster/manoach/AS/RespMon12C/subjects Script: /cluster/manoach/AS/RespMon12C/scripts/preproc_std_qc_montages_put_tpef.sh It looks like the preproc-sess finishes okay, but the problem starts afterwards, but I'm not sure how to fix this easily.. it looks like it's looking for files that aren't there, but I haven't gotten this error before. Thanks! Output, with error at end: ----------------- mkbrainmask Done ----------------------------- Thu Jul 7 17:15:21 EDT 2011 mkbrainmask-sess done ---------------------------------------- Started at Thu Jul 7 16:54:00 EDT 2011 Ended at Thu Jul 7 17:15:21 EDT 2011 preproc-sess done mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999976, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999976, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999976, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999976, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999976, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999976, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999976, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999976, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No such file or directory cp: cannot stat `./009/lightboxes/tsnr_lightbox.png': No such file or directory cp: cannot stat `./009/lightboxes/tstd_lightbox.png': No such file or directory cp: cannot stat `./009/lightboxes/tmean_lightbox.png': No such file or directory bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No such file or directory cp: cannot stat `./011/lightboxes/tsnr_lightbox.png': No such file or directory cp: cannot stat `./011/lightboxes/tstd_lightbox.png': No such file or directory cp: cannot stat `./011/lightboxes/tmean_lightbox.png': No such file or directory bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No such file or directory cp: cannot stat `./013/lightboxes/tsnr_lightbox.png': No such file or directory cp: cannot stat `./013/lightboxes/tstd_lightbox.png': No such file or directory cp: cannot stat `./013/lightboxes/tmean_lightbox.png': No such file or directory bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No such file or directory cp: cannot stat `./015/lightboxes/tsnr_lightbox.png': No such file or directory cp: cannot stat `./015/lightboxes/tstd_lightbox.png': No such file or directory cp: cannot stat `./015/lightboxes/tmean_lightbox.png': No such file or directory bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No such file or directory cp: cannot stat `./017/lightboxes/tsnr_lightbox.png': No such file or directory cp: cannot stat `./017/lightboxes/tstd_lightbox.png': No such file or directory cp: cannot stat `./017/lightboxes/tmean_lightbox.png': No such file or directory bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No such file or directory cp: cannot stat `./019/lightboxes/tsnr_lightbox.png': No such file or directory cp: cannot stat `./019/lightboxes/tstd_lightbox.png': No such file or directory cp: cannot stat `./019/lightboxes/tmean_lightbox.png': No such file or directory bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No such file or directory cp: cannot stat `./021/lightboxes/tsnr_lightbox.png': No such file or directory cp: cannot stat `./021/lightboxes/tstd_lightbox.png': No such file or directory cp: cannot stat `./021/lightboxes/tmean_lightbox.png': No such file or directory bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No such file or directory cp: cannot stat `./023/lightboxes/tsnr_lightbox.png': No such file or directory cp: cannot stat `./023/lightboxes/tstd_lightbox.png': No such file or directory cp: cannot stat `./023/lightboxes/tmean_lightbox.png': No such file or directory Cannot open tsnr_lightbox1.png for reading /autofs/cluster/manoach/AS/RespMon12C/scripts/RM12C_lightbox_runs.bash: line 35: 28671 Segmentation fault pngappend tsnr_lightbox1.png + $((gap)) tsnr_lightbox2.png + $((gap)) tsnr_lightbox3.png - $((gap)) tsnr_lightbox4.png + $((gap)) tsnr_lightbox5.png + $((gap)) tsnr_lightbox6.png tsnr_all.png Cannot open tstd_lightbox1.png for reading /autofs/cluster/manoach/AS/RespMon12C/scripts/RM12C_lightbox_runs.bash: line 36: 28672 Segmentation fault pngappend tstd_lightbox1.png + $((gap)) tstd_lightbox2.png + $((gap)) tstd_lightbox3.png - $((gap)) tstd_lightbox4.png + $((gap)) tstd_lightbox5.png + $((gap)) tstd_lightbox6.png tstd_all.png Cannot open tmean_lightbox1.png for reading /autofs/cluster/manoach/AS/RespMon12C/scripts/RM12C_lightbox_runs.bash: line 37: 28673 Segmentation fault pngappend tmean_lightbox1.png + $((gap)) tmean_lightbox2.png + $((gap)) tmean_lightbox3.png - $((gap)) tmean_lightbox4.png + $((gap)) tmean_lightbox5.png + $((gap)) tmean_lightbox6.png tmean_all.png mv: cannot stat `/autofs/cluster/manoach/AS/RespMon12C/subjects/RMAUT021/bold/all_lightboxes/*all*': No such file or directory rm: cannot remove `/autofs/cluster/manoach/AS/RespMon12C/subjects/RMAUT021/bold/0*/lightboxes/': No such file or directory Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307

1 1

longitudinal base creation error
by Jessica Liu 13 Jul '11

13 Jul '11

Hi all, I'm trying to analyze longitudinal data with for a subject with six time points. However, when I try to create a within-subject template using all six time points, I get the following error message on TP 3: Resolution: 0 Iteration(single-prec): 1MRIalloc(256, 256, 256): could not allocate 262144 bytes for 140th slice Cannot allocate memory Linux HMRI-HP.SME 2.6.35.6-45.fc14.i686 #1 SMP Mon Oct 18 23:56:17 UTC 2010 i686 i686 i386 GNU/Linux recon-all -s MKA_base exited with ERRORS at Wed Jul 13 14:55:32 PDT 2011 After trying again using only five of the six time points, this occurs on TP 4: Resolution: 0 Iteration(single-prec): 1 -- diff. to prev. transform: 0.114929 Iteration(single-prec): 2terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Abort (core dumped) Linux HMRI-HP.SME 2.6.35.6-45.fc14.i686 #1 SMP Mon Oct 18 23:56:17 UTC 2010 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Jul 13 11:52:31 PDT 2011 Is there any way to avoid these errors while using all of the time points? Is it even necessary to use all six time points when creating the base (it's over the course of ~1.5 years), or could I just use two or three? Thanks! Jessica

2 1

Re: [Freesurfer] Corrections with white matter
by Bruce Fischl 13 Jul '11

13 Jul '11

Hi Antonella, what format are the attachments in? They don't have an extension Bruce On Wed, 13 Jul 2011, Antonella Kis wrote: > > Hi Bruce, > > Sorry to bother you again. I am doing my corrections for the white matter and I have few slides where I am not sure what should I do. On the slice no. 82 do I need to > fill/edit voxels on the right hemisphere area where the white surface (yellow line) does not follow the surface of the brain, but in fact cuts into it 9the black area). Is > this a geometric inaccuracy caused by a lesion where white matter has been marked as non-white matter? I also attached the next slice no. 81 to see how things will change. > > Thank you very much for your help! > Antonella > > > >

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