Freesurfer July 2011

freesurfer@nmr.mgh.harvard.edu

129 participants
195 discussions

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. > >

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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

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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

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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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error messages in running mri_convert
by Yajun Fang 13 Jul '11

13 Jul '11

Hi, I used to be able to run command "mri_convert" in the matlab environment through "system" command. Now I received the error messages as below: mri_convert: error while loading shared libraries: requires glibc 2.5 or later dynamic linker Any suggestions ? Is it related to the new update of freesurfer ? If I switch to another server, the problem did not exist. But can I still run the command in the same server ? I am looking forward to your suggestions. Thank you ! best, Yajun

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tracula - fix bad bbregister's
by GREGORY R KIRK 13 Jul '11

13 Jul '11

Hi, I processed about 80 subjects with -prep stage and then checked the bbregister registrations with tkregister2 --mov /study5/aa-scratch/TEENEMO/freesurfer_local/toot/057/dmri/dwi.nii.gz --reg /study5/aa-scratch/TEENEMO/freesurfer_local/toot/057/dmri/xfms/anatorig2diff.bbr.dat --surf found 17 subjects with bad registrations, as always because the fsl registration initialization was bad. so now i manually fix the registeration and use the manual fix for the initialization and rerun bbregister and get a good registration. so now i need to rerun -prep phase but have it use the good registration instead of computing a new bbregister registration. will trac-all -prep -nointra -c configfile accomplish this or do i need to get in and tinker with the scripts to make it run everything including computing new fsl and inverse registration matricies but using my bbregister good registration. thanks greg

2 1

reg-feat2anat: correct anat2exf.register.dat only or also func2std?
by Agnieszka Burzynska 13 Jul '11

13 Jul '11

Dear experts, I am using reg-feat2anat to register my functional data from FSL to anatomical and starndard space in Freesurfer. For some subjects the registration is bad. I can easily fix anat2exf.register.dat. However, as specified in reg-feat2anat help, I know that the registration failed as the func2std is incorrect, too. Is it enough to correct anat2exf.register.dat to correctly transfer functional data from feat to the surface space or do I also need to correct func2std? It seems to me that in the next steps I am using, such as sampling the functional data to fsaverage and further calculations in the fsaverage space do not rely on func2std. Is this correct? Cheers, Aga

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Re: [Freesurfer] Corrections with brainmask volume
by Bruce Fischl 13 Jul '11

13 Jul '11

Hi Antonella those look good to me. Note that you can't tell defects from a single slice. You need to scroll back and forth and look in different orientations. That said, the surfaces look pretty accurate cheers Bruce On Wed, 13 Jul 2011, Antonella Kis wrote: > Good morning Bruce, > I am checking my data after recon-all data pre-process. I am not very sure about some defects (removing dura and pail surface corrections). I attached > two tiff files from > > tkmedit P1 brainmask.mgz -aux T1.mgz -surfs > > > Do I have a lot of defects to eliminate on this slides, are the gray/white boundaries good or any suggestion regarding manually corrections that should > be done on this images it will be very appreciated. > > Thank you very much for your help! > Antonella > > > > >

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-legacy flag in version 5.1
by Marie Schaer 13 Jul '11

13 Jul '11

Hi everyone, Just a quick question: I noticed that the -legacy option of recon-all was removed in version 5.1. Is there any way to keep the manual edits and all the processing from previous versions while reprocessing with 5.1? Thank you very much, Marie

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Freesurfer July 2011