Re: [Freesurfer] QC Montages error
Hello, I have tried troubleshooting this problem in various ways, but I am still not able to figure out the problem. Does anyone have any idea? Thank you! 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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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:
Re: [Freesurfer] Corrections with white matter
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 fis...@nmr.mgh.harvard.edu To: Antonella Kis ator...@yahoo.com Cc: freesurfer@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 fis...@nmr.mgh.harvard.edu To: Antonella Kis ator...@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 fis...@nmr.mgh.harvard.edu To: Antonella Kis ator...@yahoo.com Cc: freesurfer@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. ___ 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. 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.
Re: [Freesurfer] Attachement for the Corrections with white matter
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 fis...@nmr.mgh.harvard.edu To: Antonella Kis ator...@yahoo.com Cc: freesurfer@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 fis...@nmr.mgh.harvard.edu To: Antonella Kis ator...@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 fis...@nmr.mgh.harvard.edu To: Antonella Kis ator...@yahoo.com Cc: freesurfer@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. ___ 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. 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.
[Freesurfer] Choice of input surface for mris_make_face_parcellation
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 ___ 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. 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.
Re: [Freesurfer] Choice of input surface for mris_make_face_parcellation
Hi Miichael, oh, that was definitely a mistake. You want to use either ?h.sphere if you want it to be uniform in subject space or ?h.sphere.reg if you want the parcels to correspond across subjects. Sorry for the bad advice. Bruce On Thu, 14 Jul 2011, Michael Waskom wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. 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.
[Freesurfer] Saving all the edits
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___ 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. 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.
Re: [Freesurfer] Saving all the edits
yes, but you can double check by doing the save and bringing up a second instance of tkmedit with wm.mgz before exiting the first to make sure the edits are in it On Thu, 14 Jul 2011, Antonella Kis wrote: 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 ___ 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. 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.
Re: [Freesurfer] Tracula - error in pre-proc
Hi Priti, Thank you for your help. I get through the fslroi successfully by setting the nb0 variable. The lowb.nii.gz looks fine. However, when the process comes to bet, there's another error prompt for lowb.nii.gz.hdr. fslmaths /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz -Tmean /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz bet /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb_brain.nii.gz -m -f 0.3 Can't open /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz.hdr Linux guasha 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux Kindly help. Phoebe. Hi Phoebe, The fslroi part extracts all the low-b images from the 4D diffusion data and creates an average low-b mask. fslroi input output tmin tsize tsize is the number of 3D low-b volumes to be extracted from the 4D diffusion volume. For some reason tracula is unable to read the no. of low-b images from your dicom header (Is this an MGH acquisition?). If you know the number of low-b volumes you can specify that in the configuration file using the following command: set nb0 = *No. of low-b images* Once you set that value it should not throw that error. From what you ran in the commandline, I assume that in your dti acquisition 0 through 25 are low-b volumes. Creating the low-b image mask is the last step in the first stepwise directive of tracula (-corr). You can go through the rest of the steps by specifying any or all of the stepwise directives: Ex: trac-all -intra -inter -masks -tensor -prior -c ./scripts/dmrirc_single_subject Please let us know if you have any questions or problems running the same. Thanks, Priti 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 pho...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- ___ 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 pho...@nmr.mgh.harvard.edu ___ 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. 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.
[Freesurfer] tracula pub
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 ___ 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. 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.
Re: [Freesurfer] Tracula - error in pre-proc
Hi Phoebe - I don't have permission to access your files, but do you have FSLOUTPUTTYPE set to anything other than nifti by any chance? a.y On Thu, 14 Jul 2011, pho...@nmr.mgh.harvard.edu wrote: Hi Priti, Thank you for your help. I get through the fslroi successfully by setting the nb0 variable. The lowb.nii.gz looks fine. However, when the process comes to bet, there's another error prompt for lowb.nii.gz.hdr. fslmaths /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz -Tmean /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz bet /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb_brain.nii.gz -m -f 0.3 Can't open /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz.hdr Linux guasha 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux Kindly help. Phoebe. Hi Phoebe, The fslroi part extracts all the low-b images from the 4D diffusion data and creates an average low-b mask. fslroi input output tmin tsize tsize is the number of 3D low-b volumes to be extracted from the 4D diffusion volume. For some reason tracula is unable to read the no. of low-b images from your dicom header (Is this an MGH acquisition?). If you know the number of low-b volumes you can specify that in the configuration file using the following command: set nb0 = *No. of low-b images* Once you set that value it should not throw that error. From what you ran in the commandline, I assume that in your dti acquisition 0 through 25 are low-b volumes. Creating the low-b image mask is the last step in the first stepwise directive of tracula (-corr). You can go through the rest of the steps by specifying any or all of the stepwise directives: Ex: trac-all -intra -inter -masks -tensor -prior -c ./scripts/dmrirc_single_subject Please let us know if you have any questions or problems running the same. Thanks, Priti 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 pho...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. 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.
Re: [Freesurfer] tracula pub
Hi Greg - The paper has been with anonymous reviewers for the last 4 months :( a.y On Thu, 14 Jul 2011, GREGORY R KIRK wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. 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.
Re: [Freesurfer] tracula pub
Hi Greg, I think the tracula folks might have gotten their original code from Saad Jbabdi, but then the code-bases have probably diverged. (My apologizes if this is not correct!). Here is Saad's publication on global tractography: http://www.ncbi.nlm.nih.gov/pubmed/17543543/ Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki Sent: Thursday, July 14, 2011 9:48 PM To: GREGORY R KIRK Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tracula pub Hi Greg - The paper has been with anonymous reviewers for the last 4 months :( a.y On Thu, 14 Jul 2011, GREGORY R KIRK wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tracula pub
Yes, Matt is correct Bruce On Jul 14, 2011, at 10:52 PM, Matt Glasser m...@ma-tea.com wrote: Hi Greg, I think the tracula folks might have gotten their original code from Saad Jbabdi, but then the code-bases have probably diverged. (My apologizes if this is not correct!). Here is Saad's publication on global tractography: http://www.ncbi.nlm.nih.gov/pubmed/17543543/ Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki Sent: Thursday, July 14, 2011 9:48 PM To: GREGORY R KIRK Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tracula pub Hi Greg - The paper has been with anonymous reviewers for the last 4 months :( a.y On Thu, 14 Jul 2011, GREGORY R KIRK wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tracula pub
In fact it's a combination of Saad's likelihood term with an anatomical prior term that uses diffusion and anatomical data. On Thu, 14 Jul 2011, Matt Glasser wrote: Hi Greg, I think the tracula folks might have gotten their original code from Saad Jbabdi, but then the code-bases have probably diverged. (My apologizes if this is not correct!). Here is Saad's publication on global tractography: http://www.ncbi.nlm.nih.gov/pubmed/17543543/ Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki Sent: Thursday, July 14, 2011 9:48 PM To: GREGORY R KIRK Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tracula pub Hi Greg - The paper has been with anonymous reviewers for the last 4 months :( a.y On Thu, 14 Jul 2011, GREGORY R KIRK wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] retinotopy manual?
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=(xdem) groups=(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 -
Re: [Freesurfer] retinotopy manual?
I think the sliver problem means you need to update your video driver Bruce On Jul 14, 2011, at 11:08 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: 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=(xdem) groups=(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
