[Freesurfer] Fwd: Freeview display errors - Ubuntu 12.04
-- Forwarded message -- From: Richard Binney binney.ale...@googlemail.com Date: Thu, Sep 13, 2012 at 2:01 PM Subject: Freeview display errors - Ubuntu 12.04 To: freesurfer@nmr.mgh.harvard.edu Hi Freesurfers, I've recently moved onto Ubuntu 12.04. The Freesurfer installation has required me to download various libraries and create many symbolic links to have it working. Further more I've had to set the doublebufferflag=1 (whatever that is) in order for tkmedit and freeview to work (they otherwise were tranparent display boxes). Still though I'm having some issues with freeview. It struggles with rendering the tracts generated in dpath from TRACULA. the tracts will disappear when the 3D box is moved and they are displayed in the wrong colors until you change opacity or another random parameter. Has anyone else experienced this and had any success resolving it? Are there any libraries or other general settings that need to be changed? Any help would be appreciated. On a side note I'm finding that freesurfer displays are also at the forefront, meaning they block terminals and other things I'm also working with. Any help to resolve this would be great too. Thanks Richard ___ 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] Freeview display errors - Ubuntu 12.04
Hi Freesurfers, I've recently moved onto Ubuntu 12.04. The Freesurfer installation has required me to download various libraries and create many symbolic links to have it working. Further more I've had to set the doublebufferflag=1 (whatever that is) in order for tkmedit and freeview to work (they otherwise were tranparent display boxes). Still though I'm having some issues with freeview. It struggles with rendering the tracts generated in dpath from TRACULA. the tracts will disappear when the 3D box is moved and they are displayed in the wrong colors until you change opacity or another random parameter. Has anyone else experienced this and had any success resolving it? Are there any libraries or other general settings that need to be changed? Any help would be appreciated. On a side note I'm finding that freesurfer displays are also at the forefront, meaning they block terminals and other things I'm also working with. Any help to resolve this would be great too. Thanks Richard ___ 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 -prep error
Hi Anastasia et al., I previously had TRACULA running wonderfully on a test dataset. I was tasked with writing an in-house step-by-step manual for dummies. Since then, a colleague has followed my manual with a new dataset and had problems. After trying to determine whether it was her install or something about her data and failing to find anything, I returned to re-run the subject I had already successfully processed. Nothing has changed in my install (TRAC-all version etc) ODDLY, this re-run is suffering from the same problem as my colleague. We ran trac-all -prep -dmrirc and it exited without any errors. However, there seem to be some files missing from the output: control.dat data.nii.gz nodif_brain_mask.nii.gz Bedpostx will not run due to the *data* file being missing and I'm sure the other missing files will cause problems. What is going on? I knew to look for these files as at some point I found the following list for the \dmri\. I can not re-find a post with this list so I'm sorry if it related to a solution to our current problem. Please help Richard brain_anat_mni.nii.gz dtifit_L2.nii.gz dwi_orig_flip.nii.gz brain_anat.nii.gz dtifit_L3.nii.gz dwi_orig.mghdti.bvals brain_anat_orig.nii.gz dtifit_MD.nii.gz dwi_orig.mghdti.bvecs bvals dtifit_MO.nii.gz dwi_orig.nii.gz bvecs dtifit_S0.nii.gz dwi_snr.txt bvecs.norot dtifit_V1.nii.gz lowb_brain.nii.gz control.dat dtifit_V2.nii.gz lowb.nii.gz data.nii.gz dtifit_V3.nii.gz mni dtifit_FA.nii.gz dwi.ecclog nodif_brain_mask.nii.gz dtifit_L1.nii.gz dwi.nii.gz xfms ___ 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 -prep error
Yes, because of the directions given previous listing I am running bedpost outside of trac-all (is this not necessary anymore - have we a new update?) I do not remember having to manually create the symlinks last time around but I have just done that now and bedpost is whirring away happily. For future reference to other TRACULA users: dmri/data.nii.gz should be a symlink to dmri/dwi.nii.gz presumably only if you have usemaskanat=1, then: dmri/nodif_brain_mask.nii.gz should be linked to dlabel/diff/aparc+aseg_mask.bbr.nii.gz Otherwise I guess it would be linked to the dmri/lowb_brain.nii.gz, but someone may correct me on that and some of the above. Thanks for your help eveyone Richard On Thu, Aug 16, 2012 at 2:24 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: The symlinks are actually created in the -bedp step, not the -prep step. If you're running bedpostx outside of trac-all, you need to create them yourself. On Thu, 16 Aug 2012, Watson, Christopher wrote: I've just taken to making the sym links myself after running trac-prep and before running bedpostx. Then everything should run normally. __**__ From: freesurfer-boun...@nmr.mgh.**harvard.edufreesurfer-boun...@nmr.mgh.harvard.edu[ freesurfer-boun...@nmr.mgh.**harvard.edufreesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Thursday, August 16, 2012 4:24 PM To: Richard Binney Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA -prep error Hi Richard - In the listing you sent below I do see the a nodif_brain_mask.nii.gz and a control.dat, although I have no idea what control.dat is. As for data.nii.gz, it should be created as a symbolic link to dwi.nii.gz, since bedpostx indeed expects it to be called data. I have not seen this problem before, but does it occur only when you rerun and overwrite things in the same directory, or also when you start a fresh run on a previously non-existent directory? a.y On Thu, 16 Aug 2012, Richard Binney wrote: Hi Anastasia et al., I previously had TRACULA running wonderfully on a test dataset. I was tasked with writing an in-house step-by-step manual for dummies. Since then, a colleague has followed my manual with a new dataset and had problems. After trying to determine whether it was her install or something about her data and failing to find anything, I returned to re-run the subject I had already successfully processed. Nothing has changed in my install (TRAC-all version etc) ODDLY, this re-run is suffering from the same problem as my colleague. We ran trac-all -prep -dmrirc and it exited without any errors. However, there seem to be some files missing from the output: control.dat data.nii.gz nodif_brain_mask.nii.gz Bedpostx will not run due to the data file being missing and I'm sure the other missing files will cause problems. What is going on? I knew to look for these files as at some point I found the following list for the \dmri\. I can not re-find a post with this list so I'm sorry if it related to a solution to our current problem. Please help Richard brain_anat_mni.nii.gz dtifit_L2.nii.gz dwi_orig_flip.nii.gz brain_anat.nii.gz dtifit_L3.nii.gz dwi_orig.mghdti.bvals brain_anat_orig.nii.gz dtifit_MD.nii.gz dwi_orig.mghdti.bvecs bvals dtifit_MO.nii.gz dwi_orig.nii.gz bvecs dtifit_S0.nii.gz dwi_snr.txt bvecs.norot dtifit_V1.nii.gz lowb_brain.nii.gz control.dat dtifit_V2.nii.gz lowb.nii.gz data.nii.gz dtifit_V3.nii.gz mni dtifit_FA.nii.gz dwi.ecclog nodif_brain_mask.nii.gz dtifit_L1.nii.gz dwi.nii.gz xfms 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/**compliancelinehttp://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] -nobigventricles
Out of curiosity, I would like to know what the flag -nobigventricles in the ca_reg and ca_label commands does exactly. Please help. Richard ___ 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] regeneration of aseg.mgz following edits
Hi Freesurfers, I've been trying to understand the implications of various types of edits in an attempt to solidify some standardized procedures regarding editing strategies, particularly in severely lesioned (and thus highly vulnerable to RECON failure) brains. In doing so I've been comparing volumes surfaces and segmentions pre- and post- edits/re-running RECON. I've noticed that changes in surface reconstruction is, as expected, followed by changes in the aparc.2009s+aseg.mgz segmentation (exapnded/contracted in accordnace with surface) but I don't see similar alterations in the aseg.mgz segmentation.In fact the aseg.mgz is identical pre- and post-edits despite large changes in the WM.mgz and pial/WM surfaces. Could you explain why this might be? Thanks Richard ___ 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] Running Tracula -bedpostx and -path
Hi Anastasia, I ran bedpost directly: bedpostx dmri It seemed to run fine, not exiting with any errors. the only thing that concerned me was that the last output in the terminal was 50 slices processed [when I have 54] queing post-processing stage then it exited. It seemed to run rather quicker than I expected and I expected it to at least output all slices processed and/or something after queing post Is there any reason to be concerned? Furthermore, in running the -path, the terminal window constantly outputting... ERROR: Degenerate spline segment 58 81 24 56 69 24 .. ERROR: Degenerate spline segment .. but it seems to continue on without exiting. Is there any reason to be concerned about this? what doe sit mean? Thanks for your help R ___ 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] Running Tracula -bedpostx and -path
Thanks - appears as if all is well. On Tue, Apr 24, 2012 at 4:02 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Richard - I'd check your bedpostx output files, run mri_info on them to make sure they have the right number of slices. The monitoring script that produces the slices processed messages checks only every once in a while, so you won't see a separate message for each slice. The warnings from the -path part you can definitely ignore. Hope this helps, a.y On Tue, 24 Apr 2012, Richard Binney wrote: Hi Anastasia, I ran bedpost directly: bedpostx dmri It seemed to run fine, not exiting with any errors. the only thing that concerned me was that the last output in the terminal was 50 slices processed [when I have 54] queing post-processing stage then it exited. It seemed to run rather quicker than I expected and I expected it to at least output all slices processed and/or something after queing post Is there any reason to be concerned? Furthermore, in running the -path, the terminal window constantly outputting... ERROR: Degenerate spline segment 58 81 24 56 69 24 .. ERROR: Degenerate spline segment .. but it seems to continue on without exiting. Is there any reason to be concerned about this? what doe sit mean? Thanks for your help R 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/**compliancelinehttp://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] Freeview Edit Capability
Hi Freesurfers, I just want to check my observation that Freeview can not currently be used for editing the WM.mgz or the brainmask.mgz (for minor skull strip errors) as is done in TKmedit (cf., Edit Tutorial). Is that correct? I can’t find any documentation on this, and whilst I would assume it to be a straightforward thing if possible, I can’t work out how I could configure Freeview voxel edit tools to do this. I assume that the only edits currently possible in freeview are label/ROI edits and control point definition. If this is correct, will the other edits become possible in later versions of Freeview? – this would be great given the ability to load multiple volumes…for example it is nice to view the brainmask.mgz over the T1.mgz with the latter’s opacity turned down in order to quickly detect minor skull strip errors. It would be then nice to delete (or clone-in) voxels on this set of images (like TKmedit). Thanks for your help R ___ 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] Edit Capability of Freeview
So shorlty after I sent that email I figured out how to do a little of what I spoke about... a) White matter (WM.mgz) edits - joining WM fingers in the WM.mgz or filling holes, etc..Should New WM voxels in WM.mgz should be = 255 (brush value)?? b) I can delete skull/dura..should I be replacing values in dura/skull voxels with 1 or 0 or what? Can I do cloning like in TKmedit such that I could replace small bits of skull-stripped cerebellum in the brainmask.mgz by cloning from the T1.mgz? In the voxel edits toolbar, what is the reference option for? I was hoping that it would be for cloning, but apparently not R ___ 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.
