Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS
Hi Elijah - Does the directory in the error message exist? a.y On Fri, 19 Aug 2016, Elijah Mak wrote: Hi Anastasia, The error message occurs for other control points too, but it does not kill the -prior stage. I have attached the full trac-all.log file. This error message is also found in other subjects where I am struggling to get a good initialisation. The ERROR: fio_pushd:subject/dmri/xfms/cvs/final_CVSmorph_tocvs_avg35/mri Thank you! Best Wishes, Elijah -- Elijah Mak PhD Candidate | Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ 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 - difference in tracts using MNI vs CVS
Hi Elijah - This error occurs with one number of control points but not another? That would be very strange. I'd have to look at the full trac-al.log to figure it out, I can't guess what's going on just from this one line unfortunately. a.y On Fri, 19 Aug 2016, Elijah Mak wrote: Hi Anastasia, Thanks, it works, but only for MNI reg option. For the CVS stream, there was an error message during -prior. ERROR: fio_pushd: /Users/MacPro/Documents/22995_EM/dmri/xfms/cvs/final_CVSmorph_tocvs_avg35/mri This error message did not halt the process though. Could this be a clue? Thanks for your patience :) Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate | Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ 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 - difference in tracts using MNI vs CVS
Hi Anastasia, Thanks, it works, but only for MNI reg option. For the CVS stream, there was an error message during -prior. ERROR: fio_pushd: /Users/MacPro/Documents/22995_EM/dmri/xfms/cvs/final_CVSmorph_tocvs_avg35/mri This error message did not halt the process though. Could this be a clue? Thanks for your patience :) Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ 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 - difference in tracts using MNI vs CVS
Mmm, it sounds like the shape of the tract is too convoluted for it to find a good fit. I'd try increasing the # of control points. On Fri, 19 Aug 2016, Elijah Mak wrote: Hi Anastasia, Thank you for looking into that subject. I have tried reinitiliasation a few times and in all cases, it just could not find a satisfactory control point fit during the -prior stage. Therefore, the -prior stage has been running for more than 10 hours now. This occurs in other a small number of other subjects as well. WARN: Could not find satisfactory control point fit - try 596 How can I resolve this? And what type of problem could be reflected by this? Bad aparc+aseg.mgz / registration to template? If all else fails, I will exclude subjects using the criteria that you set in the Neuroimage paper: where a subject was excluded if there were failures of reconstruction in 2 or more WM tracts. Thank you for your help! Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate | Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ 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 - difference in tracts using MNI vs CVS
Hi Anastasia, Thank you for looking into that subject. I have tried reinitiliasation a few times and in all cases, it just could not find a satisfactory control point fit during the -prior stage. Therefore, the -prior stage has been running for more than 10 hours now. This occurs in other a small number of other subjects as well. WARN: Could not find satisfactory control point fit - try 596 How can I resolve this? And what type of problem could be reflected by this? Bad aparc+aseg.mgz / registration to template? If all else fails, I will exclude subjects using the criteria that you set in the Neuroimage paper: where a subject was excluded if there were failures of reconstruction in 2 or more WM tracts. Thank you for your help! Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ 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 - difference in tracts using MNI vs CVS
Dear Anastasia, I have also uploaded the file with the problem (22995_EM.zip), and this is how my config file looks like after modifications: set subjlist = (22995) set pathlist = (fmajor_PP) set ncpts = (7) set reinit = (1) Thanks again! Best Wishes, Elijah -- Elijah Mak PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ 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 - difference in tracts using MNI vs CVS
Hi Elijah - You add "set reinit =1" to the config file, (and remember to set the pathlist and subjlist to only what you want to rerun), and then rerun the -prior and -path steps in that order. Best, a.y On Thu, 18 Aug 2016, Elijah Mak wrote: Thanks for the tips on reinitialisation of tracts. Apologies if I might have missed it in the online tutorial, do you have some general guidelines for reinitialising? Can I simply add "set reinit =1" to my configuration file, and then re-run trac-all -path. Are there any other parameters I could tweak? After running through more QC on other subjects, I have also noticed other tracts that were not fully constructed. These tracts appear to be truncated or blob-like, for a lack of better word :) I have attached the screenshot to illustrate what I mean. In these cases, I do the following QC routine after the general recon-all QC 1) freeview -v dmri/dtifit_FA.nii.gz -v dlabel/diff/aparc+aseg.bbr.nii.gz 2) freeview -v $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz subjectname/dmri/cvs/dtifit_FA.bbr.nii.gz Thanks a lot for your help, Anatasia! Best Wishes, Elijah -- Elijah Mak PhD Candidate | Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ 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 - difference in tracts using MNI vs CVS
Hi Elijah - It looks like the CVS case needs to be reinitialized. In principle you're right that if the registration is good this shouldn't be a problem. It's hard to tell what might've caused this in an individual case without looking at the data. If you want me to look into it you can upload all the TRACULA directories of the subject for me here: https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks! a.y On Thu, 18 Aug 2016, Elijah Mak wrote: Dear Anastasia and List, I have been using TRACULA to process my DTI dataset using both the affine MNI and non-linear CVS options. In one subject, the forceps major (MNI) look very different from its CVS counterpart (screenshot attached). I am just wondering what could lead to this type of differences? I've checked the registrations and they look good (overlaying FA on MNI/CVS). Thanks! Best Wishes, Elijah -- Elijah Mak PhD Candidate | Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ 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.
