Dear Anastasia - Yes, I noticed the added mri_convert capability in the release notes for Freesurfer 6.0 - that will save some work - thank you.
It sounds like there is no big down side to running tracula on a scan obtained with higher b-value. At present, I am primarily interested in using tracula to identify the ROIs at which each standard pathway terminates. Any additional thoughts would be welcome. Thank you again for your help and time in getting me started on this. Best - Don From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Thursday, February 15, 2018 12:52 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI Hi Donald - If you have recent dicoms from a standard manufacturer's sequence, then mri_convert should be able to read the b-values and gradient directions from the dicom header, in which case you don't have to provide them separately. About which b-values to use - there's no short answer there. For sure the higher b-values contain additional info about white matter organization. But there are 2 "buts" here. First, with TRACULA you're not doing exploratory tractography, but instead you're trying to reconstruct some well-defined pathways, based on prior info on their anatomy. It's not clear that you need the additional info from the higher b-values for that. And TRACULA uses global tractography, where the usual issues of false positives/negatives that conventional streamline tractography gets into by either taking the wrong turn or terminating prematurely don't exactly apply. Second (or maybe third?), the ball-and-stick model may not fully take advantage of the additional info contained in those higher b-values, and it's not clear if there is a crossing-fiber model that does. We're doing post mortem validation studies at the moment to get to the bottom of these questions. I hope I answered your question! Anastasia. ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Krieger, Donald N. <krieg...@upmc.edu<mailto:krieg...@upmc.edu>> Sent: Thursday, February 15, 2018 10:18:21 AM To: Freesurfer support list Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI Dear a.y. Thanks for getting back. I've set the wheels in motion to run tracula on the control scans that we have. I found your notes in the diffusion_tutorial download for grabbing the bval and bvecs from each DTI slice which looks like the biggest difficulty. On most of our controls, we have scans at several b-values, 1000, 3000, 5000, 7000. Is there a way to use all 4? And even if there is, which would be the best single one to use? Best - Don From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Wednesday, February 14, 2018 6:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI That's correct, you'd have to run TRACULA on a subject to get those files. They're computed from those 33 subjects, but you can't get the info without running it unfortunately. ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Krieger, Donald N. <krieg...@upmc.edu<mailto:krieg...@upmc.edu>> Sent: Wednesday, February 14, 2018 5:19:48 PM To: Freesurfer support list Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI Thank you very much for getting back on this so promptly, a.y. If I understand correctly, I think it's the information in the *_fsids_all_0_0_0.txt files from tracula runs on your training subjects, trc001-trc033, that would be best to use. I see the trctrain directory with its contents in my Freesurfer 5.3 installation and presume that this is all that's here. Are those .txt files readily available somewhere? Or do I need to do my own tracula runs to get them? Or am I missing something? I am a total newbie on tracula. Best - Don From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Wednesday, February 14, 2018 4:34 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI Hi Donald - TRACULA doesn't use deterministic ROIs, instead it assigns a probability to any ROI to be the one that the specific tract intersects or neighbors at a specific position along that tract's trajectory. These prior probabilities are computed from the training subjects that make up the TRACULA atlas (where atlas here refers to a set of individuals rather than an average brain). For what you're looking for, find the files: $yoursubject/dlabel/mni/*_fsids_all_0_0_0.txt There is one file for each tract. The 0_0_0 in the file name means that you're looking at the ROIs that tract goes through (rather than the tract's left, right, etc neighbors - there are other files for those). In each of these files, each line corresponds to a different position along the tract. Since you're interested in the endpoints, you want to look at the first and the last line. The ID numbers in that file correspond to ROIs as specified in $FREESURFER_HOME/FreeSurferColorLUT.txt. Hope this helps, a.y From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Krieger, Donald N." <krieg...@upmc.edu<mailto:krieg...@upmc.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, February 14, 2018 at 10:19 AM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] List needed: pathway <==> freesurfer ROI Dear List, I need a list of Freesurfer ROIs which are typical endpoints for each standard pathway used in tracula. I think this information is likely included in the default tracula atlas which I have been unable to find although I do not need spatial coordinates but rather just the list of ROI names for each pathway. If this information is contained in publications, I would like to cite them. I hope this is clear and thank you for any help you can provide. Best - Don Don Krieger, Ph.D. Research Scientist Department of Neurological Surgery University of Pittsburgh
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