Freesurfer

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30076 discussions

tracula reinit
by Lars M. Rimol 21 Nov '16

21 Nov '16

Hi, Rerunning the tractography using reinit, is it an absolute requirement to specify number of control points? It doesn't seem like I can just set reinit = 1 and let the number of control points be the default. Also, is there a trade-off in terms of number of control points? For instance, when reconstructing the forceps major, the default number of control points is already 7, i.e. the highest of any tract. What if I double it? Apart from the fact that it takes longer, is there any drawback to using lots of controls points? Thank you! LMR

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Getting combined bvals/bvecs
by Marissa Pifer 21 Nov '16

21 Nov '16

Hello freesurfer experts, I am trying to run tracula on subjects that have separate AP/PA direction DTI files. We combined the data into one using topup, and would now like to run tracula on the subject. The problem is, the combined file doesn't have a bvals/bvecs file. When I try to use the original bval/bvec files, I get the error that the bvals and bvecs don't match up. I have tried combining the files into one, and then running a dicom to nifty conversion to get a combined bvals/bvecs output, but that results again in two separate bvals/bvecs files as well. I then tried just have two specified bvals and bvecs. This did not give us an error message, but trac-prep took only a few seconds and did not complete the steps it was supposed to to create the directories for trac-bedp to complete. I have attached our dmrirc.example file and the log for the trac-prep step for your reference. The questions then are; is there a way to get one bvals/bvecs file that has the correct parameters for the AP and PA combined file. Or, if not, is there a way to run tracula with two sets of bvals and bvecs (one for the AP and one for the PA direction)? In case you need this information, the process is being run with freesurfer 5.3, on a macbook pro OS X version 10.9.5. Thank you in advance, Marissa

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quality control of tracula tractography
by Lars M. Rimol 21 Nov '16

21 Nov '16

Hi, I have done tracula tractography on 180 subjects, and most of my isosurfaces look a lot noisier than the example on the wiki. Is there any way to gauge the noisiness of a reconstructed path? And can that information be used for quality control? For instance, here ( https://neuro.ebioscience.amc.nl/portal/web/nsg/tracula) they do not accept a somewhat noisy fminor. Another source of information on outliers is the log files that are produced when running -trac-all -stat (based on the shape of the tract). It doesn't seem to flag tracts that are (almost) completely missing (see attached figure, which was not flagged in lh.cab_PP.avg33_mni_bbr.log) - but they may fall under the minimum threshold and therefore not be evaluated? Is it recommended to automatically exclude the subjects that are flagged as outliers there? Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

2 1

quality control of tracula tractography
by Knut J Bjuland 21 Nov '16

21 Nov '16

Hi, We have done tracula tractography on 180 subjects, and most of the isosurfaces look a lot noisier than the example on the Tracula wiki (see fminor in attached figure). Is there any way to gauge the noisiness of a reconstructed path? And can that information be used for quality control? For instance, here (https://neuro.ebioscience.amc.nl/portal/web/nsg/tracula) they do not accept a noisy fminor (not unlike ours). Another source of information on outliers is the log files that are produced when running -trac-all -stat (based on the shape of the tract). It doesn't seem to flag tracts that are (almost) completely missing (see attached figure, which was not flagged in lh.cab_PP.avg33_mni_bbr.log). Do they fall under the minimum threshold and are therefore not evaluated? Is it recommended to automatically exclude the subjects that are flagged as outliers here? Thank you! Knut Jørgen Bjuland, PHD Sørlandet sykehus[cid:FE03EBE5-0A24-4D48-B88F-5929B7604E41][cid:4AB4F493-C33E-4F51-8A8A-09082A56D188]

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tracula: thresholding in pathstats.byvoxel
by Knut J Bjuland 21 Nov '16

21 Nov '16

Hi, We have two subjects, one with a lhcab that looks ~OK (somewhat noisy) and one with a lhcab that is almost completely missing (please see attached figures). And yet, looking at their respective pathstats.byvoxel.txt (under dpath/lh.cab_PP_avg33_mni_bbr) we find that both have data for this tract and that the subject with a seemingly missing tract (70) has more observations. Is this a thresholding issue? The default threshold in Freeview when viewing these files is 20% of the 99th percentile of the posterior probability distribution for the path, so how does that affect the data in pathstats.byvoxel and pathstats.overall; are they also thresholded? # subjectname 17 # pathwayname lh.cab # # pathway start x y z AD RD MD FA AD_Avg RD_Avg MD_Avg FA_Avg 56 35 27 0.000890712 0.000603441 0.000699198 0.315126 0.00105762 0.000596839 0.000750432 0.362276 56 36 26 0.00107635 0.000545558 0.000722489 0.41169 0.00104539 0.000615595 0.000758858 0.335287 56 37 26 0.00106187 0.000590571 0.000747672 0.372333 0.00105743 0.000602726 0.000754296 0.354483 56 38 25 0.00102202 0.000600078 0.000740726 0.368605 0.00100576 0.000632157 0.000756689 0.313797 56 39 25 0.00119029 0.000522558 0.000745135 0.485075 0.00107733 0.000611676 0.00076689 0.358958 56 39 24 0.000901928 0.000700433 0.000767598 0.204508 0.0010547 0.000622021 0.000766243 0.338646 56 40 24 0.000983715 0.000610012 0.00073458 0.333454 0.00105292 0.000634273 0.00077382 0.330426 56 41 23 0.00109975 0.000657692 0.000805043 0.318553 0.00115473 0.000602686 0.000786698 0.395328 57 42 23 0.00119796 0.000512441 0.000740946 0.50737 0.00119982 0.00058122 0.000787428 0.43539 57 43 22 0.00108816 0.000588772 0.000755234 0.368538 0.00120245 0.000589771 0.000793995 0.417918 57 44 22 0.00145913 0.000457154 0.000791146 0.628211 0.00131065 0.000556036 0.00080757 0.48867 57 45 21 0.00142093 0.000463346 0.000782542 0.617307 0.0013404 0.000544065 0.000809509 0.514237 57 46 21 0.00142182 0.000445771 0.000771122 0.632204 0.00139366 0.000547482 0.000829538 0.525517 57 47 20 0.000968663 0.000475497 0.000639886 0.434747 0.001285 0.000583274 0.000817181 0.448241 58 48 19 0.00121939 0.000531887 0.000761053 0.482488 0.00133092 0.000590401 0.000837236 0.462653 58 49 19 0.00159589 0.000576742 0.000916457 0.569308 0.00136598 0.000635182 0.000878787 0.437028 58 50 19 0.00164139 0.000624262 0.000963304 0.549971 0.00138664 0.000658869 0.000901467 0.426815 58 50 18 0.00157653 0.000942457 0.00115382 0.332295 0.00137177 0.000715268 0.000934107 0.385317 58 51 18 0.00118225 0.000642473 0.0008224 0.36823 0.00118518 0.000684428 0.000851342 0.330996 58 52 18 0.00109238 0.000519084 0.000710181 0.435882 0.00107605 0.000632073 0.000780059 0.324378 58 53 18 0.00129725 0.000623659 0.000848189 0.430382 0.00108778 0.000647922 0.000794535 0.315793 # pathway end # subjectname 70 # pathwayname lh.cab # # pathway start x y z AD RD MD FA AD_Avg RD_Avg MD_Avg FA_Avg 53 32 26 0.00117731 0.000928949 0.00101174 0.143923 0.00116391 0.00090839 0.000993563 0.153213 53 33 26 0.0010364 0.000859843 0.000918695 0.128905 0.00103869 0.000848443 0.000911856 0.138848 53 33 25 0.00105938 0.000877392 0.000938055 0.127225 0.00105752 0.000865256 0.000929355 0.135088 54 34 25 0.000944648 0.000719044 0.000794246 0.162868 0.000957389 0.000725472 0.000802768 0.16744 54 35 25 0.000972687 0.000738523 0.000816578 0.208351 0.000986717 0.000739063 0.000821629 0.213113 54 36 24 0.00101603 0.000621378 0.000752929 0.305637 0.0010253 0.000631396 0.000762693 0.302995 54 37 24 0.00113992 0.000642822 0.000808521 0.369124 0.0011217 0.000646204 0.000804698 0.353409 55 38 23 0.000890718 0.000584601 0.00068664 0.265622 0.000916719 0.000590972 0.000699556 0.273432 55 39 23 0.0013084 0.000657441 0.000874427 0.41632 0.00129438 0.000656492 0.000869102 0.409684 55 40 22 0.000897226 0.000549981 0.000665729 0.294657 0.000926128 0.000565056 0.000685412 0.294239 56 41 22 0.00129446 0.000643583 0.000860544 0.416518 0.00128053 0.000641873 0.000854761 0.410811 56 42 21 0.00095897 0.000527739 0.000671483 0.356436 0.000986408 0.00054246 0.000690451 0.355442 56 43 21 0.00126047 0.000576778 0.000804674 0.460586 0.00120436 0.000578402 0.000787051 0.4315 57 44 21 0.00141709 0.000815438 0.00101599 0.333322 0.00136115 0.000786714 0.000978188 0.330026 57 45 20 0.00107155 0.000547688 0.000722309 0.398732 0.0010439 0.000565023 0.000724638 0.366345 57 46 19 0.00106184 0.000688623 0.000813027 0.276355 0.00106565 0.000721324 0.000836098 0.250311 58 46 18 0.00138626 0.00111282 0.00120397 0.13344 0.00133896 0.00105932 0.00115254 0.147013 58 46 17 0.00190569 0.00154603 0.00166592 0.127639 0.0017048 0.00136742 0.0014799 0.141036 58 47 17 0.00182424 0.00136918 0.00152086 0.176476 0.00170912 0.00128364 0.00142549 0.178103 58 48 17 0.00179186 0.00155183 0.00163184 0.121897 0.0016827 0.00141198 0.00150224 0.137642 58 49 17 0.00173965 0.00152012 0.00159329 0.0828833 0.00156972 0.00134741 0.00142152 0.101404 58 50 17 0.00146827 0.00123617 0.00131354 0.105179 0.0013648 0.00113875 0.00121408 0.115824 59 51 17 0.000939683 0.000730799 0.000800427 0.151144 0.000913724 0.000729779 0.000791094 0.140851 59 52 17 0.000973182 0.000776841 0.000842288 0.136551 0.000937145 0.000762049 0.00082041 0.130533 59 53 17 0.000974158 0.000799803 0.000857921 0.120722 0.000938325 0.000778099 0.000831516 0.119775 59 54 17 0.00100004 0.000821513 0.000881023 0.135361 0.000956475 0.000793336 0.000847705 0.130042 # pathway end Thank you! sincerely yours, Knut Jørgen Bjuland, PhD Sørlandet sykehus[cid:572E458B-7D76-4529-A118-F41DFDA9D0E1][cid:8B038586-7E12-4FEB-974B-A30F6BEFF242]

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Post recon anatomic file normalization
by Bauer, Patrick M 21 Nov '16

21 Nov '16

Greetings, I had quick question as to whether the final post-recon anatomical image (ie. T1.mgz) retains the normalization provided by the MNI template or if it is somehow reverted back to a pre-normalization format? Many thanks, Patrick Bauer PGY4 Neurology resident Medical College of Wisconsin

2 1

ASL processing in Freesurfer?
by Foo Keat Mak 21 Nov '16

21 Nov '16

Hi Freesurfer Team, Is there an ASL-friendly processing pipeline embedded in Freesurfer? Something like an equivalent to that of PetSurfer? Thanks. Best Wishes, Elijah Sent from my iPad

2 1

Mris_decimate for MAC
by Dorothy Sincasto 21 Nov '16

21 Nov '16

Hi, I can't find in my freesurfer version the mri_decimate, and I tried to download it from the links in the mailing list archive but they are down. >From where could I download it? Thanks Dorothy

2 4

trouble with mailing list
by Knut J Bjuland 21 Nov '16

21 Nov '16

Hi I have posted two posts to the FreeSurfer mailing list that does not appear in the archive. Are there any trouble with the list or are there a trouble with my mailing client? Knut Jørgen Bjuland PhD

2 4

Help with Opseq: Setting Parameters
by Leshin, Joseph 21 Nov '16

21 Nov '16

Greetings, Is it possible to avoid having Optseq repeat my events more than 3 times before inserting a NULL? In other words, I get sequences that look like ev1, ev5, ev4, ev2, ev6, NULL, etc. Ideally, I'd have Optseq limit event repetitions at 2-3 followed by a NULL. I tried using "-repvar" but I don't really understand how to use it, or whether the function will help. I've provided my syntax below. Thank you, Joseph ./optseq2 --tr 2 --ev SocialFear 8 6 --ev NonsocialFear 8 6 --ev SocialSad 8 6 --ev NonsocialSad 8 6 --ev SocialNeutral 8 6 --ev NonsocialNeutral 8 6 --o SituatedNeuroscience --nkeep 30 --nsearch 10000 --psdwin 0 26 1 --ntp 180 --repvar 8 __ Joseph C. Leshin Ph.D. Student | Psychology & Neuroscience Carolina Affective Science Lab<http://www.unc.edu/~kal29/> University of North Carolina at Chapel Hill

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