Freesurfer November 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
214 discussions

how does the content of the curv files compare to that of smoothwm.H.crv
by Bernardoni, Fabio 22 Nov '16

22 Nov '16

Dear Freesurfer experts, I am having troubles interpreting the output of the recon-all output concerning the curvature, in particular in relation with the one from the command mris_curvature_stats. My aim is to compare the absolute value of both the gaussian/intrinsic and the mean/extrinsic curvatures between a group of patients and a group of controls. In particular I would like to obtain a voxelwise statistical maps for the comparison. Browsing the freesurfer mailing list I understood the following (please correct me if I am wrong): - the file $SUBJECTS_DIR/<subjid>/surf/lh.smoothwm.H.crv, produced by mris_curvature_stats, contains the mean/extrinsic curvature map for the left hemisphere, as computed on the white matter surface, for subject <subjid> - the file $SUBJECTS_DIR/<subjid>/surf/lh.curv, produced by recon-all (or by mris_curvature, right?) contains a smoothed version of smoothwm.H.crv - the files $SUBJECTS_DIR/<subjid>/surf/lh.pial.H.crv and $SUBJECTS_DIR/<subjid>/surf/lh.curv.pial are the analogues of the above, but for the pial surface Also the local gyrification index, contained in the file$SUBJECTS_DIR/<subjid>/surf/lh.pial_lgi, is computed on the pial surface and might be compared (I know it is a different measure) with $SUBJECTS_DIR/<subjid>/surf/lh.pial.H.crv and $SUBJECTS_DIR/<subjid>/surf/lh.curv.pial, not with $SUBJECTS_DIR/<subjid>/surf/lh.curv or $SUBJECTS_DIR/<subjid>/surf/lh.smoothwm.H.crv. If this is true I expect that: 1- the histograms of the above quantities for any subject be approximately symmetric around zero. Actually given that the convention chosen is to give a positive curvature to the suci and a negative to the gyri (also read in one email of this list from long time ago - so please correct me if I am wrong), I expect that the mean value would lie a bit below zero if we want the brain surface to close (with this convention a sphere has mean curvature -1/r). This expectation of mine is only a rough expectation, but it would be precise if one had normalized somehow for the area related to the vertex on which the local curvature is computed. 2- the histograms for smoothwm.H.crv and pial.H.crv would have fatter tails than curv and curv.pial, respectively 3- smoothwm.H.crv and pial.H.crv would follow quite closely curv and curv.pial, respectively, for each subject Now please have a look at the attached plots, where in red always appear unsmoothed quantities, while in blue smoothed ones. NB I have extracted the above plotted values using the functions fs_read_Y from the freesurfer longitudinal package by M. Reuter et al. Now I observe that 1,2,3 are true on the white matter surface (see attached *smoothwm* files). Also, if I average the mean curvature for one subject over all vertices I obtain a negative value. When I look at the analogue plots for the pial surface2,3 are still true, but the mean values for the curvatures are now positive! If I look at the *pial* files, the distribution looks clearly different. Therefore I have the following doubts/questions: a) is the convention for the curvature sign different on the pial and on the wm surface? b) if not, can the normalization issue I mention in point 1 above explain the negative mean of the mean-curvature I observe (the subject I used to produce the plots is a healthy control, plots are similar for other subjects)? c) in any case I expected the survatures to be more similar to each other on the wm and on the pial surface, given that they are approximately parallel. Any comment on this would be highly appreciated. d) or do you think my results are wrong/ I am not plotting the right thing? Thanks in advance for any help. Fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Psychosoziale Medizin und Entwicklungsneurowissenschaften Tel. +49 (0)351 458-5245 Fax +49 (0)351 458-7206 URL http://www.uniklinikum-dresden.de/psm; www.transdenlab.de Universitätsklinikum Carl Gustav Carus & Medizinische Fakultät an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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Re: [Freesurfer] ASL processing in Freesurfer? (Douglas Greve)
by Elijah Mak 21 Nov '16

21 Nov '16

Many thanks for the information, Doug! I will give it a go. Actually, I would like to carry out the following analyses: Get regional estimates of perfusion within a region of interest as defined by a significant cluster after mri_glmfit-sim. as well as other cortical regions that are connected to that cluster in terms of WM paths. Is it possible to do that in Freesurfer environment? How can I do PVC for perfusion in ROIs? Will the -pv ppvol flag be crucial during the mri_segstats stage? Thanks again for help. Best Wishes, Elijah

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Training Tracula to add more pathways
by Kristafor Farrant 21 Nov '16

21 Nov '16

Hi there, As a complete newbie to the Tracula tool, I have a questions about using it. Is it possible to train tracula to track additional pathways other than the 18 thats are already included? I was to track several pathways that are not included with Tracula. Best, Kris

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[FreeSurfer] TRACULA Registration transform matrix
by Ostrowski, Lauren 21 Nov '16

21 Nov '16

Hi experts, We're trying to convert an ROI in T1 MRI space to diffusion space in order to collect FA values from the ROI (using TRACULA output files). Is there a t1 to dwi transform matrix to use with TRACULA? Thanks, Lauren

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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

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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

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Freesurfer November 2016