Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30134 discussions

Left Thalamus and Pallidum segmentation problem
by Jeffrey Crawford 16 Nov '16

16 Nov '16

Hello there! I was wondering if I could get some help on an issue I am noticing in the segmentation of the left thalamus and left Pallidum on my scans. I've included pictures of tkmedit so you can see what I mean. The tkmedit uses this code: tkmedit SZ2014 brainmask.mgz lh.white -aux norm.mgz -aux-surface rh.white -segmentation aparc+aseg.mgz All of my scans have been through the entire recon-all process and , out of my sample of about 172 patients and controls, just about 29 of them show this odd segmentation on, almost always, the left hemisphere. The left thalamus seems to be over estimating the size and the pallidum is underestimating its size. I was wondering why this would be and if the community thought it would be okay to go back and manually edit the segementation to fit the subcorticals structures better? Also, since I have never done such editing, is it advisable or even possible to do so?

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Two neuroimaging post doc positions available
by Kristine Beate Walhovd 16 Nov '16

16 Nov '16

Dear all, ? two post doc positions at the Center for Lifespan Changes in Brain and Cognition at the University of Oslo, Norway, are available for excellent candidates: http://uio.easycruit.com/vacancy/1717727/65775?iso=no http://uio.easycruit.com/vacancy/1715913/65775?iso=no Best wishes, Kristine Beate Walhovd Leader of Center for Lifespan Changes in Brain and Cognition (LCBC)? Department of Psychology University of Oslo POB 1094 Blindern 0317 Oslo Norway E-mail: k.b.walhovd(a)psykologi.uio.no Phone: (+47) 22845130 Cell: (+47) 46824662

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Re: [Freesurfer] differences between OS recon all output, longitudinal data
by anonymous anonymous 15 Nov '16

15 Nov '16

Thank you so much for the extense answer! It happens that the person who analysed the first measure (of this longitudinal dataset) used two different OS (he did it in a Virtual machine on windows and a mac OS X) to speed up this step. That data has already been used in some studies. ¿So my question now would be how much does that really affect to the results? > Hi > > I am using recon-all in some longitudinal data on a ubuntu 16.04, and > using > the development version of freesurfer as I was told here, because the > other > current version doesnt work on ubuntu 16.04. > > The problem is that the first scans were probablly processed using > virtualbox in a windows and an older version of freesurfer. > > > i think I already know the answer, that I can't do this if I dont want to > bias my results. Can I? Yup. You know the answer ;) However, I did discover a way to make freesurfer 5.3 work on Ubuntu 16 by doing the following steps to install an older version of perl : 1) install perlbrew: $> sudo apt-get install perlbrew 2) use perlbrew to install perl version 5.20.3: $> perlbrew install perl-5.20.3 3) You must change the '/bin/perl' file to a link which points to the version of perl installed by perlbrew. (This technique is not the standard practice but it is the only way to get the mni tools to use the older version of perl): $> cd /bin $> sudo mv perl perl.orig (can always set back later) $> ln -s ~/perl5/perlbrew/perls/perl-5.20.3/bin/perl > > But I'm using a better computer now and I use the one with windows for > other analyses, so I wanted to know if I could install Virtual box on my > ubuntu 16.04 computer, and install the same version of linux used to > process the first measure. Should I also need to use the same version of > freesurfer? You could do that, but The Virtual Box version is not really good for processing a large number of subjects because of the limited amount of disk space on the virtual image. Its really meant more as a teaching tool for users with Windows machines. > > f the computer's specs are dfferent, does it matter? And if I assign > different cpu and ram on my virtual machine? Different specs are fine. Its the OS, OS version, and version of freesurfer that should stay the same. > > Thank you! > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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tracula missing tracts and pathstats
by Lars M. Rimol 15 Nov '16

15 Nov '16

Hi Anastasia, I have two subjects, one with a lhcab that looks ok (more or less noisy but it's there) and one with a lhcab that is almost completely missing (please see attached figures). And yet, when I look at their respective pathstats.byvoxel.txt (under dpath/lh.cab_PP_avg33_mni_bbr) I 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? Which brings me to: The default threshold in Freeview when viewing these files is 20% of the 99th percentile of the posterior probability distribution for the path, isn't it? So I was wondering how that affects 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, 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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Pial medial line crossover at hemispheres
by Hampton, Jackie 15 Nov '16

15 Nov '16

In some of my subjects, the medial pial line crosses over the hemispheres. It mislabels in both brainmask and aseg. So the part that it crosses too far over in the left hemisphere is now mislabeled. I have seen this issue in the forums before, but it didn’t seem that there was a definitive fix to the issue. I am just hoping someone will be able to give me some direction. I have tried deleting voxels to no avail. Thank you! I have attached screenshots of the issue that I am having. Jackie Hampton Clinical Research Study Assistant Nico Dosenbach, MD, PhD & Deanna Greene, PhD Department of Neurology Washington University School of Medicine 660 S. Euclid Ave. | Campus Box 8111 St. Louis, MO 63110 Phone: 314-362-4154 jackiehampton(a)wustl.edu<mailto:jackiehampton@wustl.edu> [cid:5AAC79BE-115F-42BD-8A62-90FBF1552F21][cid:9C620881-C7CB-4917-AB7E-675324F74007] ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] Cluster Color
by Timothy Hendrickson 15 Nov '16

15 Nov '16

It seems that this message has been ignored. I really do need an answer on this. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay)

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Wm edits not used in -autorecon2-wm
by jari gool 15 Nov '16

15 Nov '16

Dear all, In three of my subjects one of the sides of the T1 scan is brighter than the other side (probably a coil problem). This resulted in the recon-all processing stream identifying not enough white and gray matter, even though the brainmask.mgz included the whole brain. Since I will use my T1 scans as registration for my DTI scans only the white matter is of importance and loss of gray matter is not really an issue. I manually edited the wm.mgz using the voxel edit function. I tried to rerun the pipeline in the same subject folder with this command: recon-all -autorecon2-wm -autorecon3 -s 0008_smri_t1 with the wm.mgz being replaced by my edited version (red overlay in attached screenshot). It finished without errors according to the log files (one is attached), but no changes were made to the output files (e.g. aparc+aseg and lh.white) as can been seen in the screenshots. Do you have any idea why the white matter that I added in wm.mgz has not been included in the new output files? Secondly, do you have any idea how I could fix this? I am still a bit new to Freesurfer, so help would be very welcome! Kind regards, Jari Gool Department of Neurology - Leiden University Medical Center - The Netherlands

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localGI command
by Lauren Gascoyne 15 Nov '16

15 Nov '16

Dear Freesurfer developers, I am attempting to run the localGI command to calculate the gyrification of a group of subjects. Freesurfer version 5.3.0 was used all the way through the process. The command I have been using is as follows: recon-all -s <subjid> -localGI However it crashes straight away with the following error: ERROR: cannot find /opt/magres/freesurfer-v5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs When I look for the file mentioned in the error, the following file is there instead: lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs Do you know why the folder contains a different file from the one the command is looking for? I cannot find this error reported elsewhere. Any ideas are much appreciated, thanks. Thanks very much Lauren This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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MP2RAGEs
by Torrisi, Sam (NIH/NIMH) [E] 15 Nov '16

15 Nov '16

hi there, will FS 6.0 have any special options for MP2RAGE sequences? specifically i'm trying to decide whether to collect MPRAGE or MP2RAGE T1s; either would be at 0.7mm iso (7T data). i've heard skull-stripping is the main issue with the MP2RAGE and so i'm curious if FS 6.0 will have any adaptations for that. improved subcortical gm/wm contrast is what's drawing me towards MP2RAGE. thanks! -Sam Section on Neurobiology of Fear and Anxiety National Institute of Mental Health

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Re: [Freesurfer] nuisance dichotomous variables
by Dominic Dwyer 14 Nov '16

14 Nov '16

Hi Prof. Greve, Thanks for the response and sorry for the confusion. I mean can we use dichotomous variables in the "Nuisance Factors" box of qdec? i.e., if we don't explicitly define them as categorical variables. I was thinking that if it's a GLM then it should be ok? We want to do this because we have more than one dichotomous variable that we want to control for. Many thanks, Dom -------------------------------------------------------------------- Dom Dwyer, PhD Psychiatry & Psychotherapy LMU Munich A: Nußbaumstr. 7, Munich, 80336 E: dominic.dwyer(a)med.uni-muenchen.de T: +49 (0)89 4400 55880 I'm not sure what you mean. Dichotomous variables can be used. Our tutorial has an example of using gender. On 11/9/16 5:05 AM, Dominic Dwyer wrote: Dear FS experts, Sorry for my confusion here, but I'm wondering why dichotomous nuisance variables (e.g., gender) can't be used in qdec? I was thinking that if it uses a generalized linear model then it should be ok? I read other posts and understand why discrete factors can't be used with more than 2 levels, but was thinking that dichotomous variables should be different. NB. we're trying to run a simple two group comparison, but we two dichotomous variables that we want to control for. Many thanks for your help, Dom -------------------------------------------------------------------- *Dom Dwyer, PhD* Psychiatry & Psychotherapy LMU Munich A: Nußbaumstr. 7, Munich, 80336 E: dominic.dw...(a)med.uni-muenchen.de <mailto:dominic.dw...@med.uni-muenchen.de> T: +49 (0)89 4400 55880

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