Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Demeaning TIV
by Nasim Maleki 16 Jun '10

16 Jun '10

Hi all, I have a question with regards to using the TIV as a covariate in comparing the subcortical volumes between the two cohorts. In particular I'm wondering: 1-Should you demean the TIV at all or not? 2-1-If you are using both age and TIV as your covariates, will it make sense to demean the age but not demean the TIV? 2-If you do demean each or both, should you demean these for each of the cohorts separately or use the mean of all of your subjects? I should add that the mean age of both of my cohort are pretty much the same and I'm just interested in seeing if there is a difference in the subcortical volumes between the two cohorts. Thanks for your advices in advance, Nas

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Local gyrification index error
by Dankner, Nathan (NIH/NIMH) [F] 15 Jun '10

15 Jun '10

Hi All, I'm running the lGI script on my subjects, and recently received this error: ... remeasuring lGI value for vertex iV = 64101. It may take a few minutes. WARNING -- Problem for vertex iV = 64101, lGI value is aberrantly high (lGI=59.4571)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file '/misc/data14/jen/SurfaceStats/BCM/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'! Linux thalamos 2.6.18-194.3.1.el5 #1 SMP Thu May 13 13:08:30 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Jun 14 19:20:30 EDT 2010 I've gone to the offending vertex in tkmedit and tksurfer to try to determine if there was some manual editing that needed to be done, but the area appeared to be fine. Any ideas on what the cause/solution might be? Thanks, Nathan

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Changing tkmedit settings
by Mehul Sampat 15 Jun '10

15 Jun '10

Hi Folks, In tkmedit, the keyboard commands to view main and aux volume are 'Ctrl+1' and Ctrl+2'. Is it possible for me to change them to just '1' and '2' respectively ? (like how only 'n' is required for the navigation tool) Thanks Mehul

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Re: [Freesurfer] R: R: How means all the output file from a segmentation?
by Michael Waskom 15 Jun '10

15 Jun '10

Hi Leonardo, You might want to check out 3D slicer: http://www.slicer.org/ It sounds like it might be able to do what you're looking for. Best, Mike On Sun, 13 Jun 2010, Leonardo Chesi wrote: Hi bruce, my goal is to obtain a 3D surface of the hippocampal region for a visual comparison with a manual segmentation made by a neuroradiologist. Today I managed to extract the volume with mri_binarize but I can't transform it in a surface that tkurfer can visualize. For that I try to use mri_vol2surf but I obtain a surface with 0 vertices. Can you help me?? Cheers Leonardo

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Antw: Re: V5/MT label anatomical borders
by Carl Schultz 15 Jun '10

15 Jun '10

Hi Bruce, thank you for your fast reply. Is that the work you referred to ? Cytoarchitectonic analysis of the human extrastriate cortex in the region of V5/MT+: a probabilistic, stereotaxic map of area hOc5. Malikovic A, Amunts K, Schleicher A, Mohlberg H, Eickhoff SB, Wilms M, Palomero-Gallagher N, Armstrong E, Zilles K. Cereb Cortex. 2007 Mar;17(3):562-74. Best regards Christoph Christoph Schultz, MD University of Jena Department of Psychiatry 07743 Jena Germany Dr. C. Schultz Universitätsklinik für Psychiatrie und Psychotherapie Philosophenweg 3 07743 Jena >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 15.06.10 14.56 Uhr >>> Hi Christoph, the V5/MT label we distribute is based on the work of Karl Zilles and Katrin Amunts who defined it histologically. I don't have the reference handy, but it shouldn't be too hard to find. cheers Bruce On Tue, 15 Jun 2010, Carl Schultz wrote: > Dear all, > > is there an anatomical description for the V5/MT label? > (Freesurfer Version 4.0.5) > > Thank you in advance > > > Christoph > > Christoph Schultz, MD > University of Jena > Department of Psychiatry > 07743 Jena > Germany > > Dr. C. Schultz > Universitätsklinik für Psychiatrie und Psychotherapie > Philosophenweg 3 > 07743 Jena > > ____________________ > Universitätsklinikum Jena > Körperschaft des öffentlichen Rechts und Teilkörperschaft der > Friedrich-Schiller-Universität > Jena Bachstraße 18, 07743 Jena > Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; Medizinischer > Vorstand: Prof. Dr. Klaus Höffken; > Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer > Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse > Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; > Gerichtsstand Jena > Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777 > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ____________________ Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777

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micro-parcellation
by Christian Lambert 15 Jun '10

15 Jun '10

Hello, I've been through the threads and can't find the answer to this one. Problem: - Subdivide the cortex into 5000++ (ideally>10,000) units per hemisphere I've tried using mris_divide_parcellation but unfortunately it got very upset trying to find a "unique rgb colour" after I had managed to achieve >2700 new labels (also I was not entirely sure how to transfer these annot labels to the annot.mgz but that's a side issue): CTABfindRGBi: rgb was invalid CTABfindRGBi: rgb was invalid CTABfindRGBi: rgb was invalid .. etc., I'm not really bothered about visualising the result per se, I just want each small area_ through _the cortical mantel to be assigned an unique value (like in the annot.2009s.mgz images but with many many more areas) so I can then convert to nifti and run numerous MATLAB scripts across multiple coregistered scans. Is this approach going to work?? Cheers, - Chris

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V5/MT label anatomical borders
by Carl Schultz 15 Jun '10

15 Jun '10

Dear all, is there an anatomical description for the V5/MT label? (Freesurfer Version 4.0.5) Thank you in advance Christoph Christoph Schultz, MD University of Jena Department of Psychiatry 07743 Jena Germany Dr. C. Schultz Universitätsklinik für Psychiatrie und Psychotherapie Philosophenweg 3 07743 Jena ____________________ Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777

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MMIL postdoctoral position
by Don Hagler 14 Jun '10

14 Jun '10

Postdoctoral Research Scholar Position, Multimodal Imaging Laboratory, University of California, San Diego The Multimodal Imaging Laboratory (MMIL) at the University of California, San Diego invites applications for a postdoctoral research scholar position under the direction of Drs. Donald Hagler and Anders Dale. The successful candidate will join a multi-disciplinary team of scientists, programmers, and support staff addressing a variety of neuroscience questions using multimodal brain imaging, electrophysiology, behavior, and genetics. An important component of the work done at MMIL, and an integral role of the currently announced position, is the development and improvement of methods for the analysis of neuroimaging data. This will include extending our recent work on a white matter fiber tract atlas (Hagler et al., HBM 2009) to encompass a more diverse population of subjects, additional fiber tracts, and a larger age range, including infants. The postdoctoral researcher will receive training in brain imaging and methods development, and will be encouraged to develop his or her own research projects. Applicants for the position must have completed relevant Ph.D. research activities within the past five years. Applications from many disciplines may be considered, and the position is open to qualified international applicants. Proficiency in the following areas is required: 1. computer programming (e.g. MATLAB, C/C++) 2. scientific writing Experience and/or interest in the following areas is desired: 1. structural MRI, diffusion MRI 2. neuroimaging analysis software (e.g. FreeSurfer, FSL) This posting is for a 2-year appointment beginning immediately. Salary will be consistent with the NIH/NRSA levels in accordance with the University of California, San Diego policies for Postdoctoral trainees. Compensation includes full staff benefits, including health insurance, and vacation time. Review of applications will begin immediately and will continue until the position is filled. To apply, please send your CV, a brief statement of research interests and goals, and any selected reprints to dhaglerjr(a)hotmail.com with the subject line "MMIL postdoctoral position". Letters of reference will be required before final approval of hiring. Informal inquiries for more details are welcome. _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28…

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Calc stats on ROI in qdec
by Jeff Sadino 14 Jun '10

14 Jun '10

Hello, I am wondering if it is possible to calculate t-values and significance of a whole ROI in qdec, version 1.2. Right now, I have no problem doing it on a point-by-point basis, but I want to do whole ROI analysis within qdec. For example, I want to know the p-value of the whole lh_superiorparietal region for the "Does the average thickness differ between HIV and Control?" contrast. Your help is always appreciated! Mahalo, Jeff

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Re: [Freesurfer] make_average_subject with large cohorts
by Nick Schmansky 14 Jun '10

14 Jun '10

Marie, I fixed the memory leak that was causing your out-of-memory error when running mris_make_average_surface. A new mris_make_average_surface for Mac Intel Leopard is posted here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-int… I'm still looking into the mri_average failure. I dont know what to say about the license error, as the code that handles the license hasnt changed since v2.0. As an aside, I'm skeptical of the utility of a volume or surface composed of 400+ subjects. The volume will be too blurry to be of use, and the surface will have lost any group-specific patterns that might have existed. If retaining the unique morphometric properties of your subject set is important, you might want to consider using just 20 or so randomly chosen subjects. Perhaps Bruce or others can comment. Nick On Wed, 2010-06-02 at 18:53 +0200, Marie Schaer wrote: > Hi Nick, > > Thank you for your response. I added the flag --debug, please find in > attachment the log. I am working on a Mac Intel Quad-Core Intel Xeon, > Processor 3 GHz, RAM 5GB. I also tried with another similar machine > which 9GB, but it exited with the same error exactly at the same > point. Even using the -no-aseg option it stops exactly at the same > point. I also provide you a screenshot with the top command running, a > few minutes before the error, and just after the error. > > As for the license error, I just had this problem using the Freesurfer > version 4.5, and you are right, it may be a connection problem because > our data are on a server (mounted with afp). It is however strange > that it exits always at exactly the same point... Anyway, no license > problem with version 4.4 or 4.3. > > Many thanks for your help, > > Marie > > On 1 juin 10, at 16:54, Nick Schmansky wrote: > > > can you try adding the flag --debug to make_average_volume? it will > > output a lot of stuff, but will pinpoint at which stage it is running > > out of memory. also, try running 'top' in another terminal to monitor > > the amount of memory it's consuming while running. > > > > as for the license error, that is bizarre, i can't think of a reason > > for > > that, unless your subjects are located on an NFS drive (a network). > > we've seen lots of problems with NFS and the Mac OS, where the > > connection drops for a couple seconds. > > > > n. > > > > > > On Mon, 2010-05-31 at 22:39 +0200, Marie Schaer wrote: > >> Hi everyone, > >> > >> I did not find a solution to my problem yet: how to launch > >> make_average_subject / make_average_volume / make_average_surface > >> on a > >> large number of subjects on a Mac Intel? Did someone encounter this > >> error before? > >> > >> Many thanks in advance for your help, > >> > >> Marie > >> > >> On 29 mai 10, at 20:07, Marie Schaer wrote: > >> > >>> > >>> Hi Nick, > >>> > >>> Sorry for disturbing again. As advised, I tried to launch separately > >>> make_average_volume and make_average_surface. Even with the --no- > >>> aseg > >>> option with make_average_volume I got the "cannot allocate memory" > >>> error. And with the make_average_surface I got the "license error" > >>> in > >>> the middle of one subject processing... Any idea? > >>> > >>> Thank you very much, > >>> > >>> Marie > >>> > >>> > >>> On 28 mai 10, at 21:37, Nick Schmansky wrote: > >>> > >>>> try adding --no-aseg to the command line. that out-of-memory error > >>>> seems to originate with creation of the average aseg.mgz file > >>>> (hopefully > >>>> you wont need it for your subject set, typically you dont need > >>>> aseg.mgz > >>>> since aseg stats are usually gathered from a set of aseg.stats > >>>> files, > >>>> not from an average aseg.mgz). > >>>> > >>>> doug: maybe we should make --no-aseg the default? > >>>> > >>>> n. > >>>> > >>>> > >>>> On Fri, 2010-05-28 at 21:31 +0200, Marie Schaer wrote: > >>>>> Hello everybody, > >>>>> > >>>>> I have a problem running make_average_subject for a large number > >>>>> of > >>>>> subjects (>400) on a Mac Intel. I tried with different Freesurfer > >>>>> versions (all the log outputs are attached). Using the freesurfer > >>>>> version 4.3 and 4.4 the make_average_subject script always stop at > >>>>> the > >>>>> 297th subject with the error "Cannot allocate memory". I already > >>>>> tried > >>>>> to uncomment the line "limit descriptors unlimited" or to set it > >>>>> to > >>>>> various values, as proposed in the mailing list, but without > >>>>> success > >>>>> (it always stop at the 297th subject). Then I tried with the > >>>>> Freesurfer version 4.5 (therefore I had to recompute the > >>>>> lh.inflated.H > >>>>> and lh.inflated.K which are not automatically produced in previous > >>>>> versions), but with the 4.5 version I got a strange "license > >>>>> error" > >>>>> message in the middle of the script (and my licence is certainly > >>>>> fine > >>>>> as I can run any other script without problems). > >>>>> > >>>>> Does anyone have an idea? Many thanks in advance for your precious > >>>>> help, > >>>>> > >>>>> Marie > >>>>> > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer(a)nmr.mgh.harvard.edu > >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer(a)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. > >>>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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