Freesurfer November 2009

freesurfer@nmr.mgh.harvard.edu

92 participants
135 discussions

Research Assistant/ Lab Manager Position at OSU
by Ruchika Shaurya Prakash 22 Nov '09

22 Nov '09

Full-time Research Assistant/Lab Manager temporary position available in the Clinical Neuroscience Laboratory at Ohio State University. We employ both fMRI and behavioral paradigms to investigate the efficacy of psychosocial interventions on brain and cognitive plasticity. The job involves both administrative and research duties, with the potential candidate being involved in participant recruitment, maintenance of lab databases, data collection and analyses. A bachelor's degree in psychology, neuroscience or a related field is required. Prior research experience, background in computer programming is preferable. Start date is negotiable and the position can start as early as first week of January. For more information, interested candidates may contact Ruchika Prakash at prakash.30(a)osu.edu. To apply for the position, please visit : http://jobs.osu.edu/; (Job # : 348100) Ruchika Shaurya Prakash, Ph.D. Assistant Professor Department of Psychology Ohio State University Email: prakash.30(a)osu.edu Phone: (614) 292-8462 URL: http://faculty.psy.ohio-state.edu/prakash/lab/The_Lab.html

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missing vertices in mri_glmfit
by Julien Cohen-Adad 22 Nov '09

22 Nov '09

Hi, I'm using 'mri_glmfit' with surface inputs. However, from subject to subject, some vertices have zero-values. One solution is to use the 'prune' flag to keep only non-zeros vertices across subjects. However, this solution seems too conservative as too many vertices are discarded, producing gruyère-like significance maps. Is it possible to adopt a softer version of prune, i.e., only do the inference on non-zeros frames, without including frames that have null signal? In other words, this solution would consist in having different degrees of freedom throughout the surface. thanks, julien -- Julien Cohen-Adad, PhD Athinoula A. Martinos Center for Biomedical Imaging MGH, Harvard Medical School 149 Thirteen St, Charlestown, MA 02129, USA Work: +1 617 724 2463 ; Cell: +1 857 544 6110 ; Fax: +1 617 726 1383

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Bonferroni multiple comparison correction
by Jonathan DuBois 21 Nov '09

21 Nov '09

When correcting for multiple comparisons with Bonferroni for FS parcilation statistics, is it necessary to adjust for all parcellations (35) or just the variables (in our case mean thickness and surface area)? Assuming that no prior hypothesis is used to constrain the number of parcellations. Thanks for you input! Jon

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how to use my own template
by Guang Zeng 20 Nov '09

20 Nov '09

Hello, there, I built our own template, and gonna use it to test some subjects. Currently, I have two questions, (1) How can I use my template, In "recon-all.sh", I found that their two places where ?h.average.curvature.filled.buckner40.tif are called, so I just need to change all the "?h.average.curvature.filled.buckner40.tif" in "recon-all.sh" to "?h.average.curvature.filled.owntemplate.tif", is it correct? I think I need not do anything to ?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs, right? How about RB_all_withskull_2007-08-08.gca? (2) How can I test if my template is good? I am going to test some subjects using my template and the FS default template, measure the volumes of some ROIS, compare the percentage overlapping ratio and correlation coef, does it sound reasonable? Thanks a lot! Guang _________________________________________________________________ Windows 7: It works the way you want. Learn more. http://www.microsoft.com/Windows/windows-7/default.aspx?ocid=PID24727::T:WL…

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mri_robust_register
by Jared Price 20 Nov '09

20 Nov '09

Hi gurus, The output of mri_robust_register includes some instruction for checking the registration. In my case the ouput said I could check the registration by running "tkregister2 --mov 0110837_20090425/mri/001.anatomicalspace.mgz --targ 0311501_scan1_20061205/mri/001.anatomicalspace.mgz --lta 0110837_20090425/mri/transforms/robustreg.lta --reg 0110837_20090425/mri/transforms/robustreg.reg" However, when I run this I get the error that file 0110837_20090425/mri/transforms/robustreg.reg does not exist. Mri_robust_register appears to exit without error and creates the linear transform array file, but it did not create a file called robustreg.reg. Did something go wrong?

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talairach registration-result
by Rajagopalan, Venkateswaran 19 Nov '09

19 Nov '09

Dear Freesurfer Users, Could anyone please tell me what is the name of the image file after talairach registration for instance like nu.mgz (after intensity correction). Thanks venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Question about longitudinal outputs
by Weisinger, Brian (NIH/OD) [E] 19 Nov '09

19 Nov '09

Is there any way to view the change in deeper cortical structures in freesurfer in a longitudinal stream run study like you can see with tksurfer and cortical thickness?

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GLM model for cortical thickness!
by Dalwani, Manish 19 Nov '09

19 Nov '09

Hi All, If you don't have a linear trend in the Cortical thickness vs age correlation, is there a way to use a polynomial (quadratic, cubic) regression model to best fit the cortical thickness vs age using the GLM mechanism of freesurfer? Regards, Manish Dalwani Sr. PRA Univ. of CO

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Error in Recon-All nu_correct
by mmoayedi＠uhnres.utoronto.ca 19 Nov '09

19 Nov '09

Hi Everyone, We're having a problem in our preprocessing (see below). Any ideas what the problem may be? Many thanks, Massih #-------------------------------------------- #@# Nu Intensity Correction Thu Nov 19 13:40:47 EST 2009 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /usr/local/freesurfer/subjects/zeel3/skconF010304/F001/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.7.2.2 2009/05/04 16:16:27 nicks Exp $ Linux mpm-fmri.uhnres.utoronto.ca 2.6.9-55.ELsmp #1 SMP Fri Apr 20 16:36:54 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux Thu Nov 19 13:40:47 EST 2009 Can't do setuid (cannot exec sperl) tmpdir is ./tmp.mri_nu_correct.mni.21813 /usr/local/freesurfer/subjects/zeel3/skconF010304/F001/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.21813/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.21813/nu0.mnc $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from orig.mgz... TR=10.06, TE=4.20, TI=400.00, flip angle=20.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.21813/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Nov 19 13:40:50 EST 2009 nu_correct -clobber ./tmp.mri_nu_correct.mni.21813/nu0.mnc ./tmp.mri_nu_correct.mni.21813/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.21813/0/ Can't do setuid (cannot exec sperl) ERROR: nu_correct Linux mpm-fmri.uhnres.utoronto.ca 2.6.9-55.ELsmp #1 SMP Fri Apr 20 16:36:54 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Nov 19 13:40:50 EST 2009

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Re: [Freesurfer] recon-all -all error with version 4.5
by Bruce Fischl 19 Nov '09

19 Nov '09

thanks. Did it also write the aseg.auto_noCCseg.mgz volume? That is, did mri_ca_label complete? On Thu, 19 Nov 2009, Xiangchuan Chen wrote: > Hi Bruce, > > I don't know if recon-all exactly stopped in the same place, but I think the > lines in the end of recon-all.log showed the same message. BTW, > aseg.auto_noCCseg.label_intensities.txt was written and saved on the hard > disk. I could open it and it looked similar to those in the non-error cases. > > Thanks, > Xiangchuan > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Wednesday, November 18, 2009 7:37 PM > To: Xiangchuan Chen > Cc: 'Freesurfer Mailing List'; 'Narly A Golestani' > Subject: Re: [Freesurfer] recon-all -all error with version 4.5 > > Hi Xiangchuan, > > so you found recon-all stopped in the same place (writing > aseg.auto_noCCseg.label_intensities.txt)? > > Bruce > On Wed, 18 Nov > 2009, Xiangchuan Chen wrote: > >> I had got the same error output with v4.50 but not v4.01 for one of my >> subjects. I guessed that something might be wrong with the skull-strip >> process. So, I ran this step with different wsthresh values (from 20 to > 30, >> increased by 1), and found that the brainmask looked very similar if the >> wsthresh value was set as 20-22 (if it was larger than 22, too much >> non-brain tissue was left in the brainmask). Then, I ran autorecon2. If > the >> wsthresh was 20, no luck; if it was 22, the autorecon2 went through > without >> error. >> >> There were other strange outputs from the skull-strip process for this >> specific subject (sorry, it is off-topic): when wsthresh=23~30, too much >> non-brain tissue was left in the brainmask, except for wsthresh=25 (part > of >> the cerebellum was removed). >> >> Hope that this information helps. >> >> Xiangchuan >> >> -----Original Message----- >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Narly A >> Golestani >> Sent: Wednesday, November 18, 2009 8:15 AM >> To: Bruce Fischl >> Cc: Freesurfer Mailing List >> Subject: Re: [Freesurfer] recon-all -all error with version 4.5 >> >> >> Hi Bruce, >> >> There is plenty of disk space, and the >> 'aseg.auto_noCCseg.label_intensities.txt' file *has* successfully been >> written to the subject's 'mri' directory. >> >> best, >> Narly. >> >> On Wed, 18 Nov 2009, Bruce Fischl wrote: >> >>> did you run out of disk space? Is the file >>> aseg.auto_noCCseg.label_intensities.txt writeable in the subject's dir? >>> On >>> Wed, 18 Nov 2009, Narly A Golestani wrote: >>> >>>> >>>> >>>> Dear all, >>>> >>>> I am encountering a problem with 'recon-all -all' with one subject using >>>> freesurfer version 4.5 which I did not encounter when using version 4.4. >>>> With the older version, the stream ran without error, whereas the >>>> processing produces the following error with version 4.5: >>>> >>>> >>>> ######################## >>>> >>>> ..... >>>> >>>> gca peak WM_hypointensities = 0.15609 (88) >>>> gca peak non_WM_hypointensities = 0.10304 (57) >>>> gca peak Optic_Chiasm = 0.34849 (76) >>>> mri_ca_label GCA sequential renormalization: label 28 not consistently >>>> computed. >>>> >>>> not using caudate to estimate GM means >>>> setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 >>>> estimating mean gm scale to be 1.00 x + 0.0 >>>> estimating mean wm scale to be 1.00 x + 0.0 >>>> estimating mean csf scale to be 0.97 x + 0.0 >>>> Left_Pallidum too bright - rescaling by 0.998 (from 1.000) to 107.8 (was >>>> 108.0) >>>> Right_Pallidum too bright - rescaling by 0.998 (from 1.000) to 107.8 >> (was >>>> 108.0) >>>> saving intensity scales to aseg.auto_noCCseg.label_intensities.txt >>>> Linux aria 2.6.16.60-0.39.3-smp #1 SMP Mon May 11 11:46:34 UTC 2009 >> x86_64 >>>> x86_64 x86_64 GNU/Linux >>>> >>>> recon-all exited with ERRORS at Wed Nov 18 04:02:23 CET 2009 >>>> >>>> ######################## >>>> >>>> I have tried simply rerunning the recon-all -all stream but the error is >>>> reproduced consistently. This seems strange since there was no such >>>> error with the very same data using version 4.4. >>>> >>>> Is there any way to correct for this problem so that the stream can run >>>> successfully? >>>> >>>> >>>> Thanks in advance and best wishes, >>>> Narly. >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >> >> ==================================== >> Narly Golestani >> Institute of Cognitive Neuroscience >> 17 Queen Square >> London WC1N 3AR >> United Kingdom >> Tel: +44 (0)20 7679 7529 >> ==================================== >> >> _______________________________________________ >> 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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Freesurfer November 2009