Freesurfer

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Research Fellow Positions on Imaging Genetics of Infant Brain
by Anqi Qiu 09 Dec '13

09 Dec '13

Postdoctoral Fellow Position on Imaging Genetics of Infants Job description: Computation functional anatomy laboratory at National University of Singapore (http://www.bioeng.nus.edu.sg/cfa) focuses on brain and cognition studies using neuroimaging techniques. Our group is leading a large-scale longitudinal neurodevelopmental project from birth onwards in Singapore. The project examines neurocognition using EEG and eye trackers, brain development using diffusion tensor imaging (DTI), resting-state fMRI, and structural MRI, genetic and epigenetic influences on cognition and brain. Thus far, we have collected both functional and anatomical imaging as well as genetic and epigenetic data of 200 newborns and their follow-up at six months. The follow-up scanning at 4, 6, and 8 years will start soon. We are looking for a research fellow who is interested in developing and (or) employing pattern recognition approaches to understand the relationship of the brain with psychopathology in early life and how environmental factors and genetics influence such relationship. Or the candidate is interested in developing spatial-temporal analysis tools for this longitudinal datasets. Requirements: Ph. D or MD Neuroimaging Research background is preferable but necessary Knowledge in multivariate statistical analysis is necessary Good communication and writing skills in English language If you are interested in the jobs listed above, please send your CV to Associate Prof. Anqi QIU Department of Biomedical Engineering National University of Singapore Email: bieqa(a)nus.edu.sg Phone: +(65) 6516 7002

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Re: [Freesurfer] Fwd: Problems with longitudinal analysis
by jorge luis 08 Dec '13

08 Dec '13

Hi Knut There are a few confusing things in your question post. First, it seems that your attached images are depicting p-values. We usually use -log10(pvalue) format for visualization in tksurfer. The sig.mgh file saved by lme should be in that format. However we didn't use tksurfer to build the figures for the paper you mentioned. We instead just used matlab-based geometric objects and figures. Second, for mass-univariate analyses the contrast matrix is given to lme as a matlab structure CM.C = [0 0 1 0 0 0] not a plain matrix C. Perhaps you should try first the vertex-wise lme model to ensure that all your parameters (design matrix, data matrix, contrast matrix, etc...) are right and then give it a try to the more complex spatio-temporal lme model using the same parameters. eg.lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex); Then you can compare the results to have a better idea about what is going on. Best -Jorge El Jueves 5 de diciembre de 2013 13:29, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> escribió: Hi Jorge, > >this was on the freesurfer list. Do you know what is going on ? > >Best, Martin > > > > >-------- Original Message -------- >Subject: [Freesurfer] Problems with longitudinal analysis >Date: Wed, 4 Dec 2013 22:04:07 +0100 >From: Knut J Bjuland <knutjorgen(a)outlook.com> >To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > > >Hi, I have used a linear mixed model for longitudinal data analysis on a FreeSurfer 5.3, Matlab 2013b on a system with Ubuntu 12.04. I used mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh to concatenate thickness surf files, and smoothed with mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval lh.thickness_sm30.mgh --fwhm-trg 30 --cortex –noreshape. I then used the same command and options in a Matlab script, as shown at http://freesurfer.net/fswiki/LinearMixedEffectsModel found in the example for mass-univariate data analyses. . I used this design matrix: interception, time, group, group*time, gender, gender*time, and I used two random effect on interception and time. I did not compare the two random effect models with one random effect model. I used this contrast vector C=[0 0 1 0 0] for these images which are included in the email. The script ran fine but when I looked at sig.mgh, it contained many visible quadrate shapes boxes even after FDR correction, and the image looks quite different than the image in the paper in Neuroimage (Spatiotemporal Linear Mixed Effects Modeling for the Mass-univariate Analysis of Longitudinal ). Any idea what went wrong here? Thank you! Best regards, Knut Jørgen > > > >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. > >

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Segmentation misses sulci in posterior
by Eve M. LoCastro 07 Dec '13

07 Dec '13

We have a T1 image that has been problematic to process. This patient has thicker skull and extensive hypointensities in the white matter along with big vents. Skullstripping by modifying the watershed parameter either leaves too much skull or removes entire chunks of the brain in this Siemens image; unfortunately there seems to be no middle ground. In recon-all FreeSurfer has been unable to discern the gray matter boundary in the posterior of the brain and omits folding detail of the sulci. I am attaching a screenshot overview of the "best" attempt so far, which finished this morning (there is a bit of skull left over on this run; on previous runs where the skull is cleanly removed this problem persists). As a last-ditch effort I had re-sliced the axis-reformat T1 images as additional images (002.mgz, 003.mgz, 004.mgz) (any feedback on the feasibility of this approach is welcomed also). Any suggestions to improve the processing on these cortical problem areas are very much appreciated (ventricles are as good as I can hope for today; that's matter for a whole other post!). Much thanks, Eve LoCastro Senior Research Assistant IDEAL, Radiology Department Weill Cornell Medical College 515 E. 71st St S118 Tel: 212-746-1289 Fax: 212-746-4189 http://ideal-cornell.com/<http://ideal-cornell.com>

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LGI　error
by 王康程 07 Dec '13

07 Dec '13

Dear all， When I run "recon-all -s ${subject} -localGI", it appear "rm: remove regular file `/tmp/tmp4653077.mgh'? ". Then, I write yes, however, it didn't response anyway. How shold I do next? Thank you! The echo for the process is followed -------------------------- running subject Emotion_xunlian_s12002 -------------------------- Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/fmri/desktop/test Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r--. 1 root root 544815 Dec 6 20:54 /home/fmri/desktop/test/ Emotion_xunlian_s12002/scripts/recon-all.log Linux localhost.localdomain 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/fmri/desktop/test/Emotion_xunlian_s12002/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Dec 6 21:07:40 CST 2013 mris_compute_lgi --i lh.pial ================= rm -Rf /home/fmri/desktop/test/Emotion_xunlian_s12002/surf/ tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /home/fmri/desktop/test/Emotion_xunlian_s12002/surf/ tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /home/fmri/desktop/test/ Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /home/fmri/desktop/test/ Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial/ lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/home/fmri/desktop/test/Emotion_ xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial. filled.mgz',15,'/home/fmri/desktop/test/Emotion_xunlian_ s12002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2012 The MathWorks, Inc. R2012a (7.14.0.739) 64-bit (glnxa64) February 9, 2012 Toolbox Path Cache read in 0.02 seconds. MATLAB Path initialized in 0.79 seconds. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> reading filled volume... -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/fmri/desktop/test MNI_DIR /usr/local/freesurfer/mni FSL_DIR /opt/fsl -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/fmri/desktop/test MNI_DIR /usr/local/freesurfer/mni FSL_DIR /opt/fsl rm: remove regular file `/tmp/tmp4653077.mgh'? -- kangcheng Wang

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paradigm file - condition codes
by Eryilmaz, Huseyin Hamdi 06 Dec '13

06 Dec '13

Hi all, I'm trying to run a simple event-related analysis, in which the conditions are determined based on subject's performance. It is possible that some of the predicted conditions do not appear in the paradigm file (mostly because the subject performs well). In these cases, do I need to renumber the conditions (I don't prefer this since I want the condition codes to be consistent across subjects) ? If I run the design with some conditions missing I get the following error. I checked the created Xtmp.mat, and XtX matrix contains NaNs in the columns corresponding to the conditions that don't appear in the paradigm file. Does anyone know a robust solution to this problem? Many thanks! -Hamdi ******************************************************* Creating Design Matrix ... creation time = 0.006 sec DoMCFit = 1 ntptot = 235, nX = 22, DOF = 213 Saving X matrix to /autofs/cluster/roffman/users/Stable5_PerRun/MTH20067AA/bold/ER_SIRP_TEST2/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 39) s = svd(A); Error in fast_selxavg3 (line 256) XCond = cond(XtX);

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Re: [Freesurfer] Fwd: white matter and pial surface don't track sulcus
by Darren Gitelman 06 Dec '13

06 Dec '13

Yes. That's it. I tried editing the wm.mgz earlier and deleting all voxels labels as ventricle (250) but that didn't solve the problem. Do I edit the aseg.mgz file and just label it as none in this region? Would I use the command tkmedit <subjid> brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt When done do I run recon-all -autorecon2-noaseg -autorecon3? Thanks, Darren On Sun, Sep 16, 2012 at 4:38 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Check the aseg and see if it was labeled ventricle (and make sure it > really isn't). You may need to edit the aseg > > > > On Sep 16, 2012, at 5:19 PM, Darren Gitelman <d-gitelman(a)northwestern.edu> > wrote: > > Hi > > I have run into an issue that I'm not sure how to correct. What happens > is that in some subjects the surfaces don't seem to properly track sulci > coming off the medial part of temporo-occipital cortex. Please see green > arrows on the attached image. > > In fact the tutorial on topological defects shows an image with a > similar issue, but fixing it is not discussed. > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect?actio… > > I have checked and these are sulci and not the occipital extent of the > lateral ventricle. > > Perhaps it is not a problem, or if it is then how to approach fixing it? > > Thank you, > Darren > -- > Darren Gitelman, MD > Northwestern University > 710 N. Lake Shore Dr. > Abbott 11th Floor > Chicago, IL 60611 > Ph: (312) 908-8614 > Fax: (312) 908-5073 > > <3809-error.png> > > _______________________________________________ > 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. > -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

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trac-all version 5.3 crash
by Jon Wieser 06 Dec '13

06 Dec '13

Hi freesurfer experts, I've recnetly upgraded to freesurfer 5.3 (lion) 64bit version on our Mac Pro when I run trac-all -prep, I get the following error: writing to /Studies/MJMRI/MJ0030/freesurfer/dmri/dwi_orig.nii.gz... mri_probedicom --i /Studies/MJMRI/MJ0030//s1869/i1560627.MRDC.1 > /Studies/MJMRI/MJ0030/freesurfer/dmri/dcminfo.dat Trace/BPT trap Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Dec 6 11:20:50 CST 2013 I've included the trac-all.log and trac-all.error file the trac-all log indicates in incompatible library version: Reason: Incompatible library version: mri_probedicom requires version 10.0.0 or later, but libX11.6.dylib provides version 9.0.0 Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 I have reinstalled Xquartz and rebooted, but I still get the same error. what else can I do? system info: mac pro 6-core intel Xeon MAc OS 10.6.8 snowleopard Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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bad skull strip but pial and white matter borders ok
by krista kelly 06 Dec '13

06 Dec '13

Hi, I have one subject with a poor skull strip - much of the skull and neck are left over. I have used one of the automated processes to remove the problems areas and I now the skull strip is fine. If the talarairching, pial and white matter borders, and labels were fine, do I need to rerun any of the recon-all steps? Thanks! Krista

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Freeview question
by Alan Francis 06 Dec '13

06 Dec '13

Hi Bruce et al, Is it possible to load just the Hippocampal mask/ROI from the ASEG onto a brain in Freeview? thanks, Alan

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empty norm.mgz file {Disarmed}
by Adam Mezher 06 Dec '13

06 Dec '13

Hi all, I'm having a similar issue to the one described below - the mri_cc step seems stuck and goes on for days (still going); I'm using FreeSurfer version 5.1 as well. Like Bruce said in another thread, this could be due to an empty norm.mgz file. This seems like it is my exact problem, as that file is empty. Is there a way to skip this step, or to re-run from autorecon1 and ensure the norm.mgz file is created? Thanks, Adam *Adam Mezher* Staff Research Associate II Center for Imaging of Neurodegenerative Diseases San Francisco VA Medical Center 4150 Clement St. (114M) San Francisco, CA 94121 Tel: 415-221-4810 Ext. 4629 Fax: 415-668-2864 If someone can send us and example of this behavior I will fix it Cheers Bruce On Feb 20, 2013, at 12:23 PM, Matt Glasser <matt at ma-tea.com <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> wrote: >* I've noticed this at well when something goes wrong before mri_cc. It gets stuck in some kind of infinite loop. You might check that the linear and nonlinear registration worked correctly. *> >* Peace, *> >* Matt. *> >* From: Dawei Liu <ldw70171 at gmail.com <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> *>* Date: Wednesday, February 20, 2013 10:49 AM *>* To: <freesurfer at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> *>* Subject: [Freesurfer] unusually long running time in autorecon2 *> >* Dear Freesurfer experts, *> > > >* I am running autorecon2 using Freesurfer verion 5.1.0 on Linux. For some subjects, it looks that the pipeline stucked in the middle of mri_cc and keeps running for days (without any error message). Last time when it occurred I thought it may be caused by some hardware-related problem, so I killed these jobs and re-launched recon-all -autorecon2 on a different machine. Now these jobs have been running for over 40 hours and they are still running. Do you know why they take so long? For your reference, I copied the most recent processing information below: *> > > >* mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/transforms/cc_up.lta 0057_34479 *> > > >* will read input aseg from aseg.auto_noCCseg.mgz *> >* writing aseg with cc labels to aseg.auto.mgz *> >* will write lta as /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/transforms/cc_up.lta *> >* reading aseg from /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/aseg.auto_noCCseg.mgz *> >* reading norm from /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/norm.mgz *> >* 24076 voxels in left wm, 23641 in right wm, xrange [73, 130] *> >* searching rotation angles z=[65 79], y=[-54 -40] *> >* searching scale 1 Z rot 75.6 global minimum found at slice 103.0, rotations (-50.09, 68.60) *> >* final transformation (x=103.0, yr=-50.093, zr=68.597): *> >* 0.234 -0.931 -0.280 230.831; *> >* 0.597 0.365 -0.714 75.219; *> >* 0.767 -0.000 0.642 3.440; *> >* 0.000 0.000 0.000 1.000; *> > > >* Thanks in advance for your help! *> > > >* Dawei*

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