Freesurfer December 2013

freesurfer@nmr.mgh.harvard.edu

107 participants
197 discussions

qdec analysis with 2 covariates
by Jon Wieser 09 Dec '13

09 Dec '13

HI freesurfer experts I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? Thanks 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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mris_anatomical_stats error
by krista kelly 09 Dec '13

09 Dec '13

Hi, I'm trying to run mris_anatomical_stats to get cortical thickness from labels for each participant but I keep getting the following error: MRISread: file '/Applications/freesurfer/subjects/MB19/surf/lh.thickness' has many more faces than vertices! Probably trying to use a scalar data file as a surface! Here is the command I'm using: mris_anatomical_stats -l MB07/label/lh.V1.thresh.label -b -f MB07/stats/lh.V1.thresh.thickness.stats MB07 lh thickness I wasn't able to find a suitable solution from the archives. I used the same command to get area.pial stats without any problems. Any help is appreciated! Krista

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Paired analysis: use of covariates
by Aldo Cordova 09 Dec '13

09 Dec '13

Dear FreeSurfer experts, I'm trying to implement the steps you indicate in the Paired Analysis' wiki site, but I still don't get something: In this site, you show the next FSGD file: GroupDescriptorFile 1 Class Main Variables Age Input subject1pair Main 30 Input subject2pair Main 40 Input subject3pair Main 50 Input subject4pair Main 60 Accordingly, "Age" is a variable whose value is the same for each pair of subjects (i.e., it is a measure of between-pair differences, but does not contain information about differences found in subjects of the same pair). Nevertheless, I need to introduce some covariates of interest whose value would indicate within-pair differences (i.e., the difference between "subjectN" and "subjectNmatch", where "N" is the arbitrarily assigned pair number). I made the next FSGD, but I'm wondering it's not correct (is it?): GroupDescriptorFile 1 Title trait1_trait2_paired MeasurementName thickness Class male Class female Variables Age trait1_diff trait2_diff Input subject1pair female 24 150 1850 Input subject2pair male 41 -200 -2090 Input subject3pair female 48 50 -6508 Input subjec4tpair male 53 -100 -7100 Input subject5pair female 36 150 1950 . . . In this FSGD, the last two variables ("trait1_diff" and "trait2_diff") would represent within-pair differences. As you can see, there are both positive and negative values, depending on the random order of individuals within a pair. Afterwards, contrast files such as "0 0 0 0 0.5 0.5 0 0" or "0 0 0 0 0 0 0.5 0.5" would be used to check whether "trait1_diff" or "trait2_diff" have an effect on cortical thickness, regressing out the effects of "gender", "Age" and either "trait2_diff" or "trait1_diff". Could you please tell me if the FSGD table is correct? If it isn't, how to implement such an approach? (I.e., how to use both between-pair and within-pair variables?) Also, are the contrast files mentioned above correct? Thank you in advance, Aldo

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New features in TRACULA
by Anastasia Yendiki 09 Dec '13

09 Dec '13

Hi all - I have just posted a tracula software update. This update adds some new functionality without any changes to any existing functionality, so you can use it with any analyses you have already done in 5.3. What's new: 1. Compute measures of head motion, as in our recent paper: http://www.sciencedirect.com/science/article/pii/S1053811913011312 2. Makes it easier to perform "along-the-tract" type analyses by combining the FA/MD/etc values from multiple subjects by position along each tract. 3. Gradient vector tables can now be different for each scan, they can be formatted in columns or rows, and blank lines at the end of the table should not pose a problem. 4. Fixed a small scripting bug that was causing the longitudinal stream not to run at all on certain platforms. You can get the update here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates Download the file for the appropriate platform (same as your freesurfer 5.3 distribution), unzip it, and copy the files directly into your $FREESURFER_HOME/bin. The trac-all wiki page has been updated, with the new command-line options shown in red: http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Arguments The tracula tutorials have also been updated with info on how to use these new features. Specifically: 1. For measures of head motion, see "Outputs from quality assessment" in: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs 2. For along-the-tract analyses, see "Anisotropy and diffusivity along the trajectory of a pathway" in: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics 3. For new options for specifying gradient tables, see "Specify the diffusion-encoding gradient table" in: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Enjoy and thank you for your feedback, a.y

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

09 Dec '13

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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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Freesurfer December 2013