Freesurfer June 2014

freesurfer@nmr.mgh.harvard.edu

155 participants
234 discussions

Tracula preprocessing error ( set dob0 = 1 )
by Elia S. 17 Jun '14

17 Jun '14

Dear Freesurfer community, Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 " and the following command line: trac-all -prep -no-isrunning -c '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tracula.config It stops, giving me errors like these: niiRead(): error opening file /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz ERROR: reading /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.gz While setting "dob0 = 0" everything runs smoothly. Can you help me please? I'll attach the log + dmrirc (tracula.config) Best,Elia. -------------------------------------------------------------------------------------------------------------- Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

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pial edits near cerebellum and problems in sagittal view
by Elissa McIntosh 16 Jun '14

16 Jun '14

Hi, I'm new to manual editing and I'm noticing some potential problems in my data. There are several sagittal slices that seem to be showing the dura as gray matter. Also, by the cerebellum, I cannot tell if non gray matter is being included. There are some dips by the cerebellum (especially on outer edges in screen shot) and I'm not sure if that area should be included. I have attached screen shots of these potential problems. Please let me know if you have advice on what to do in both cases. I want to avoid over editing. Thank you.

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template registration and wm edits
by Walton, Matt 16 Jun '14

16 Jun '14

Hello Freesurfer experts, I have two separate questions. 1. I am doing an MRI study on young children (3-5 years old). I have read in a few a different places that Freesurfer isn't ideal for analyzing young subjects. It does seem to be processing my subjects just fine though, with the exception of needing a bit of editing on a few images. Out of curiosity, I would like to try using a different template to register my subjects to. I know Freesurfer uses an MNI based adult template, and I have acquired a template for my specific age group. Is it possible for me to replace the Freesurfer template with my own. How would I go about doing this, and do you expect the results I get to be better or worse than using the adult template. 2. When I do white matter edits, they seem to be getting overwritten when I rerun the subject. I am editing the wm.mgz volume, making sure that I save it, and then rerunning the following line recon-all -s subject -autorecon2 -autorecon3 I've also tried running from different places in the pipeline (-autorecon2-cp, -autorecon2-wm) and it still does not work. Any idea whats going wrong here, and how I might fix this. Greatly appreciate any help with this Matt

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Announcing PySurfer version 0.5
by Michael Waskom 16 Jun '14

16 Jun '14

Hello everyone, We are pleased to announce the release of PySurfer <http://pysurfer.github.io/> version 0.5. PySurfer is a Python library for making beautiful and reproducible visualizations of Freesurfer data. Changes in this version include - The statistical overlay functions can now use a wider variety of colormaps, with any matplotlib colormap <http://matplotlib.org/examples/color/colormaps_reference.html> (including the "_r" reversed versions) accepted. - Surface normals are used when rendering the cortex for a smoother visualization. - Changed the default colormap for some functions to more perceptually appropriate options. - Added control over the width of label and annotation borders. - Added 2D grids of images when saving a montage. Additionally, we have substantially improved the docs with a new example gallery <http://pysurfer.github.io/examples/index.html> and an updated installation guide <http://pysurfer.github.io/install.html> describing how to get over some hurdles that can be encountered on OSX. To install or upgrade, just run: pip install -U pysurfer We hope you find it useful. As always, contributions, suggestions, and bug reports are welcome on our github page <https://github.com/nipy/PySurfer/>. - PySurfer Devs

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Re: [Freesurfer] Linear Mixed Models in FS‏
by jorge luis 16 Jun '14

16 Jun '14

Hi LMR 1) Yes, you should use n-1 (0/1) covariates to model n groups. Eg. (Controls, Case 1 and Case 2) the model would be: intercept(random effect) + centered age (might be a random effect too) + Case1 + Case1 x centered age + Case2 + Case2 x centered age + sex 2)In model: intercept(random effect) + centered age + group + group x centered age + sex the fourth coefficient is the interaction term that represents the difference in slope between the patient and control groups. This is easy to see from your Question 1 equations. It's also easy to see from those equations that [0 1 0 0 0] tests the effect of time in the control group since the group-specific slope is only equal to the coefficient of the time covariate (the second covariate) when the group covariate is zero (i.e for the controls). Hope this makes sense. Best -Jorge >________________________________ > De: Lars M. Rimol <lmr1999(a)hotmail.com> >Para: jorge luis <jbernal0019(a)yahoo.es> >CC: Ørjan Bergmann <orjan.bergmann(a)gmail.com> >Enviado: Lunes 16 de junio de 2014 8:25 >Asunto: RE: Linear Mixed Models in FS‏ > > > > >Hi Jorge, > >I have a couple of questions which I hope you can assist us with. We have run some analyses with the model you kindly assisted us with in previous e-mails: > >intercept(random effect) + centered age + group + group x centered age + sex > >We have two groups in these analyses; one control group and one patient group (Case 1), denoted 0 and 1 respectively. > >1) If we have more than two groups (Controls, Case 1 and Case 2), in the context of GLM we would model it like this: >Group variable 1, Group variable 2 >0 0 <-- Control >1 0 <-- Case 1 >0 1 <-- Case 2 > >Would a scheme like this be appropriate in the context of lme? In other words, do we use two columns with three groups (with controls as implicit baseline), three columns with four groups etc. Or are we supposed to have just one group column in your lme software, where the groups would be denoted by labels, e.g. 'ctrl','case1','case2' etc. (or by 1,2,3,4....)? > >2) We are a little puzzled by the following contrast vectors and their interpretations. Given the model above, in a previous e-mail you wrote (in red): > >Question 1: Is there a significant interaction between time and group? >Slope group1 (group covariate=0): coefficient of centered age >Slope group2 (group covariate=1): coefficient of centered age + coefficient of group x centered age >Contrast: [0 0 0 1 0] > >This contrast would seem to ask the question: In which regions of the cortex is there an effect of centered age for Case 1 and no effect for controls? Is this the correct interpretation? > >If you want to test if the volume tend to increase within group1 then test the coefficient (slope) of centered age>0 >Contrast: [0 1 0 0 0] > >Why would this contrast yield only the effect of time for group 1 (which we assume is the control group == 0) and not for both groups? Since the second column of the design matrix contains centered age for all subjects, regardless of group, wouldn't this contrast yield the effect of time irrespective of group? > >And finally: If Question 1 not significant then both groups have the same slope otherwise you can test the coefficient of centered age + coefficient of group x centered age > 0 >Contrast: [0 1 0 1 0] > >I have tested both 0 1 0 0 0 and 0 1 0 1 0and I get very similar results for cortical surface area (figures attached). So the question is how do I interpret this. It seems to me, although I may have misunderstood, that you're saying that 0 1 0 0 0 tests the effect of time in the control group and 0 1 0 1 0 tests the effect of age in the patient group Case 1. But I don't understand why 0 1 0 0 0 doesn't test the effect of time in both groups. > >And also, if 0 1 0 0 0 is the effect of time only in the control group, wouldn't 0 -1 0 1 0 (or 0 1 0 -1 0) be a better test of interaction? > > >Thank you! > >yours, >LMR > > > > > >________________________________ >Date: Wed, 11 Jun 2014 19:09:51 +0100 >From: jbernal0019(a)yahoo.es >Subject: Re: Linear Mixed Models in FS‏ >To: lmr1999(a)hotmail.com > > >This is the standard linear mixed-effects statistical procedure, so yes it's valid and correct. Lme and SStat (a toolbox for survival data analysis) are now on github: > > >https://github.com/NeuroStats > > > >I'll update them when I have time. > > >Best >-Jorge > > > > > > > > > > >>________________________________ >> De: Lars M. Rimol <lmr1999(a)hotmail.com> >>Para: jorge luis <jbernal0019(a)yahoo.es> >>Enviado: Miércoles 11 de junio de 2014 13:40 >>Asunto: RE: Linear Mixed Models in FS‏ >> >> >> >>Hi Jorge, >> >>I just wanted to check with you whether this procedure is OK for analyses of cortical data. I use: >> >>lme_mass_fit_vw.m >> >>and then >> >>lme_mass_F.m >> >> >>I do not use any of the Regrowth functions. I know regrowth is more advanced but is the procedure I have used here valid? >> >> >>Thank you! >> >>LMR >> >> >> >> >> >>________________________________ >>Date: Mon, 28 Apr 2014 20:30:47 +0100 >>From: jbernal0019(a)yahoo.es >>Subject: Re: Linear Mixed Models in FS‏ >>To: lmr1999(a)hotmail.com >> >> >>Hi LMR >> >> >>1- The effect size is usually equivalent to the absolute value of the Beta coefficient you test in your contrast for being different from zero. >> >> >>2- The residual vector r at each vertex/voxel can be computed as: >> >> >>r = y - X*Beta >> >> >>where y is the vertex/voxel data, X is the design matrix and Beta is the estimated population regresion coefficients at that vertex/voxel. >> >> >> >>Best >>-Jorge >> >>El Lunes 28 de abril de 2014 9:32, Lars M. Rimol <lmr1999(a)hotmail.com> escribió: >> >> >>>Hi Jorge, >>> >>> >>>1) I'm looking for a way to obtain effect size estimates from the lme longitudinal analyses. So for instance, for the effect of time in a model that is: >>> >>>intercept(random effect) + centered age + group + group x centered age + sex >>> >>>With a contrast vector that is [0 1 0 0 0] I would like to obtain a corresponding effect size measure. >>> >>>2) I would like to calculate the residuals from a linear mixed model. The residuals are part of the output from lme_fit_FS but it doesn't seem to be part of the output from lme_FSfit, lme_mass_fit_vw, or lme_mass_fit_Rgw. Could you please explain how I can calculate the residuals using values in the stat struct output from lme_mass_fit_vw? >>> >>> >>>Thank you! >>> >>> >>>LMR >>> >>> >>> >> >> > >

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Vol stats of precentral gyrus
by Hugh Pemberton 16 Jun '14

16 Jun '14

Hi everyone, I was wondering if someone could comment on which portion of the precentral gyrus is used to produce subcortical volume stats? Is it just medial or lateral the whole gyrus? Many thanks and all the best, Hugh

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registration of functional data to inflated brain
by Sherryse Corrow 16 Jun '14

16 Jun '14

Hi Douglas, This worked. Thank you so much! Just in the knick of time as the presentation is Wednesday! For anyone having issues of reg-feat2anat not producing register.dat or anat2exf.register.dat . . . The link below should solve your problem! Best, Sherryse Message: 19 Date: Mon, 16 Jun 2014 12:42:54 +0200 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Messages not appearing on Mail Archive To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <539ECA2E.8020709(a)nmr.mgh.harvard.edu<mailto:539ECA2E.8020709@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="iso-8859-1" Hi Sherryse, sorry for the delay, I've been traveling. I think the problem may be with your version of reg-feat2anat. I've put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat Copy that into $FREESURFER_HOME/bin (after making a backup of the one that is there) let me know if that does not work doug -- Sherryse Corrow, Ph.D. / Postdoctoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 360A-2550 Willow Street Vancouver, BC, V5Z 3N9 Tel: 604-875-4111 ext 67672 Cell: 604-315-6717 sherryse.corrow(a)eyecarecentre.org<mailto:sherryse.corrow@eyecarecentre.org>

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Re: [Freesurfer] Fwd: How to extract significant result for each subject
by kangchengwang0808＠gmail.com 16 Jun '14

16 Jun '14

Hi dr Jerome J Maller The analysis I do this research was followed as the tutorials of freesurfer group analysis (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) The detailed was followed: (1) recon-all <subject> autorecon-all; (2) recon-all -s <subject> -localLGI; (3) recon-all -s <subject> -qcache/recon-all -s <subject> -qcache -measure pial_lgi ; (4) mris_preproc --fsgd --catch-in thickness --target --out ;(5) mri_glmfit --y --fsgd --C --surf --cortex --glmdir ;(6) using matlab to do clusterwise correction for multiple comparisons with mri_surfrft_jlbr. In the result file, there are files (sig.cw.neg.mgh,sig.cw.pos.mgh,sig.vw.neg.mgh.sig.vw.pos.mgh). Lastly, I look the result with command of mri_surfcluster. I want to extract the data of each subject in the regions of significant. Thank you Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0808(a)gmail.com / wangkangcheng.001(a)163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China From: Jerome Maller Date: 2014-06-13 13:50 To: 王康程 Subject: Fwd: [Freesurfer] How to extract significant result for each subject Hi Wang, Here are my instructions for extracting data from Freesurfer: How to export the data from Freesurfer into SPSS 1. After you have conducted a QDEC analysis, a new directory will have been created in the “qdec” directory called “stats_tables”. Navigate to this directory 2. Copy all of the files in the directory (they will all have a .dat extension) onto a Windows computer 3. Open MS Excel 4. Select on a .dat file (although it may appear with a .stats extension) and then open it (you may have to select “delimited”, then “tab”) 5. Save the file in Excel 97-2003 format 6. Close Excel 7. Open SPSS 8. Change the option in the navigation window to show “All files” 9. Select the Excel file which you have just saved 10. The Excel file will now open in SPSS. 11. Save As 12. Complete this process for all of the .dat files 13. Once all .dat files have been converted to SPSS format, merge them (using the merge feature in SPSS: Data à Merge Files à Add variables) Regards, Jerome Maller ---------- Forwarded message ---------- From: kangchengwang0808(a)gmail.com <kangchengwang0808(a)gmail.com> Date: 13 June 2014 12:53 Subject: [Freesurfer] How to extract significant result for each subject To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Dear freesurfers, I contrast depression and control and find that patients have a lower thickness in region of inferior frontal gyrus. Now, I want to extract the data of thickness for each subject. Could you tell which command could do this? Thank you Wang Kangcheng ( New learner of 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. -- Dr Jerome J Maller BSc,GradDipPsych,MSc,PhD Neuroscientist NHMRC Industry Career Development Fellow (CDF) CETBIR (Centre for Excellence in Traumatic Brain Injury) Postdoctoral Research Fellow Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School, Monash University and Alfred Hospital 4th Floor, 607 St Kilda Rd, Melbourne VIC Adjunct Associate Professor Centre for Research on Ageing, Health and Wellbeing, Research School of Population Health, ANU College of Medicine, Biology and Environment at the Australian National University. Phone: +61 3 9076 2404 Fax: +61 3 9076 6588 Mobile: +61 419 221 454

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epidewarp.fsl
by XJ Kang 16 Jun '14

16 Jun '14

Hi, The script "epidewarp.fsl" included in the FreeSurfer package for field map correction only works for fsl 3.X and 4.X. I searched the mail archive and find the link ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl This new script is supposed to work for fsl 5.X, but I cannot download it. Is the link still valid? Please check or send me a new link to download the file. Thank you very much. XJ Kang

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mri_segstats
by shahin＠nmr.mgh.harvard.edu 16 Jun '14

16 Jun '14

Hi, I have two questions about mri_segstats. I want to measure the surface area of a functionally-defined ROI. I used the mri_segstats as below and I want to be sure that it is correct. Please note that ROIs were defined in the native space. mri_segstats --i $SUBJECTS_DIR/SBJ1/surf/rh.area --slabel SBJ1 rh rh.FFA --sum SBJ1.txt --accumulate The second question is about the report file. I assume that the 'Mean' value for seg0001 is the measured surface area of my ROI in this particular subject. But what is the meaning of 'StdDev', 'Min', 'Max' and 'Range' in this report? Also, is 'Mean' value for Seg0000, the surface area of the whole (right or left) cortex? If no, how can I measure the whole rh or lh cortex surface area? Regards

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Freesurfer June 2014