Freesurfer April 2013

freesurfer@nmr.mgh.harvard.edu

131 participants
220 discussions

announcement for MGH email list (fwd)
by Bruce Fischl 12 Apr '13

12 Apr '13

FYI ---------- Forwarded message ---------- Date: Fri, 12 Apr 2013 00:27:38 +0200 From: Jorge Jovicich <jorge.jovicich(a)unitn.it> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: announcement for MGH email list Ciao Bruce, would you mind forwarding for me the postdoc position announcement below? Thanks, Jorge ----------------------------------------------------------------------------- POST-DOCTORAL POSITION IN USING BRAIN DATA TO SUPPORT THE DEVELOPMENT OF EMOTIONALLY PLAUSIBLE VIRTUAL AGENTS AT CIMEC/CLIC, UNIVERSITY OF TRENTO A postdoctoral position will soon become available at the CLIC laboratory of the Center for Mind / Brain Sciences, University of Trento (http://clic.cimec.unitn.it/) starting as soon as possible from June 2013. The successful candidate will join a team of computational linguists and computational neuroscientists whose research is focused on using machine learning methods to analyze recordings of neural activity (EEG, MEG and fMRI) to gain insights about conceptual knowledge and other aspects of the cognitive models of agents involved in language use and interaction. This particular position will be in the PRESTO project, a collaboration between CIMEC, Delta Informatica, the University's Computer Science Department, and Fondazione Bruno Kessler (FBK). The objective of the project is the development of training environments based on immersion in virtual reality situations in which the trainee interacts with artificial agents (avatars). The role of the postdoc in the project will be to run experiments testing the emotional plausibility of the artificial agents, and studying the interaction between emotions and decision making in the trainees. The ideal candidate for the position is a cognitive neuroscientist with a strong research curriculum in the use of fMRI and/or EEG to study emotions and interaction. Familiarity with machine learning methods to analyze such data (eg MVPA) a plus. The fellowship has a duration of 1 year with the possibility of renewal for a second year if the results of the first year are satisfactory. The Language Interaction and Computation Lab (CLIC) is a unit of the University of Trento's Centre for Mind/Brain Sciences (CIMEC) (www.cimec.unitn.it) an interdisciplinary Centre for the research in brain and cognition including neuroscientists, psychologists, (computational) linguists, computational neuroscientists, and physicists. CLIC consists of researchers from the Departments of Computer Science and Cognitive Science carrying out research on a range of topics, including concept acquisition and information extraction from very large multi-modal corpora, combining brain data and data from corpora to study cognition, and theoretical linguistics. The official call for the position can be found at: http://www.unitn.it/en/cimec/11882/study-and-job-opportunities Deadline for the application is April 30th. For additional information please contact Massimo Poesio (massimo.poesio at unitn.it), attaching your CV. -- Jorge Jovicich, Ph.D. MR Lab Coordinator Center for Mind Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it http://www.cimec.unitn.it/ http://polorovereto.unitn.it/~jovicich

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problem about cortical area values
by 仙豆 12 Apr '13

12 Apr '13

Dear teacher, I haven't found the page describes the workflow to extract freesurfer cortical area values for a region-of-interest (ROI) defined by myself (used another software), I only saw how to calculate cortical thickness values, please help me~ Thank you very much! Student: He Qin

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mri_glmfit & .nii.gz & FSF_OUTPUT_FORMAT
by Xiangzhen Kong 12 Apr '13

12 Apr '13

Hi, all. I have come across a problem when using mri_glmfit. We know that the output format is controlled by the $FSF_OUTPUT_FORMAT. I have checked that in my environment, $FSF_OUTPUT_FORMAT is nii.gz. But the output fils are all in mgh format. How can I get output files in nii.gz? Thanks! Xiang-zhen 【小孔成像】http://www.conxz.net

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setting thresholds in qdec
by Michael Harms 12 Apr '13

12 Apr '13

Hello, Is it no longer possible to set the Min, Mid, and Max thresholds directly on the Qdec display tab? The only way I seem to be able to change them is via the sliders in the histogram at the bottom, which I don't recall previously being the case. This is Qdec 1.4 (FS 5.2) on a RHEL 5.9 system using freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 distribution. I can't change the FDR "Rate" either. thanks, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu

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LME and clusterwise correction
by Benjamín Garzón 12 Apr '13

12 Apr '13

Hi, I am doing a longitudinal analysis using the LME toolbox, and I would like to perform a clusterwise correction for multiple comparisons. Would it be correct to use mri_surfcluster on the resulting maps, or do you suggest any alternative otherwise ? I can only find functions implementing FDR correction in the toolbox. Thanks, Benjamin -- Benjamín Garzón, Ph.D. Karolinska Institutet Department of Neuroscience Retzius Väg 8 17177 Stockholm (SWEDEN)

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bblabel values for DLPFC
by Anupa AV 12 Apr '13

12 Apr '13

Dear All, I 'd like to know the xmin, ymin and zmin for creating DLPFC label using bblabel string. I want to make a coronal cut at y=26 for seperating DLPFC from premotor cortex. I tried by giving a value of xmin=0, ymin=26 and zmin= 0. I'd like to know whether I'm on right track. Thanks in advance for your response.

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Fwd: Sample size estimation from LME models
by nicolas guizard 11 Apr '13

11 Apr '13

Hi, I am new to Freesurfer and the Linear Mixed Effects (LME) Models packages. And I would like to compute sample size from volumetric measures for 2 groups. I followed the longitudinal example provided in the wiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#a.29Univa…) with the ADNI example. But I am not sure what to use for the "common random effect design matrix" Zi and "column" ZiCol with the lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,dr,pw,alpha,gr_pr) function: Here is what I do in matlab: > load('ADNI791_Hipp_and_Entorh.mat') > total_hipp_vol_stats = lme_fit_EM(X_Hipp,[1,2],Y(:,1)+Y(:,2),ni); > lme_plannedSampleSize(total_hipp_vol_stats.X,[1,2] ,total_hipp_vol_stats.Dhat,total_hipp_vol_stats.phisqhat,1,.2,.8,0.05) > ans = 1.0e+07 * 1.3584 0.0154 0.0154 0.0100 Is that right? Regards, Nicolas

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"final" skull-stripped file?
by Marco Loggia, PhD 11 Apr '13

11 Apr '13

Dear all, what is the 'best' skull stripped file produced by freesurfer? From what I see, it would seem to be 'brainmask'. However this file -if I understand correctly- is produced in the very first stages of recon-all, and therefore does not take advantage of the detailed reconstruction of the brain 'borders' which is achieved in the subsequent stages of recon-all. For this reason, I have been masking my brainmask.mgz file with a binary file created using the aparc+aseg file (which labels only the brain), slightly smoothed to be conservative in the stripping. Or is there already a file skull-stripped this way? Thanks, Marco ______________________________ Marco L. Loggia, PhD Instructor in Radiology Harvard Medical School Massachusetts General Hospital 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 726-7422 marco(a)nmr.mgh.harvard.edu

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Re: [Freesurfer] Transform SMOOTHWM to DTI B0
by Daniel Haehn 11 Apr '13

11 Apr '13

Thanks, Satra! This is helpful!! On Thu, Apr 11, 2013 at 12:32 PM, Satrajit Ghosh <satra(a)mit.edu> wrote: > hi all, > > here you go: > > https://gist.github.com/satra/1451812 > > this goes from trackvis streamlines to freesurfer surface space. you > would do the inverse of this transform to go the other way. > > cheers, > > satra > > On Thu, Apr 11, 2013 at 12:26 PM, Daniel Haehn < > daniel.haehn(a)childrens.harvard.edu> wrote: > >> Hi Satra et al, >> >> thanks a lot and it would be great if you could find some code! >> >> In the meantime, I tried the following based on information from Kiho >> Im: >> >> # we have to first remove transformation of 'vertex to RAS' embedded in >> smoothwm surface. >> mris_transform lh.smoothwm identity.xfm ./lh.smoothwm.clean >> >> # then use the flirt T1-to-b0 matrix converted from .mat to .xfm format >> to transform the surface >> mris_transform lh.smoothwm.clean T1-to-b0.xfm lh.b0.smoothwm >> >> And of course: it didn't work.. In the attached screenshot, the red >> surface is the original one which kind of fits the b0 image but not very >> well (it obviously fits the original T1 very well). The blue is the >> transformed surface (lh.b0.smoothwm) and is completely off. >> >> [image: Inline image 1] >> >> Do you know what I could be doing wrong? I also attached both >> tranforms. Maybe I just converted them wrong. >> >> Thanks!! >> Daniel >> >> >> On Thu, Apr 11, 2013 at 10:53 AM, Satrajit Ghosh <satra(a)mit.edu> wrote: >> >>> hi dan, >>> >>> if you use bbregister to match the DTI b0 to freesurfer space, then >>> you can transform the surface back (no guarantees on the tesselations >>> though i think). the only additional component here would be a tkr >>> transform that's based on the conformed space. i might even have some >>> python code lying around to do this. i'll take a look. >>> >>> cheers, >>> >>> satra >>> >>> On Thu, Apr 11, 2013 at 10:40 AM, Daniel Haehn < >>> daniel.haehn(a)childrens.harvard.edu> wrote: >>> >>>> Hi all, >>>> >>>> I want to transform the Freesurfer Smoothwm surfaces to DTI B0 space. >>>> >>>> I found >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransformsbut this describes transforming the B0 to T1 space and then match the >>>> surfaces. I don't want to change the DTI B0 image. >>>> >>>> What is the best way to do that? >>>> >>>> Thank you very much! >>>> Daniel >>>> >>>> -- >>>> Daniel Haehn >>>> FNNDSC / BCH >>>> +1.857.218.5140 >>>> >>>> _______________________________________________ >>>> 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. >>>> >>>> >>> >> >> >> -- >> Daniel Haehn >> FNNDSC / BCH >> +1.857.218.5140 >> > > -- Daniel Haehn FNNDSC / BCH +1.857.218.5140

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DTI: problems with (high) FA values
by Rotem Saar 11 Apr '13

11 Apr '13

Hi Douge, In your last reply to my email (that contained questions regarding some really high FA values - see recent emails below), u asked me to write u the first value in register.dat.mincost - I'm copying the line I have: 0.280554 140.210312 156.795241 11.152485 Does this takes us one step further towards understanding the problem and its solution ? Thanks for your time, Rotem On 04/07/2013 06:48 AM, Rotem Saar wrote: > Hi Doug, > > Thanks for your answer. > I changed the last step as u suggested, but I think I need to clarify > my question: > Indeed values of the CC looks OK, but don't u think other values, like > the ventricles are too high ? *yes, the ventricles look too high* > > When I first run the script, I got all values and looked the the CC - > it looked fine. Then, I wanted to validate with some other regions, > just to show that I got the appropriate (low) FA values for regions I > don't expect to see high values in - and things looked odd (too high). > > I remember Bruce also writing me that the values seems a little high, > but we didn't further discuss. I read the following this link: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual > > "The CC has an average FA of about 0.75, gyral parcellations are about > 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as > expected because the CC is highly directional with no crossing fibers > so we would expect the CC to have the highest FA. The gyral white > matter is also directional but has fibers crossing in them, so one > expects the FA to be lower than CC. The gray matter (putamen) is still > lower. The ventricle has no fibers, so we expect it to have the lowest > FA". > > All my values are above 0.4.... > > Additionally, if in the last step I'm writing --seg > /usr/local/freesurfer/ subjects/Rotem_try/mri/wmparc.mgz > > why do I get 182 regions ? in my wmparc.stats I have only 70... The wmparc includes all the subcortical and cortical regions too, but only the WM regions are reported in the wmparc.stats file. *To only report the WM regions, add to mri_segstats --ctab $FREESURFER_HOME/**WMParcStatsLUT.txt* > > I'm probably doing something wrong, but I can't really point to the > problem, thus asking for your help. *I don't know either. If I had to guess, I'd say it is a registration problem. What is the first value in register.dat.mincost?* doug > > Attached is the table again, > > Thanks > Rotem > > > The values look about right in the table. Your pipeline looks ok, > thought the last step uses fa_FOLDER-NAME.mask.nii instead of the > output > of mri_vol2vol (fa_FOLDER-NAME.nii). > doug > > > > On 03/17/2013 02:16 AM, Rotem Saar wrote: > > > > Hi all, > > I run into somthing that seems odd to me and wanted to consult - > > I run the following script for getting the FA values from my DTI > > scans: > > > > 1) dt_recon --i > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s > > FOLDER-NAME --o > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec > > 2) tkregister2 --s fsaverage --surf white --reg > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg > > --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii > > 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz > > -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > > -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii > > -fthresh 0.2 -fmax 1 > > 4) mri_vol2vol --mov > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s > > FOLDER-NAME --interp nearest --o > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > > --reg > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > > 5) tkregister2 --mov > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > > --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz > > --reg > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg > > 6) mri_segstats --seg > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab > > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii > > --sum > > > /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME > > > > > > I got a table with all the FA values (see attached), for each > > segment, but I suspect a problem: I think that the values > are too > > high (I set the threshold to 0.2-1), am I right ? > > Can u guide me regarding what I can do to solve the problem ? in > > addition I attached a figure of the corpus-callosum, in > which I'm > > interested - i't seems that the green area in not big enough, is > > this fixable ? > > > > Thanks ! > > > > Rotem > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Freesurfer April 2013