Freesurfer November 2017

freesurfer@nmr.mgh.harvard.edu

110 participants
198 discussions

Reference on measures computed by dt_recon
by Mehta, Chintan 11 Nov '17

11 Nov '17

Dear FreeSurfer users, I'm using FS 6.0 and have computed summary statistics for different measures including adc, ivc, volume ratio, and radial diffusivity. Is there a reference on how the FreeSurfer software computes these measures (i.e. mathematical formulas)? Thank you. Best, Chintan

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Destrieux (aparc2009) atlas in MNI 2mm space?
by Daya P 11 Nov '17

11 Nov '17

Hi All, How can I get the aparc2009 atlas in MNI 2mm space? I want the labels to be in MNI 2mm space. Are there Destrieux labels in 2mm space already somewhere? I could only find them in 1mm ... Thank you, Daiana

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QDEC
by Kinzel, Phillipp 10 Nov '17

10 Nov '17

Hi, I have problems loading project files in QDEC. I get the following error: Loading data table /tmp/qdec_project_archive/qdec.table.dat... ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat Error loading the project file. I would be greatful for any advice. Best, Philipp

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Re: [Freesurfer] dt_recon and Tracula
by Mehta, Chintan 10 Nov '17

10 Nov '17

Dear Doug, I figured out the mistake I was making, which was that I ran: > freeview -v orig.mgz wmparc2diff.mgz:colormap=lut lowb.nii.gz:reg=register.dat -f lh.white:edgecolor=green rh.white:edgecolor=green -viewport coronal & Here the lowb, orig, and white surfaces were consistent. Since wmparc2diff.mgz is in diffusion space, it was bound to be mismatched with the lowb & white surface lines. When replacing wmparc2diff.mgz with wmparc.mgz, it is no surprise that there is a much better match between the white matter parcellation & lowb. There is a very good match between lowb and wmparc2diff, when running, per the documentaiton, > freeview -v lowb.nii.gz wmparc2diff.mgz:colormap=lut -f lh.white:edgecolor=green rh.white:edgecolor=green -viewport coronal & However, the lh.white and rh.white surfaces do not change. I suppose this is because those surfaces are not for volumes registered to the diffusion space. Does that make sense? Or would the lh.white and rh.white automatically adjust to diffusion space? Thank you. Best, Chintan

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Flux Satellite Conference
by Margaret Sheridan 10 Nov '17

10 Nov '17

*UNC Chapel Hill, in association with The Flux Society, *will host a conference highlighting research using large, representative, or publicly available datasets to investigate developmental cognitive neuroscience. This conference will address the unique ability of larger, more representative datasets–and particularly those with multiple time points–to ask questions about brain development that have historically been impossible to address with the smaller, cross-sectional samples utilized in most neuroimaging research studies. The focus will be on research leveraging large datasets to understand functional and structural brain development in the context of connectomics, environmental influences on brain development, and typical and atypical trajectories of brain development. The conference will take place at UNC Chapel Hill May 6 – May 8, 2018. Abstract submission deadline: 1/22/18 Registration opens: 2/1/18 For more information and to submit your abstract, visit: http://fluxsatellite.web.unc.edu/ You may also sign up for the conference listserv on the site to receive future announcements.

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Re: [Freesurfer] Trans. : VBM question
by Douglas N Greve 10 Nov '17

10 Nov '17

Hi Mohamed, please remember to post to the list. As for your question, what aparc files are you looking at? Those measures are in, eg, lh.aparc.stats On 11/06/2017 04:05 AM, Mohamed Ali Bahri wrote: > > Dear Douglas, > > Many thanks for your answer! > > We are interested on one region belonging to the Brodmann areas > "Perirhinal". Cortical thickness as well as volume values appear on > the BA stat list and not on the aparc or aseg lists. Does the > ROI-based analysis could be used for this BA region? > > Best regards, > > Mohamed > > > On 05/11/2017 18:46, Douglas Greve wrote: >> >> Do you just want to do an ROI analysis? Or do you want to do a >> voxel-based analysis? If ROI-based, then follow the steps on the ROI >> tutorial (ie, aparcstats2table and mri_glmfit with --table input). >> >> >> On 11/3/17 4:08 PM, Bruce Fischl wrote: >>> Hi Mohamed >>> >>> Doug is away this week and can give you a more details answer next >>> week. Certainly you could use mris_anatomical_stats -l <BA label >>> file name> to compute the volume/thickness/area for each subject >>> then do whatever GLM analysis you want outside of FS. >>> >>> cheers >>> Bruce >>> >>> >>> On Fri, 3 Nov 2017, m.bahri(a)uliege.be wrote: >>> >>>> Dear All, >>>> Does anyone have an answer to the following VBM question? >>>> >>>> Many thanks in advance, >>>> Regards >>>> >>>> -----Mail original----- >>>> De: "Mohamed Ali Bahri" <m.bahri(a)uliege.be> >>>> À: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> >>>> Envoyé: Jeudi, Novembre 2, 2017 06:08:33 PM >>>> Objet: [Freesurfer] VBM question >>>> >>>> Dear Freesurfer users, >>>> >>>> I would like to study the between groups changes of volume/cortical >>>> thickness of one region (Perirhinal) belonging to the Brodmann >>>> areas. I >>>> tried to do that with Qdec tool but unfortunately Qdec does not >>>> load the >>>> Brodmann areas stat list. I am wondering if I could use the GLM >>>> formalism with of course regressing out the ITV. Any suggestion/advice >>>> will be very welcome. >>>> >>>> Many thanks in advance, >>>> >>>> Best regards, >>>> >>>> Mohamed >>>> >>>> >>> >>> >>> _______________________________________________ >>> 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 >> >> >> 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. Mohamed Ali Bahri, > 1er Logisticien de Recherche, > Cyclotron Research Centre, > University of Liège, Belgium > m.bahri(a)uliege.be -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Optseq and de convolution for rapid designs
by fmri2013 10 Nov '17

10 Nov '17

Many thanks Douglas If I optimise my design using Optseq, do you know if this de convolution process is implemented in SPM or any other software? and it is part of the processing behind th3 scenes? Or do I have to account for this using a specific software. Aser Sent from my Samsung Galaxy smartphone. -------- Original message --------From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Date: 10/11/2017 19:24 (GMT+00:00) To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Optseq and de convolution for rapid designs It is because the random jitter creates differential amounts of overlap. Imagine if you have A=C+D and B=C-D. You know A and B, but you want C and D. You have two equations and two unknowns, so you can solve for C and D from A and B eventhough C and D "overlap" in A and B and you never see C or D by themselves. This is a type of deconvolution On 11/10/17 11:38 AM, Aser A wrote: Hi all I used Optseq to optimize rapid event designs with multiple conditions . I have a theortical question : how it is possible to distingwoh the close by trials ? Is it by de convoution ? How is it possible to deal with overallped trials ? Is it because the conditions are random so that when averaging them the distingwoh is possible? Many thanks Aser _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Creating cached versions of Xhemi registrations
by Mehta, Chintan 10 Nov '17

10 Nov '17

Dear Doug, I think that is essentially what I figured. Based on remarks in other posts, my steps for evaluating laterality index entail applying: (1). Apply mri_preproc for each subject $SUB and $meas (area or thickness) individually using -xhemi flag but without any paired differences via: > mris_preproc --target fsaverage_sym --hemi lh --xhemi --srcsurfreg fsaverage_sym.sphere.reg --meas $meas --out ${SUB}_out.mgh --s $SUB Result is a surface file with two volumes (lh and xhemi-lh) called ${SUB}_out.mgh for each subject. (2). Smooth the two volumes in ${SUB}_out.mgh at a given $fwhm (5, 10, 15...): > mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm $fwhm --i ${SUB}_out.mgh --o ${SUB}_out-sm${fwhm}.mgh to create a surface file with two volumes whose values are smoothed at fwhm = $fwhm. (3). Compute laterality index over the surface for each subject via paired-diff-norm: > mri_concat ${SUB}_out-sm${fwhm}.mgh --paired-diff-norm --o ${SUB}_latIndex-sm${fwhm}.mgh where ${SUB}_latIndex-sm${fwhm}.mgh is the surface file with laterality index for subject $SUB (after smoothing measures over left and right hemispheres). (4). Stack laterality indices for each subject in sample G (of n subjects) into a single mgh, > mri_concat --i SUB1_latIndex-sm${fwhm}.mgh --i SUB2_latIndex-sm${fwhm}.mgh ....... --i SUBn_latIndex-sm${fwhm}.mgh --out --i sampleG_latIndex-sm${fwhm}.mgh. (5) Run glm with designed matrix sampleG_design.txt containing n rows of covariates for SUB1, SUB2, ..., SUBn (in order) via: > mri_glmfit --y sampleG_latIndex-sm${fwhm}.mgh --X $sampleG_design.txt --no-rescale-x --glmdir glm_sampleG --C con1.mat --surf fsaverage_sym lh The whole purpose of this exercise + question was that I need to fit the GLM over subsets of the sample for sensitivity analysis to determine whether significance for the contrast in con1.mat (say slope of an IV, such as age) depends on patterns of based on demographics groups (such as gender). I suppose alternatively, I could just as well fit another GLMs with a design matrix modeling interactions between age and gender to make my evaluation, over the same set of stacked surfaces for the full sample. Thank you. Best, Chintan 1.

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Re: [Freesurfer] dt_recon and Tracula
by Mehta, Chintan 10 Nov '17

10 Nov '17

Dear FreeSurfer users, Sorry for adding the questions, I found most of my answers at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0#dMRIData… I used FreeView and found that registrations of the lowb.nii, orig.mgz, lh.white, and rh.white aligned very nicely. Alignments of lowb.nii with wmparc.mgz and aparc+aseg.mgz are also very nice. However, I'm finding that resampling wmparc.mgz to diffusion space via mri_vol2vol (inverse of dti/register.dat with nearest neighbor interpolation) yields poor alignments with the white surfaces and lowb.nii. Is this inevitable if there is a difference in resolutions between DWI and T1-weighted MRI? Thank you. Best, Chintan

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Optseq and de convolution for rapid designs
by Aser A 10 Nov '17

10 Nov '17

Hi all I used Optseq to optimize rapid event designs with multiple conditions . I have a theortical question : how it is possible to distingwoh the close by trials ? Is it by de convoution ? How is it possible to deal with overallped trials ? Is it because the conditions are random so that when averaging them the distingwoh is possible? Many thanks Aser

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Freesurfer November 2017