Freesurfer January 2019

freesurfer@nmr.mgh.harvard.edu

119 participants
167 discussions

LME
by Tefera, Getaneh B 07 Jan '19

07 Jan '19

Dear Freesurfer experts, I have three groups g0, g1, and g2. I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ ... The slope of g0 : 0 1 0 0 0 0 The slope of g1: 0 1 0 1 0 0 The slope of g2: 0 1 0 0 0 1 The slope difference between g0 and g1: 0 0 0 1 0 0 The slope difference between g0 and g2: 0 0 0 0 0 1 The slope difference between g1 and g2: 0 0 0 -1 0 1 1) Is this contrast matrix correct to observe pairwise slope difference? In the tutorial the contrast matrix C = [zeros(3,3) [1 0 0 0 0; -1 0 1 0 0; 0 0 -1 0 1] zeros(3,6)] 2) Is it necessary to combine contrast matrix of the pair difference the same as the tutorial? If so, my contrast matrix can be C=[0 0 0 1 0 0; 0 0 0 -1 0 1] 3) How can we interpret the result for this contrast matrix? 4) How can I obtain B1, B2, ... ? [sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,... dr,pw,alpha,gr_pr) 5) For sample size calculation how can I get Dhat ( Estimated random effects covariance matrix) and phisqhat (Estimated intra-subject variability)? With regards Getaneh

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Calculating volume using pial files
by Song, Da-Yea 07 Jan '19

07 Jan '19

External Email - Use Caution Hello, I'm trying to calculate the volume using pial files. Is there a way to convert ?h.pial files into nii formats? Or is there a command to calculate the volume? Thank you so much in advance for your help. Best regards, Da-Yea Song ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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(no subject)
by Larissa Bechtle 07 Jan '19

07 Jan '19

External Email - Use Caution Hi everybody, after finishing my group analysis I am currently trying to run a ROI analysis. However I have some problems/general questions. I am trying to draw a ROI on fsaverage in order to use the mri_label2label command afterwards. I opened Freeview, clicked on "load surface" first and then chose lh.inflated_avg (fsaverage -> surf) which worked fine but I cant choose "New ROI" (in order to crate the ROI). So is it possible to draw a ROI when focussing only on the surface? And if this is the case why cant I? Did I chose the wrong file? I am really thankful for any help!! Larissa

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[PETsurfer] Use of MGX and RBV partial volume correction
by Matthieu Vanhoutte 07 Jan '19

07 Jan '19

External Email - Use Caution Dear Freesurfer's experts, I tried to use PETSurfer to correct partial volume effect on my FDG PET images, testing both Muller-Gartner and RBV corrections. I ran the commands specified in PETSurfer website and used the two following commands for both MGX and RBV corrections respectively: mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51 --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o ./gtmpvc.output mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51 --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o rbv.output.orig 1) However, I found that cortical output mgx.ctxgm.nii.gz of MGX correction encompass more than just GM and values at the boundaries of mgx.ctxgm.nii.gz seem to me very high or aberrant. 2) Concerning RBV correction, output rbv.nii.gz seems to me following more precisely the GM ribbon. However contrary to what is said in PETSurfer website, rbv.nii.gz seems to be in the anatomical space (not in native PET) at the resolution of gtmseg.mgz. How then map rbv.nii.gz to the anatomical space when mapping the volume to the surface ? 3) What are the advantages/inconveniences of RBV vs GMX ? 4) Would it be beneficial to upsample native PET to the anatomical resolution before launching gtmpvc in order to preserve the high resolution of the anatomical tissues during partial volume correction ? Could you have a look at and give me back your opinion on these questions ? I could send the associated files if needed. Thank you. Best, Matthieu

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Robust PET signal projection
by Matthieu Vanhoutte 07 Jan '19

07 Jan '19

External Email - Use Caution Dear Freesurfer's experts, In order to have a robust PET signal projection, is it possible compute the projected PET signal as a weighted average of the PET signal intersecting with the surfaces ranging from 35 to 65% of the cortical tickness with a step t=5% ? More weight would be given to the surfaces located near the mid distance between the pial and white surfaces as they have a higher probability to be well located within the cortex (using a normal distribution for example). Thank you for helping. Best, Matthieu

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Setting the origin in native space
by Nillo, Ryan Michael R 06 Jan '19

06 Jan '19

External Email - Use Caution Hello FreeSurfer users, I want to use the suit software to segment the cerebellum, however the software requires the origin be set at the anterior composure. I know the Talairach image’s origin is set at the anterior commisure and that there is a Talairach transformation in mri/transforms. Is there a way to use this information to set the origin to the anterior commisure in the native space image? Thanks in advance, Ryan Nillo Staff Research Associate UCSF Department of Radiology and Biomedical Imaging

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FSGD file
by Raffaele Dubbioso 06 Jan '19

06 Jan '19

External Email - Use Caution Dear Freesurfer team, I'm running a group analysis where I'd like to compare myelination between two groups regressing out cortical thickness. Unfortunately I get always the same error message: dimension mismatch between X and contrast group.diff.mtx X has 3 cols, C has 4 cols. Is my group.mtx correct? My command line is: mri_glmfit --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd thickness.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --C group-x-thick --Cg1g2.intercept.mts --C g1g2.thick.mtx --surf fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness.glmdir My group_diff.mtx: 1 -1 0 0 This is my FSGD FILE: GroupDescriptorFile 1 Title Myelin Class HC Class CMT Input fs_VF HC ........ Thank you very much for your help Best regards, Raffaele

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Re: [Freesurfer] PSIR to refine pial surface?
by Vriend, C. (Chris) 05 Jan '19

05 Jan '19

External Email - Use Caution Hi Bruce, So sorry, your reply totally escaped my attention! Attached a screenshot of a PSIR scan. Do you think that Freesurfer can work with these contrasts? Thanks, Chris [cid:image002.png@01D49944.2B806E50] Van: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> Namens Vriend, Chris Verzonden: donderdag 16 augustus 2018 8:12 Aan: 'freesurfer(a)nmr.mgh.harvard.edu' <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Onderwerp: [Freesurfer] PSIR to refine pial surface? External Email - Use Caution Dear Freesurfers, In our centre we acquire T1 MPRAGE scans and phase-sensitive inversion recovery (PSIR) scans. Because of its better contrast between brain and non-brain I thought that we could use this scan in the freesurfer pipeline (v6.0) to refine the pial surface. I've already tried to use the -FLAIRpial flag (even though it's obviously not a FLAIR) but that actually makes it worse. Does anyone know if it is at all possible or have any experience with using PSIR scans in freesurfer and can point me in the right direction? Thanks, Best wishes Chris [cid:image001.png@01D40E30.9B2FFEE0] Dr. C. Vriend | Assistant Professor Anatomy & Neurosciences - section Neuropsychiatry | Psychiatry Location VUmc | O|2 13W09 | De Boelelaan 1118, 1081 HZ Amsterdam T: + 31 (0) 6 25 69 49 12 | E: c.vriend(a)vumc.nl<mailto:c.vriend@vumc.nl> P: p/a sec. Anatomy & Neurosciences, postbus 7057, 1007 MB Amsterdam www.amsterdamumc.nl<http://www.amsterdamumc.nl> | www.vumc.nl<http://www.vumc.nl/> | http://www.neuroscience-amsterdam.nl/?page_id=189 _____________________________________________________ VUmc disclaimer: www.vumc.nl/disclaimer<http://www.vumc.nl/disclaimer>

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Tracula longitudinal tract reconstruction problems
by Nick Vogt 05 Jan '19

05 Jan '19

External Email - Use Caution Dear TRACULA experts, I’m hoping someone can provide some insight about why I’m having a little trouble with tract reconstruction using the longitudinal TRACULA pipeline. As background, the analysis contains 75 middle-aged, cognitively-unimpaired subjects with two time points of imaging (T1 and multi-shell DWI) separated by approximately 2 years. The T1 images have been sent through the longitudinal Freesurfer (6.0) pipeline successfully. The multi-shell data is 2x2x2mm and has 3 b-values (6 b=0, 9 x b=500, 18 x b=800, 36 x b=2000). Prior to use in TRACULA, each DWI volume is noise and Gibbs ringing corrected in MRTrix3, then motion and eddy current corrected using ‘eddy’ in FSL. I then run the longitudinal TRACULA pipeline according to the instructions online, and everything completes, but some of the tract posterior distributions look a little funny. I’m attaching some images of the CST where the right side is good but the left side is weird. In case those don’t make it through, here’s a description: While some tract posterior distributions look like good, smooth distributions, some of the tract distributions have a distinct high-value single-voxel running through them. My understanding is that if a tract just has this single line, it means there was an issue with the path initialization (this also occurs in my dataset occasionally), but what about if a tract has both a semi-decent looking distribution, but also has this single-voxel high probability tract? Is there a step or an output that I could check to help understand why this is occurring? I’ve checked the DWI to T1 bbregister outputs, and those look honestly pretty good (considering this DWI data is non EPI-distortion corrected using field maps or topup). For the longitudinal TRACULA pipeline, what’s the best way to check if the control points calculated from trac-all -prior are good? In cross-sectional TRACULA, the control point coordinates are output in diffusion space (which seems easy to check), but in the longitudinal they’re only in MNI or anatorig (which I assume means base template?). Any ideas? Thanks in advance! Nick

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run preproc-sess wrongly and some other question about FSFAST
by xi star 05 Jan '19

05 Jan '19

External Email - Use Caution dear experts, I try to run FSFAST with a block design paradigm. there a few question i can figure out on my own. the 1st question: the directory structure was set as: -meridian --sess01 --bold -001 -002 --lpx (subjectname folder contian anatomical data run by "recon-all" previously) --subjectname (a file) Since there was only one subject, i didn't create sessid. then i run: preproc-sess -s sess01 -fsd bold -per-run -fwhm 5 -sliceorder odd -surface fsaverage lhrh -init-fsl but i got this warning (the full log is in the attachment): if: Expression Syntax. I wonder what's wrong with the command. -------------------------------------------------- the 2nd question: following the website http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastLinkAnatData I create a subjectname file which contains: cd $SUBJECTS_DIR/$SUBJECT echo "$SUBJECT">>lpx is it work? How to link the functional data to anatomical data? -------------------------------------------------- the 3rd question: i use a stationary wedge stimuli to activate the horizontal and vertical meridian representations in visual cortex. the design parameters: TR=2, 8hz flickering checkerbords, 16s fixation followed by 4 conditions（20s each）, each condition show a wedge in up, down, left and right meridian, 3 repetitions the meridian.par was set as: 0.0 0 16.0 1.0 fix 17.0 1 20.0 1.0 up 37.0 2 20.0 1.0 down 57.0 3 20.0 1.0 left 77.0 4 20.0 1.0 right 97.0 1 20.0 1.0 up 117.0 2 20.0 1.0 down 137.0 3 20.0 1.0 left 157.0 4 20.0 1.0 right 177.0 1 20.0 1.0 up 197.0 2 20.0 1.0 down 217.0 3 20.0 1.0 left 237.0 4 20.0 1.0 right my question is, in the first-level analysis, is right to write the command: mkanalysis-sess \ -analysis meridian \ -event-related -paradigm meridian.par \ -TR 2 -nconditions 4 \ -mcextreg best, star

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Freesurfer January 2019