Freesurfer

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30132 discussions

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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recalculate mean cortical thickness and/or regional thickness using a SD threshold or exclusion mask
by lindsay hanford 04 Jan '19

04 Jan '19

External Email - Use Caution Hello Freesurfer Community, I am wondering if it is possible to recalculate cortical thickness metrics (perhaps using mri_segstats or aparcstats2table) while including either a SD threshold or an exclusion mask. Using mri_surf2surf to register scans to the same space and then mri_surface_stats to create the std maps I have been comparing the variability of cortical thickness across the cortex for multiple scans across the same subject. From this I can determine a SD threshold point (0.5 say) or create a mask that includes all regions above that threshold. I would like to use this to threshold the regions showing the highest variability out of my calculations for mean hemispheric thickness and also regional thickness. Is there a way to use an SD threshold within mri_segstats or aparcstats2table? Otherwise apply a mask image to exclude specific vertices? Thank you in advance, Lindsay

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gammafit flag in mkanalysis-sess
by Nasiriavanaki, Zahra 04 Jan '19

04 Jan '19

Hi Freesurfers I have a few questions about gammafit flag in mkanalysis-sess command and I appreciate if you could respond whenever you had time. -How should we decide which function is best to apply on hemodynamic response signal? I have used both spmhrf and gammafit and I see slightly different results. -Does Freesurfer has a default function that applies on hemodynamic response signal if I don't use these flags? -Where should I get gfdelta and gftau from? Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Freesurfer 5.3 vs 6
by Nasiriavanaki, Zahra 04 Jan '19

04 Jan '19

Dear Freesurfers Hi I have a bunch of data that is preprocessed in Freesurfer version 5.3 (both recon and preprocessing). My question is whether I can do the first level and group analysis on this data using Freesurfer version 6? Or should I do everything in version 6 from the beginning? I need to compare their results with my other data set in FS v 6. Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Postdoctoral Fellowship: Neurobiology of Reading {Disarmed}
by Meaghan Perdue 04 Jan '19

04 Jan '19

External Email - Use Caution *Postdoctoral Fellowship: Neurobiology of Reading* The LandiLab (PI: Nicole Landi https://landi.lab.uconn.edu/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__landi.lab.uconn.edu_&d…>) at Haskins Laboratories and the University of Connecticut is seeking to hire a full-time postdoctoral research fellow. Haskins Laboratories *https://haskinslabs.org/ <https://haskinslabs.org/> *is located in New Haven, CT and is closely affiliated with Yale University and the University of Connecticut. This postdoc will join an NIH funded project investigating the neurobiological basis (brain structure, genetics) of reading. The successful applicant will be responsible for conducting and interpreting analyses of neuroimaging data (primarily gray matter structure and diffusion imaging). This position is part of a multi-site project (Haskins Laboratories, Yale University, University of Houston, Baylor College of Medicine, Florida Center for Reading Research) that is analyzing neuroimaging and genotyping data from 9000+ individuals to explore gene-brain-behavior relationships. *Required qualifications:* · PhD or equivalent in Psychology, Neuroscience, Cognitive Science, Computer Science, or related field · Experience analyzing neuroimaging data · Experience with one or more imaging analysis packages (e.g., FSL, SPM, AFNI, FreeSurfer) · Programming skills, including knowledge of at least one language and Unix commands · Proficiency with writing academic manuscripts · Leadership, communication, and organizational skills *Preferred qualifications:* · Experience analyzing diffusion weighted imaging data · Experience with advanced neuroimaging analysis techniques, e.g., independent components analysis, functional and context-dependent connectivity, VBM, machine learning · Demonstrable interest in the neurobiology of language and/or reading · Familiarity with genetic analyses or imaging genetic analyses This postdoctoral scholar will work with an interdisciplinary and highly collaborative team of PIs and affiliated scientists from the *LandiLab <https://urldefense.proofpoint.com/v2/url?u=https-3A__landi.lab.uconn.edu_&d…>* (PI: Nicole Landi, University of Connecticut, Haskins Laboratories, Yale Child Study Center) and the *GENESIS <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.uh.edu_class_psycho…>* lab (PI: Elena Grigorenko, University of Houston & Baylor College of Medicine, Houston TX).This position is based at Haskins Laboratories (New Haven, CT), but will coordinate with research partners at multiple locations. Interested candidates should send 1) a CV; 2) the names and contact information of three references; and, 3) a cover letter to Dr. Nicole Landi at *Nicole.Landi(a)UConn.edu <Nicole.landi(a)uconn.edu>* . This position will remain open until filled; desired start date is Spring 2019. Salary will be commensurate with NIH postdoctoral funding levels. Haskins Laboratories is an equal opportunity employer. -- Meaghan Perdue PhD Student Developmental Psychology Neurobiology of Language University of Connecticut Bousfield A302

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