Freesurfer

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30089 discussions

manual edits
by John Anderson 30 May '18

30 May '18

External Email - Use Caution Dear FS experts, My question is very basic and I appreciate your help. I ran recon-all on a low quality T1 image. I'd like to fix the segmentation error (attached). Wm.mgz seems to be fine and the wm intensity is ~110. Can this error be fixed by setting control points in the region then re run the command : recon-all -s <subject> -autorecon2-cp -autorecon3 Thanks for any advice John

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QDEC, order of groups for interpretation of results
by Avi Gharehgazlou 30 May '18

30 May '18

External Email - Use Caution Hello experts, I am using QDEC to compared LGI values between groups (typically develping and ASD). I made a "diagnosis.levels" file, putting my 2 groups in the following order: Typically developing ASD However, when I upload my qdec.table.dat file on QDEC, it recognizes my diagnosis levels in the following order: 1 Diagnosis discrete 2 1 ASD 2 TD 2 age continuous 0 3 SA continuous 0 Will you please tell me which order I have to interpret my results according to? i.e. significant regions in Blue colour would indicate less LGI in TD relative to ASD (if I consider TD first then ASD- like the order I designed my diagnosis.levels file) BUT blue regions would mean less LGI in ASD vs. TD if I consider order my groups appear on QDEC when I upload qdec.table.dat file. Would appreciate your reply, Avi

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Open Position in Neuroimaging: Barcelonaβeta Brain Research Centre – Pasqual Maragall Foundation, Barcelona, Spain
by Juan Domingo Gispert López 30 May '18

30 May '18

External Email - Use Caution *Doctoral Position in the Neuroimaging Research Group in the Barcelonaβ**eta Brain Research Centre – Pasqual Maragall Foundation, Barcelona, Spain* Barcelonaβeta Brain Research Center (BBRC) invites applications for a full-time graduate student position within the context of the AMYPAD project, as part of the Neuroimaging Research Group from the Alzheimer’s Prevention Program. *Principal Responsibilities:* In collaboration with other AMYPAD partners, the responsibilities for this position includes: · Develop technical procedures to enhance amyloid PET quantification; · Modelling of amyloid PET data in disease progression models; · Participate in analysis and publication of results; · Participate in regular meetings with our partners throughout Europe; · Engage in the management of the project; *Required Qualifications:* · MSc in Engineering, Physics, Neuroscience or any other related field · Experience in analysis of medical brain images · Excellent communication and writing skills in English; · Ability to think independently and work collaboratively. *Benefits:* · Starting date: Sept 2018. · Possibility of undergo a PhD programme · The position is scheduled initially for three years (open to renewal). · Salary will depend on experience. *Additional Information:* To apply, please submit a single PDF file containing the following: 1) Cover letter describing research interests and relevant background; 2) CV; 3) The names of up to three individuals who could provide reference letters. All files or inquiries should be submitted electronically to: rh(a)barcelonabeta.org. For more information: https://fpmaragall.org/wp-content/uploads/2014/07/Job- advert-Doctoral-Position-in-Neuroimaging.pdf -- *Juan Domingo Gispert*Group Leader - Neuroimaging *BarcelonaBeta* * Brain Research Center (BBRC) *jdgispert(a)barcelonabeta.org T. (+34) 93 326 31 67 C/ Wellington, 30 <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> 08005 Barcelona <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> www.barcelonabeta.org www.fpmaragall.org ------------------------------ Aquest missatge i els seus annexos poden contenir informació confidencial i exclusiva per al destinatari. El seu contingut no constitueix un compromís per part de l'emissor. Si rep aquest missatge per error, si us plau elimini’l sense revisar-lo ni reenviar-lo i notifiqui-ho al remitent. Gràcies per la seva col·laboració. *Este mensaje y sus anexos pueden contener información confidencial y exclusiva para el destinatario. Su contenido no constituye un compromiso por parte del emisor. Si recibe este mensaje por error, por favor elimínelo sin revisarlo ni reenviarlo y notifíquelo al remitente. **Gracias por su colaboración. *This message and attachments may contain confidential and exclusive information intended only for the individual named. The content of this message does not imply any commitment by the sender. If you have received this e-mail by mistake, please delete it before reading or distributing and notify the sender. Thank you for your cooperation. Gràcies per estalviar paper. *Gracias por ahorrar papel. *Thanks for saving paper.

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LME model and contrast for longitudinal covariate and different scanners
by Donatas Sederevicius 30 May '18

30 May '18

External Email - Use Caution Dear Freesurfer experts, I have some doubts while running LME analysis on longitudinal data. The main goal is to check whether longitudinal BMI scores have any impact on the longitudinal cortical thickness changes. The model I’m thinking of is as follows: Y_ij = b0 + b1*time_ij + b2*BMI_ij + b3*Skyra_ij + b4*Prisma_ij + b5*gender_i + b6*bslAge_i. And here is an example design matrix X for the model above: ------------------------------------------ ones|time|BMI |Skyra|Prisma|gender|bslAge| ------------------------------------------ 1 |0 |0.62|0 |0 |0 |1.89 | 1 |3.2 |1.56|0 |0 |0 |1.89 | 1 |7.2 |2.04|1 |0 |0 |1.89 | ------------------------------------------ 1 |0 |1.1 |0 |0 |1 |1.67 | 1 |1.5 |0.9 |0 |0 |1 |1.67 | 1 |4 |0.9 |1 |0 |1 |1.67 | 1 |5.3 |1.3 |0 |1 |1 |1.67 | ------------------------------------------ 1 |0 |0.7 |0 |0 |0 |0.89 | 1 |1.2 |0.5 |0 |0 |0 |0.89 | ------------------------------------------ Note that BMI and bslAge are z-scored, and there are 3 different scanners: Avanto (base), Skyra and Prisma. I’m trying to account for differences between scanners as well. For some participants, the first two timepoints were scanned with one scanner and the last time point with a different one, so it varies within the subject. Do I account for the scanner differences in a correct way? Should I add interactions with the time variable, as time*Skyra? Another question. Since BMI is longitudinal, time-variant, should I add an interaction with time as well? Assuming that the above design matrix is “correct”, I would use the following contrast [0 0 1 0 0 0 0] to answer my question whether longitudinal BMI scores have any impact on longitudinal cortical thickness changes, right? P.S. I’m running spatiotemporal models with one random effect - intercept. Thank you for the answer! Best, Donatas

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Re: [Freesurfer] Subfields Development Version MATLAB:scriptNotAFunction
by Iglesias Gonzalez, Eugenio 30 May '18

30 May '18

External Email - Use Caution Dear Lachian (and everyone), I am SO sorry about this. I’ll be fixed very soon, I promise. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Lachlan Strike <l.strike1(a)uq.edu.au> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 07:42 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Subfields Development Version MATLAB:scriptNotAFunction External Email - Use Caution Hi I’m attempting to run the hippocampal/amygdala subfields segmentation in the most recent daily build of FreeSurfer (Centos7). The T1 only and multispectral variations run fine, but attempting the segmentation without the T1 (USE_T1=0) produces the following error: Attempt to execute SCRIPT segmentSubjectT2_autoEstimateAlveusML as a function: /tmp/MCR_3555778206/.mcrCache8.4/segmen0/segmentSubje/segmentSubjectT2_autoEstimateAlveusML.m MATLAB:scriptNotAFunction Error:Attempt to execute SCRIPT segmentSubjectT2_autoEstimateAlveusML as a function: /tmp/MCR_3555778206/.mcrCache8.4/segmen0/segmentSubje/segmentSubjectT2_autoEstimateAlveusML.m Linux vagrant 4.4.0-75-generic #96-Ubuntu SMP Thu Apr 20 09:56:33 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Any ideas? I am running this within a singularity container, but as the T1 and multispec versions ran without error I’m hoping it’s not related to that. Thanks Lachlan Queensland Brain Institute The University of Queensland, Australia

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Installing different versions of FreeSurfer on Same computer (error)
by miracle ozzoude 29 May '18

29 May '18

External Email - Use Caution Hello, My Mac has v5.3 installed in the default location ( application). However, whenever I try to install v6.0 in a different location ( desktop) it deletes the existing v5.3 from application. Any solution to this? I’m trying to run the brainstem and hippo&amygdala subfields on v5.3 processed data. Thank you. Best, Paul Sent from my iPhone

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Postdoctoral Scholar positions in neuroimaging
by Roeland Hancock 29 May '18

29 May '18

External Email - Use Caution NIDL and brainLENS-east labs (Neurobiology of Individual Differences in Language Lab http://nidl-lab.org, PI: Roeland Hancock PhD; and Laboratory for Learning Engineering and Neural Systems http://brainlens.org, PI: Fumiko Hoeft MD PhD) at University of Connecticut’s Brain Imaging Research Center (UCONN’s BIRC) are seeking: (1) two full-time neuroimaging postdoctoral fellows, and (2) two full-time Research Coordinators. BIRC is also seeking one full-time IT staff. *TWO NEUROIMAGING POSTDOC POSITIONS @ UCONN* We are seeking two postdoctoral scholars. The postdocs will manage and execute a large-scale neuroimaging project investigating the neurobiological mechanisms underlying: (1) language, literacy and cognition in generally healthy young adults using multimodal neuroimaging techniques such as MRI, MRS and TMS (“Perturbation Postdoc”); or (2) intergenerational transmission of language and literacy in parent-offspring dyads using MRI techniques (“Intergenerational Postdoc”). In addition, the successful candidates will have the opportunity to be involved in other federally and non-federally funded-research projects in the laboratories, gain experience in grant and manuscript writing and large-scale project management, outreach and community engagement projects, and access to a wealth of archival developmental and longitudinal neuroimaging data on language and literacy. *Required qualifications:* · PhD or equivalent in cognitive and systems neurosciences, computer science, engineering, psychology or a closely related field · Computational skills, including knowledge of at least one programming language and Unix commands · Strong written and verbal communication skills · Leadership and organizational skills *Preferred qualifications:* · Exceptional skills in collecting and analyzing MRI, MRS, and/or TMS data · Experience in M/EEG · Documented history of productivity and leadership · Advanced knowledge and expertise in statistics, e.g. multivariate statistics, behavioral genetics, Bayesian and Monte Carlo methods The position will be formally advertised at a later date. In the meantime, interested candidates should email *info(a)nidl-lab.org <info(a)nidl-lab.org>* with *"[Postdoc Job (YOUR FULL NAME)]" in the subject line*. In the email they should include (a) a current CV, (b) a one-page cover letter describing qualifications, interest, career goals and which postdoc position they are interested in (refer to as *“Perturbation Postdoc/Project” *or *“Intergenerational Postdoc/Project”)*, and (c) a list of 3 potential referees with their contact information. The position can begin immediately. *Postdoctoral scholars from the lab have gone onto a range of research faculty and imaging director positions at institutions such as Stanford, Caltech, Boston College, and University of Texas.* *The University of Connecticut is committed to building and supporting a multicultural and diverse community of students, faculty and staff. The diversity of students, faculty and staff continues to increase, as does the number of honor students, valedictorians and salutatorians who consistently make UConn their top choice. More than 100 research centers and instates serve the University’s teaching, research, diversity, and outreach missions, leading to UConn’s ranking as one of the nation’s top research universities. UConn’s faculty and staff are the critical link to fostering and expanding our vibrant, multicultural and diverse University community. As an Affirmative Action/Equal Employment Opportunity employer, UConn encourages applications from women, veterans, people with disabilities and members of traditionally underrepresented populations.*

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Re: [Freesurfer] QDEC, order interpretationof Gracias @batmarandua for aqaa
by Markus Gschwind 29 May '18

29 May '18

External Email - Use Caution On Tue, May 29, 2018, 20:16 Avi Gharehgazlou <avighareh(a)gmail.com> wrote: > External Email - Use Caution > > Hello experts, > > I am using QDEC to compared LGI values between groups (typically develping > and ASD). I made a "diagnosis.levels" file, putting my 2 groups in the > following order: > > Typically developing > ASD > > However, when I upload my qdec.table.dat file on QDEC, it recognizes my > diagnosis levels in the following order: > > 1 Diagnosis discrete 2 > 1 ASD > 2 TD > 2 age continuous 0 > 3 SA continuous 0 > > > Will you please tell me which order I have to interpret my results > according to? i.e. significant regions in Blue colour would indicate less > LGI in TD relative to ASD (if I consider TD first then ASD- like the order > I designed my diagnosis.levels file) BUT blue regions would mean less LGI > in ASD vs. TD if I consider order my groups appear on QDEC when I upload > qdec.table.dat file. > > Would appreciate your reply, > > Avi > _______________________________________________ > 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. >

1 0

FS-FAST error:
by 高寒 29 May '18

29 May '18

External Email - Use Caution FS-FAST error: analysis language.sm05.lh does not exist, see mkanalysis-sess Hello FreeSurfer Developers, I'm attempting to run FS-FAST on my own data, as described on the FS-FAST tutorial (http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastFirstLevel) but I get the following error when I run the selxavg3-sess command: ERROR: analysis language.sm05.lh does not exist, see mkanalysis-sess I assume there is something wrong with my mkanalysis-sess command because I can finish the whole process with the fsfast-functional data without an error. My research paradigm is like this: Task-fMRI*, 􏰕􏰗Picture Naming􏰞, Block-design with 30s On - 30s Off. 3 Trials. TR = 3000 ms; TE = 30 ms; flip angle = 90 degrees; matrix size = 96 􏰝 96; FOV = 240 􏰝 240 mm; 46 contiguous transversal slices; voxel size = 2.5 􏰝 2.5 􏰝 3 mm3; 3 dummy scans􏰘Scanning time = 3 min 09s. The first 3 TR have already been removed before I got the data. So I got 60 TR. And this the paradigm file<http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastDirStruct> I set up: 0.000 1 30.000 1.000 recited 30.000 2 30.000 1.000 null 60.000 1 30.000 1.000 recited 90.000 2 30.000 1.000 null 120.000 1 30.000 1.000 recited 150.000 2 30.000 1.000 null This is the mkanalysis-sess command I set up: mkanalysis-sess \ -fsd bold -stc up -surface fsaverage lh -fwhm 5 \ -event-related -paradigm language.par -nconditions 2 \ -spmhrf 0 -TR 3 -refeventdur 30 -nskip 0 -polyfit 2 \ -analysis my-language.sm05.lh -per-run -force \ Thank you for help. Sincerely yours. Gao Han

2 1

mri_label2label: Empty label file
by Emmanuel Nwosu 29 May '18

29 May '18

External Email - Use Caution Dear FreeSurfer users, I want to extract the thickness value of a significant cluster from all the subjects used for a comparison for further statistical analyses. I ran the mri_surfcluster first to create the ROI label with fsaverage and then used mri_label2label to map this label to all the subjects but the label generated for some of the subjects are empty (i.e the label file size is 0kb). Does anyone know the reason for this? and how it can be resolved? I need the label for all the subjects before running the mris_anatomical_stats and aparcstats2table. Any help on this will be appreciated. Kind regards Emmanuel

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