Freesurfer August 2018

freesurfer@nmr.mgh.harvard.edu

104 participants
167 discussions

Fwd: Postdoctoral Position on Imaging Genetics
by Florence M 30 Aug '18

30 Aug '18

External Email - Use Caution Title : *Postdoctoral Position on Imaging Genetics* No. of Position(s) : One (1) position Location : Paris, France Starting date : November 2018 *JOB DESCRIPTION* The successful applicant will work in the Clinical Research Group on Alzheimer Precision Medicine (GRC-APM) at the site of Pitié-Salpêtrière Hospital of Sorbonne University under the supervision of Prof. Harald Hampel, holder of AXA Research Fund & Sorbonne University Chair « *sur le dépistage de la maladie d’Alzheimer*». The GRC-APM has as main objective the advancements in detecting, treating, and preventing Alzheimer’s disease (AD) by the implementation of a Precision Medicine (PM) strategy. The successful applicant will collaborate in the area of imaging genetics involving the development of algorithms for the identification of novel multi-modal (imaging and genetic) feature combinations and probabilistic models that explain these imaging-genetic interactions and facilitate diagnoses and prognoses in cognitive intact older adults at risk for AD and AD dementia patients. The candidate will benefit from the collaboration with our multidisciplinary team members and from our on-going collaborations with European and US research centres. *JOB RESPONSIBILITIES* · To conduct analyses of neuroimaging and genetics data on large datasets · To develop statistical models and/or use softwares that incorporates information across different modalities of data such as imaging (3D-T1; rs-fMRI; DTI; amyloid-Pet and FDG-PET, genetic, gene expression, biofluids) · To write scientific publications · To collaborate with other Team research scientists · To present findings at international conferences * EDUCATION* PhD in bio-/Statistics, Computer Science, Machine Learning, Electrical Engineering or related fields, with research experience in statistical machine learning using complex multivariate data. *KNOWLEDGE – SKILLS – ABILITIES* Experience on probabilistic graphical models, and/or dimensionality reduction, and and/or sparse learning is highly desirable. Researchers with image processing pipelines and gene expression analysis are particularly encouraged to apply. Strong programming skills (working knowledge of Linux, C/C++, Python, Matlab) is desirable *REQUIREMENTS* The candidate for this position is expected to have: strong background in machine learning, advanced statistical modeling and data analysis, possess excellent writing and communication skills. Experience in biostatistics and particularly analyzing genetic and imaging data. Position length: The position is supported for 4 years. However, candidates will be appointed for 1 one year, with an extension possible based on progress Salary: The salary compensation is very competitive: 3700,00 € gross / month Please send a brief letter of motivation and your detailed CV as one pdf (<2MB) to patrizia.chiesa(a)icm-institute.org

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Fwd: Biostatistician Position
by Florence M 30 Aug '18

30 Aug '18

External Email - Use Caution Title : Biostatistician No. of Position(s) : One (1) position Location : Paris, France Starting date : as soon as possible *JOB DESCRIPTION* The successful applicant will work at the Pitié-Salpêtrière University-hospital site under the supervision of Prof. Harald Hampel, holder of AXA Research Fund & Sorbonne University Chair « sur le dépistage de la maladie d’Alzheimer». The AXA Research Fund & Sorbonne University Chair conceptualized that substantial advancements in detecting, treating, and preventing Alzheimer’s disease (AD) will evolve from the generation and systematic implementation of a Precision Medicine (PM) strategy. The successful applicant will collaborate on several projects and cohorts around AD, as the sole statistician of a six-member research group but will also interact with other statisticians at the Pitié-Salpêtrière University-hospital. *JOB RESPONSIBILITIES* § Analyzing data and assisting in the interpretation of the results § Performing sample size and power calculations § Making recommendations to the Team members for the appropriate design of statistical analyses § Performing analyses of “big and deep data”, including omic(s) data, and genetic epidemiology data § Writing program codes to analyze data via statistical analysis software § Responsible for suitability, accuracy, and timeliness of statistical inputs into reports and projects § Interacting with other Team research scientists, external statisticians, and data managers in the analyses of the results, interpretation of biostatistical findings, and collection of the information for formulating advanced statistical programs * EDUCATION* § Master’s degree or PhD in Statistics, Biostatistics or related areas (e.g., Bioinformatics). *KNOWLEDGE – SKILLS – ABILITIES* Expertise in statistical software such as R, Python, Matlab and working knowledge of data management softwares such as Microsoft Excel and Microsoft Access Expertise in basic and advanced statistical analyses (such as Bayesian statistics) High proficient level of English (both in oral communications and in writing) is mandatory *REQUIREMENTS* § A minimum of 2 years (for Master’s degree education level) of demonstrated experience in statistical analyses and in summarizing findings Position length: The position is supported for 3 years. However, candidates will be appointed for 1 year, with an extension possible based on progress Salary: between 2,183 € gross / month and 2,443 € gross / month Please send a brief letter of motivation and your detailed CV as one pdf (<2MB) to *patrizia.chiesa(a)icm-institute.org <patrizia.chiesa(a)icm-institute.org>*

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freesurfer development version for mac incomplete
by Anik Dar 30 Aug '18

30 Aug '18

External Email - Use Caution Hi When I try to download the development version of freesurfer for mac, the file size is only 138 MB and doesnt unzip once downloaded. Is there another link where the complete development version for mac can be found ? Thanks Ani

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error in longitudinal stream command
by Barletta, Valeria 30 Aug '18

30 Aug '18

Dear Freesurfers, I am trying to re-launch a longitudinal time point after edits by using the command: recon-all -long MS069_R01_01_Bay8_3T_03102014.long.MS069_base MS069_base -all But I am obtaining this type of error: Unmatched ". I also tried to launch it on Launchpad but I have an error all the same and the process immediately aborts. Do you know what could be the reason? Thank you, Valeria

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Using a cluster as an ROI for further analysis
by Martin Juneja 29 Aug '18

29 Aug '18

External Email - Use Caution Hi experts, I found a cluster X1, which showed significant difference in cortical thickness between two groups C1 and P1, determined using mris_preproc, mri_surf2surf and mri_glmfit commands. I am interested in determining if the same cluster X1 has significantly different cortical thickness group between two other groups P2 and P3. I would really appreciate if you could please give me the step-by-step guidance how this can be done. Thanks.

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mri_label2label dependencies
by Krieger, Donald N. 29 Aug '18

29 Aug '18

External Email - Use Caution Dear freesurfers, I am using mri_label2label with -regmethod volume . The only other switches I am using are minimal as you can see below. The thing is that none of the freesurfer stuff is in the srcsubject's directory. Why is there no error message? Where is it getting the stuff below the line: Src2TrgVolReg: ----------- ? Actually, I just need to know what to put into those directories so this function will work properly. I see from the documentation that I need mri/transforms/talairach.xfm in both the src and trg subject directories. Is there anything else that needs to be there? mri_label2label --trgsubject 174 --srcsubject subNo1 --trglabel /dev/shm/32089_labels --srclabel /dev/shm/32089_tmp0-2 --regmethod volume srclabel = /dev/shm/32089_tmp0-2 srcsubject = subNo1 trgsubject = 174 trglabel = /dev/shm/32089_labels regmethod = volume usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/pkg/freesurfer//subjects FREESURFER_HOME /usr/local/pkg/freesurfer/ Loading source label. Found 33 points in source label. Starting volumetric mapping 33 points Src2TrgVolReg: ----------------- 0.963 -0.002 -0.044 0.330; 0.034 0.930 -0.328 -0.544; 0.044 0.285 0.919 13.268; 0.000 0.000 0.000 1.000; 0 55.0000 17.0000 23.0000 52.2444 9.6043 41.6544 1 47.0000 1.0000 39.0000 43.8696 -10.7903 51.4429 2 52.0000 -4.0000 28.0000 49.1826 -11.6594 40.1300 3 55.0000 17.0000 16.0000 52.5536 11.8998 35.2230 4 50.0000 -10.0000 23.0000 47.4912 -15.6659 33.7380 Writing label file /dev/shm/32089_labels 33 mri_label2label: Done Thanks - Don

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Designing Constrats for 3 Group 1 Covariate Analysis
by O'Dell, Ryan 29 Aug '18

29 Aug '18

External Email - Use Caution Dear freesurfers, I have what is likely a basic question but I'm new not only to FreeSurfer but contrast matrix design and group analysis as well, and was hoping for some help/clarification. Basically I want to run a GLM on our structural/functional data in order to determine if there's any significant correlation between cortical thickness and cortical amyloid deposition (measured by PiB), factoring in any potential effects of APOE genotype (e3e3, e3e4, e4e4). This means I want to construct an FSGD file with a 3 groups (the 3 APOE genotypes) and 1 covariate (our calculated cortical composite PiB value) for this analysis. However, I'm struggling with the proper contrast designs which test the various hypotheses in such a setup. Any answers, thoughts, or insights would be greatly appreciated. I know this type of analysis is also likely QDEC-able, but I think the FSGD approach would be more beneficial for my understanding of contrast matrix design. Please let me know if I've left out any information that could potentially help clarify my question/request. Best, Ryan O'Dell MD/PhD PGY2 Psychiatry Resident, NRTP Yale University

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Convert mgh to gii
by David.Mackarthy 29 Aug '18

29 Aug '18

External Email - Use Caution Hi FS experts, I ran surface based analysis between two groups. The final output "is cache.th13.pos.sig.cluster.mgh" I would like to convert this file to gii format using "mris_convert" I tried: mris_convert -c cache.th13.pos.sig.cluster.mgh cache.th13.pos.sig.cluster.gii Please what I am doing wrong? Thanks for help -Dev

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mri_gtmpvc for partial volume
by miracle ozzoude 29 Aug '18

29 Aug '18

External Email - Use Caution Hello, Can i specify a lookup table when using mri_gtmpvc? This is because I have a non-freesurfer segmentation (MALPEM) and i would like to perform partial volume on it without having to run freesurfer on the subject for PET analysis. I have a lookup table for the segmentation. I know mri_gtmpvc expects (?.ctab) file from the segmentation however, it will require processing the subject with freesurfer and petsurfer. I only want to use the partial volume command. How do I make it use the lookup table i made rather than ?.ctab file? Thank you. Best, Paul

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input to mris_preproc
by Alon Baram 29 Aug '18

29 Aug '18

External Email - Use Caution Hello, I have a surface measure calculated for each of my subjects, which I have already resampled and smoothed on fsaverage using mri_surf2surf, i.e for each subject I run: mri_surf2surf --hemi <hemisphere> --s fsaverage --sval <surfMeasureSubjX> --fwhm <FWHM> --cortex --tval <output> I now want to stack the outputs of the commands above, so that I can give the stacked image as an input to PALM. I think I should use mris_preproc for that, but I'm not sure if the subjects (the argument after the --s flags) should be the original subjects or fsaverage - given that my surface measures are already resampled to fsaverage. That is, I'm not sure if the correct command is (for 2 subjects) mris_preproc --out <outfile> --target fsaverage --hemi <hemisphere> *--s subj1 --s subj2* --is <surfaceMeasureFileSubj1> --is <surfaceMeasureFileSubj2> *or * mris_preproc --out <outfile> --target fsaverage --hemi <hemisphere> *--s fsaverage --s fsaverage* --is <surfaceMeasureFileSubj1> --is <surfaceMeasureFileSubj2> Thanks!

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Freesurfer August 2018