Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Vertex coordinates of pial surface: mris_convert, read_surf(), tksurfer
by M. Jordan 30 Aug '18

30 Aug '18

External Email - Use Caution Hello, considering the surface 'lh.pial' of the reconAll process: When I apply 'mris_convert' in order to convert to .vtk, there is a shift with respect to the .pial file when viewing in freeview. When using the --cras_correction option for converting, the shift is gone. Nevertheless, the displayed vertex RAS coordinates in Freeview are different. Can anyone explain that? Respectively, what is '--cras_correction'actually doing? Moreover, when using the function 'read_surf()' in MATLAB to read 'lh.pial' I obtain the vertex coords, but when I compare the vertex with index 1923 to the corresponding "Vertex RAS" in tksurfer, there is a slightly mismatch. Can someone explain this? (I considered that MATLAB starts at index 1 and tksurfer at index 0!) I read, that tksurfer is actually displaying the coordinates of the 'orig' file and not the coords of the file which is actually visible? is that true? So the main questions are: - What are the coordinates of the 'lh.pial' file? (surface RAS / tkrRAS, or something different?) - Why and how do these coordinates change when converting (mris_convert) or reading in MATLAB (read_surf)? - Is vertex with index 1000, the same after mris_convert (vtk) and read_surf()? - Why there is a mismatch between the coordinates of a certain vertex in tksurfer and after read_surf - Does label2label only work with tkrRAS coordinates? Thank you very much!!

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MRIread error
by Song, Da-Yea 30 Aug '18

30 Aug '18

External Email - Use Caution Hi everyone, I'm trying to pre-process subjects through the pipeline but keep getting a handful of subjects that error out within seconds of running them. The error message I get is: MRISread(/subjects/002_1006/surf/rh.white):could not open file When I go into the subject's folder, I find the rh.white file in the stats folder. I've run about 100 subjects without an issue but for some reason there are a few subjects that will stop processing with the same error message. Any suggestions or comments would be greatly appreciated. Thanks! Dayea ---------------------------------------------------------------------- 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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Segmentation of hippocampal subfields and nuclei of the amygdala
by Meena M. Makary 30 Aug '18

30 Aug '18

External Email - Use Caution Hi; My Linux machine has FreeSurfer 6.0 with MATLAB runtime2012bLinux (MCRv80) which allows me to do the hippocampal subfields segmentation without errors. Now, I'd like to use [segmentHA_T1.sh] for hippocampal and nuclei of the amygdala segmentation which exists in the development version of 2018 but not in vr 6.0. I copied this bash file and other related files from the development version to my vr 6.0 /freesurfer/bin directory but I stuck with errors related to the MATLAB runtime version (it needs MCRv84). I downloaded runtime2014bLinux (MCRv84), but still same errors. Any recommendation to overcome this problem?. Will it be okay if I just replaced my vr6.0 /freesurfer/bin folder by the one from the recent development version? - given that I analyzed my data using recon-all by vr6.0. Thanks; --Meena -- *Meena M. Makary, Ph.D.* Assistant Professor | Cairo University <http://bmes.cufe.edu.eg/> Postdoctoral Fellow | Yale University School of Medicine <http://people.yale.edu/search/meena_beshara.profile> Postdoctoral Associate | The John B. Pierce Laboratory <http://jbpierce.org/postdoctoral-associates/> Treasurer | OHBM Student and Postdoc SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449> 290 Congress Avenue, New Haven, CT 06519 +1 (475) 731-5592 <+1%20475-731-5592>

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Fwd: Biomedical Research Engineer Position
by Florence M 30 Aug '18

30 Aug '18

External Email - Use Caution Title : *Biomedical **Research Engineer* No. of Position(s) : One (1) position Location : Paris, France Starting date : November 2018 *JOB DESCRIPTION* The successful applicant will work in the Group of Clinical Research 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 be tasked with coding in efficient ways analytical methods and build internal capabilities and gears for these methods. He/she would also be responsible for setting up and running statistical and neuroimaging analysis pipelines for scientific studies. It would be expected for the Biomedical Research Engineer to regularly monitor and assess data quality for on-going projects and provide feedback to collaborators. *Duties include:* - To develop MRI pipelines and data analyses in particular DTI data and their integration with structural MRI and functional MRI - To support researchers in the team during the scientific writing process - To manage the internal database, which may include the development of new user interfaces. *Desired qualifications:* - Experienced in processing structural MRI and DTI neuroimaging data - Demonstrated high level capacity for scripting with different languages, such as Python, R, MATLAB - Familiarity with system administration, project and neuroimaging data management - Familiarity with neurological concepts and/or experience with Alzheimer’s disease is desirable - Ability to integrate multimodal data, including neuroimaging data, biological markers and genetic data will be appreciated. *Education & experience * Master's degree Biomedical Research Engineer or related field. Two years of relevant experience is highly desirable though not necessary *Knowledge, skills and abilities:* - Strong analytical and organizational skills. - Ability to learn and utilize relational databases, data integration, and statistics. - Strong written and oral English communication skills. - Ability to understand scientific literature, experimental procedures and their limitations, and current needs of the research community, as applied in clinical neuroscience and neuroimaging research. Position length: The position is supported for 4 years. However, candidates will be appointed for 1 year, with an extension possible based on progress Salary: 2,183 € 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: 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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