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Subject: Re: Zero cortical thickness
by A Nunes 16 Aug '16

16 Aug '16

Hi Douglas, I meant a surface area extracted from a surface based atlas. Thanks Adonay

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pial_lgi table
by Chatzi, Vasiliki 16 Aug '16

16 Aug '16

Dear developers, I was wondering if you could let me know how can I extract a table for the measure pial_lgi. Best wishes, Vasiliki Vasiliki Chatzi, BA(Hons) MSc PhD student | Department of Psychosis studies Institute of Psychiatry, Psychology and Neuroscience | King's College London

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recon-all -base -all, "Word too long" error.
by Hanbyul Cho 16 Aug '16

16 Aug '16

Dear FreeSurfer experts, I am FreeSurfer longitudinal processing the thirty time points data. When I tried the step 2 process to make a template, the process stopped with an error. The error message as the below. =============== ... mri_diff --notallow-pix /home/Desktop/MyProject/CO30/mri/rawavg.mgz /home/Desktop/MyProject/CO30/mri/rawavg.mgz Volumes differ in geometry row=1 col=1 diff=0.054242 (0.054242) ************************************************************ ******************* WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. ************************************************************ ******************* Word too long. ================== My command line was: recon-all -base SET1template -tp CO01 -tp CO02 ... -tp CO30 -all How can I fix the error? Best wishes, Han

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Iglesias paper: Hippocampal subfields
by Jacobs H (NP) 15 Aug '16

15 Aug '16

Hi! I would like to create a 3D rendering of the hippocampal subfields generated by FreeSurfer (as done in the Iglesias paper). I have tried to do this using Slicer, but the results are not that nice (making a model based on the 1mm mgz file). How were the surfaces in the paper generated? Do you have any suggestions for me on how to do this? Many thanks Heidi

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Zero cortical thickness
by A Nunes 15 Aug '16

15 Aug '16

Hi, I have read in the mailing list about zero cortical thickness, but I still have some doubts. I am calculating the average cortical thickness of some areas, and there are a few that almost all the subjects' thickness is zero, others only some subjects score zero. For the ones that almost all subjects is zero, I would guess is not considered cortical, however, all my areas are cortical. - If I compute a ttest against two groups, should I set the zeros as NaNs? or are the zero thickness meaningful (a genuine measure or a segmentation artifact)? -Should I use the -l ?h.cortex.label to avoid having zero thickness in some areas? If so, at which point? the commands used are: mri_surf2surf --srcsubject fsaverage --trgsubject subjid --hemi ?h --sval-annot fsaverage/label/?h.areas.annot --tval $SUBJECTS_DIR/subjid/label/?h.areas.annot mris_anatomical_stats -a $SUBJECTS_DIR/subjid/label/?h.areas.annot$SUBJECTS_DIR/subjid/label/?h.areas.annot -f $SUBJECTS_DIR/subjid/stats/?h.areas.stats -b subjid ?h Thanks Adonay

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Job postings: Post-doc & Data manager/programmer
by Gregory Book 15 Aug '16

15 Aug '16

The Olin Neuropsychiatry Research Center, located in Hartford CT, USA is looking to fill 2 open positions. The Olin Neuropsychiatry Research Center has an opening for a post-doc specializing in neuroinformatics, big-data analysis, and machine learning. The Olin Center is the psychiatric research center within Hartford Hospital’s Institute of Living campus, in Hartford, CT. We house a Siemens Skyra 3T whole-body MRI, multiple EEG, TMS, and eye tracking systems, an internal historical database of nearly 13,000 MRI sessions, and a 400-core Linux compute cluster. The candidate will pursue their own research with a focus on neuroinformatics and big-data analysis and assist multiple principle investigators with large scale analyses. The candidate will contribute to the development of the open-source Neuroinformatics Database ( http://github.com/gbook/nidb) and publish journal articles on their own research and software development. MS degree in engineering, science, neuroscience, or psychology is required, PhD preferred. Candidate is expected to have experience in SQL programming and at least one other programming language. Proficiency in multiple programming languages such as Perl, C, C++, JavaScript, PHP, Matlab, and Python is highly desirable. Contact Greg Book at gregory.book(a)hhchealth.org The Olin Neuropsychiatry Research Center is seeking a data manager/programmer to help maintain neuroimaging databases in support of multiple NIH funded projects. The Olin Center is a neuropsychiatric research center within Hartford Hospital’s Institute of Living campus. We house a 3T MRI, multiple EEG, TMS, and eye tracking systems, an internal database of nearly 13,000 MRI sessions, and a 400-core compute cluster. The primary responsibilities of the data manager will be to maintain internal and public imaging databases by performing the following tasks: remove personally identifiable information, perform uploads to NIH repositories, identify missing data, organize identifiers, support remote sites with data importing/uploading, and ensure data redundancy and backups. Additionally, the data manager may contribute to the development of the Neuroinformatics Database (http://github.com/gbook/nidb) using SQL, PHP, Perl, C++ and other programming languages for the purpose of making data management more efficient and robust. The data manager also will have the opportunity to participate in research projects and contribute to manuscripts. Bachelor’s degree in engineering, science, neuroscience, or psychology is required, Masters or higher is preferred. Candidate is expected to have experience in SQL programming. Proficiency in multiple programming languages is highly desirable. Contact Greg Book at gregory.book(a)hhchealth.org

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dividing Freesufer subfields into one anterior, middle and posterior region
by Erik Lindberg 15 Aug '16

15 Aug '16

Dear FS experts. I want to divid the FS subfield segementation into a anterior part, one middle part and posterior segment - or potentially divide the rang into 10% of the whole rang - and then move backword until I extracted 10 subparts. Is there some way I can do that? Thanks Erik

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How to run part of TRACULA
by Athanasia Metoki 15 Aug '16

15 Aug '16

Dear Freesurfer Developers, I am fairly new to image analysis and this is the first time I use Freesurfer. I have some DTI data and I have already preprocessed them and ran bedpostX using FSL. I ran probabilistic tractography on FSL as well to get the connectivity between two distinct brain areas. I am also interested in getting the probability distribution for the uncinate fasciculi so I am trying to use TRACULA. My question is: Can I use TRCULA without doing preprocessing and dedpostX again? If so, will I need to do the cortical parcelation and subcortical segmentation with recon-all and get the aparc+aseg.mgz file in order to use TRACULA? Which argument would I need to use when I run recon-all? Thank you! *Athanasia Metoki* Psychology Doctoral Student - Brain and Cognitive Sciences Program Cognitive Neuroscience Laboratory Temple University Department of Psychology 1701 N 13th St. Philadelphia, PA 19122 Email: athanasia.metoki(a)temple.edu _______________________________________________________________________________ The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient of this message or their agent, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited.

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TRACULA extracting diffusion measures using ASEG or WM parc
by Chung, Yoonho 15 Aug '16

15 Aug '16

Hi Anastasia, Is it possible to extract diffusion measures FA, ADC etc. within the subcortical (ASEG) or WM parc ROI regions using the Freesurfer tools? If possible, can you show how it can be done? Thank you in advance. Best, Yoon

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Fwd: Recon-all with flair
by Eelco van Duinkerken 15 Aug '16

15 Aug '16

Dear FreeSurfers, I've been preprocessing, in FS5.3, 3T GE data in controls, obese and diabetes patients and adding the available flair to do the pial refinement as follows: recon-all -i t1 -s bla -all -FLAIR flair -FLAIRpial This works excellent for most of the scans. Unfortunately, for some scans adding the flair leads to some interesting refinements, either extending outside of the brain.mgz or going deep into the white matter. I didn't notice any misregistrations of the flair to the T1 scan when checking the bb-registration, nor were there any errors in the recon-all.log. I have added some screenshots. The red lines represent the pial with the flair refinement, and the blue lines the pial without the refinement. As you can see, these interesting segmentations are not there when the flair is no used. Does anyone know what is going on? Thanks a lot, Eelco

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