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Re: [Freesurfer] segmentHA znzread failed error
by Maksimovskiy, Arkadiy 27 Oct '17

27 Oct '17

Thank you so much for your help with this. Much appreciated, * Arkadiy

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hippocampal subfields downsampling question
by NIELS JANSSEN . 26 Oct '17

26 Oct '17

In the mri output folder, I noticed that both the 0.33 mm and 1 mm (voxelspace) maps have subfields that do not overlap in space, meaning that each subfield occupies a unique location in space that does not overlap with other subfields (i.e., 12 subfields and 12 unique voxel intensities). I am wondering how this is achieved for both resolutions simultaneously. Do you 'fit' the subfields first to the 0.33 mm data and then transform the data to the 1mm space, or do you fit to both spaces separately? I would like to transform the subfields to 1.5 mm data and are able to do so accurately, but I run into problems with subfield overlap because of the down sampling. I am wondering how to best deal with this issue, and from seeing non-overlapping subfields at both 0.33 and 1 mm I am thinking there must be someway to deal with this issue. -- Niels Janssen Brain Imaging Laboratory Institute of Biomedical Technologies Center for Biomedical Research of the Canary Islands University of La Laguna Tenerife, Spain https://sites.google.com/view/nielsjanssen/

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Preproc-sess Error
by Hsu, Eugene 26 Oct '17

26 Oct '17

Hi FreeSurfer Experts, We're trying to run preproc-sess on FreeSurfer 6, but we're encountering an error when motion correcting: ERROR: cannot find AFNI command 3dvolreg.afni When we tried Freesurfer 5.3 the preproc-sess ran to completion. Thanks for your help! --Eugene

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freesurfer errors-windows bash
by Alexandre Obert 26 Oct '17

26 Oct '17

Dear all, I'm would like to run a hippocampal segmentation on my data. However, I'm a beginner with freesurfer thus, I juste try to run the commands with subject training data. I first try to run commands following the recent development ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) However, terminal says that the command segmentHA.sh doesn't exist. I guess that it could be linked to the fact that I used bash in Windows but I can't find a way to check this..; Any idea ? Regards, Alexandre

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Postdoctoral Fellow Positions in a longitudinal birth cohort imaging study
by Anqi Qiu 26 Oct '17

26 Oct '17

Postdoctoral Fellow Positions Job description: Growing Up in Singapore Towards Healthy Outcomes (GUSTO) is the most comprehensive birth cohort study over the world. The GUSTO mothers were recruited during pregnancy between 2009 and 2010. We have followed the GUSTO family since then. The GUSTO study collects the unique data on cognitive functions, children behaviors, psychopathology, and brain imaging at multiple points from birth to 7 years of age. We aim to study whether mothers mood, diet, and family lifestyle since pregnancy affect 1) their babies cognitive and brain development; 2) psychopathology later in life. We also aim to examine the role of genetics in such maternal influences. We are looking for postdoctoral fellows who are interested in the GUSTO study. Requirements: 1. PHD in Cognitive Neuroscience, or Psychology, or Imaging Genetics; 2. Experience with MRI-based neuroimage techniques; 3. Knowledge in statistical analysis is necessary; 4. Good communication and writing skills in English language; 5. Knowledge in longitudinal analysis will be plus plus. If you are interested in the jobs listed above, please send your CV to Deans Chair, Associate Prof. Anqi QIU Department of Biomedical Engineering National University of Singapore Email: bieqa(a)nus.edu.sg Phone: +(65) 6516 7002

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Errors in LGI computation
by k.ohmstedt＠stud.uni-heidelberg.de 26 Oct '17

26 Oct '17

Dear Freesurfers, I try computing the local gyrification index following the method developed by Marie Schaer and her colleagues. The process itself finishes without errors, yet there remain large grey areas of variable size on the cortex, indicating errors in the computation of the gyrification index. They are mainly situated in the regions next to the ventricles. I checked the reconstructed surfaces after running the recon-all command and there do not seem to be any errors or lesions. My system is a Mac with macOS Sierra (Version 10.12.6) and freesurfer Version 6.0.0 is running. Do you have any ideas what could cause these problems? Any help is appreciated! Thank you in advance and best regards, Kai Ohmstedt

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Postdoctoral Research Fellow Position in Infant and Child Brain MRI analysis
by Lilla Zollei 25 Oct '17

25 Oct '17

See the attached pdf or the text below. Lilla >>>>>>>>>>>>>>>>>>> A postdoctoral fellow is recruited for two NIH funded projects focusing on developing Freesurfer-compatible brain image analysis tools for children. One project aims to extend the tools for brain imaging data for children between 2-6 years of age. The second project aims to extend the tools for longitudinal analysis of developmental data from older children and adolescents as part of the Human Connectome Project in Development. Code development will focus on pair- and group-wise registration tools, segmentation methods and surface-based image analysis algorithms. The successful applicant should have a doctoral degree in a field related to medical imaging (e.g., computer science, electrical engineering, biomedical engineering, applied mathematics, computational neuroscience). She/he is expected to have a strong research background in method development and brain image analysis and should be able to work independently. Strong programming skills (for example, C/C++, MATLAB, and/or Python) are a must and prior experience with brain image-analysis packages (such as SPM, FSL, FreeSurfer, AFNI) is desirable. In addition, the candidate must also possess excellent English verbal and written communication skills. This position will be hosted by the Laboratory of Computational Neuroimaging, MGH and it will offer great opportunities to collaborate with a large group of scientists from diverse research disciplines. Approximate start date is winter 2017. Successful applicants will be appointed at Massachusetts General Hospital, Boston. For consideration please send a statement of interest, a CV and a list of three potential references via email to Lilla Zöllei, PhD (lzollei(a)nmr.mgh.harvard.edu) The search will continue until the position is filled. We are an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability status, protected veteran status, or any other characteristic protected by law.

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Re: [Freesurfer] segmentHA znzread failed error
by Iglesias Gonzalez, Eugenio 25 Oct '17

25 Oct '17

Dear Arkadiy Andrew Hoopes just pinpointed that they have tracked down these warnings to a recent code change. It’s happening for everyone using dev. You can ignore these znz error statements, they are completely innocuous. It’s just caused by a print statement that shouldn’t have been added. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Maksimovskiy, Arkadiy" <AMAKSIMOVSKIY(a)mclean.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, 24 October 2017 at 14:31 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] segmentHA znzread failed error Dear Hipp. Segmentation experts, I keep getting the following error when running the segmentHA script from the Dev. Version. Wondering if this is serious or something that can be ignored, as the process keeps running to the end: Transforming points znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory threshold mask volume at 0.5 znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory threshold mask volume at 0.5 znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed Thank you for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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smoothing a surface map
by Eryilmaz, H. Hamdi 25 Oct '17

25 Oct '17

Hello all, How can I simply smooth a surface map (constructed using MRIwrite) using a specific FWHM? mri_surf2surf requires source subject as an input but all I want to do is to smooth a single group map. Thanks in advance for your help! Best, Hamdi

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Freesurfer mkbrainmask-sess
by Rebecca Sheley 25 Oct '17

25 Oct '17

Hello Freesurfer Team, I'm having trouble running preproc-sess, but only with the mkbrainmask-sess step. I tried just running this step and got this output. Do you have any insights on why this might be happening? My tmp folder is empty. The cwd directory is the folder where my data are located. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 OS: Ubuntu Here is the command I ran: mkbrainmask-sess -s FS_0184 -d `pwd` Here is the output: /home/rebecca/SC/FS_0184 Wed Oct 25 11:59:31 EDT 2017 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_29130 /home/rebecca/SC/FS_0184/bold mri_convert template.nii.gz /tmp/mkbrainmask_29130/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_29130/in.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from template.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /tmp/mkbrainmask_29130/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /home/rebecca/SC/FS_0184/bold bet.fsl /tmp/mkbrainmask_29130/in.nii /tmp/mkbrainmask_29130/brain -m -f 0.1 Segmentation fault (core dumped) mri_binarize --i /tmp/mkbrainmask_29130/brain_mask.nii --min .01 --o /tmp/mkbrainmask_29130/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_29130/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/rebecca/SC/FS_0184/bold cmdline mri_binarize --i /tmp/mkbrainmask_29130/brain_mask.nii --min .01 --o /tmp/mkbrainmask_29130/brain_mask.nii sysname Linux hostname wernickesarea machine x86_64 user rebecca input /tmp/mkbrainmask_29130/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_29130/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0 Thanks! --Rebecca Sheley

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