Freesurfer

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Post-Doctoral Position: Molecular Imaging in Geriatric Neuropsychiatry
by Gwenn Smith 13 Aug '17

13 Aug '17

[JHM2.gif] Post-Doctoral Position: Molecular Imaging in Geriatric Neuropsychiatry An immediate full-time opening is available for an outstanding, highly motivated post-doctoral research fellow in the laboratory of Gwenn S. Smith, PhD. The laboratory focuses on applying pharmacologic, neuropsychological and multi-modality PET and MR imaging methods to investigate the neurobiology of late life depression, mild cognitive impairment and Parkinson's disease and of interventions, including pharmacotherapy and brain stimulation. The laboratory, based in the Division of Geriatric Psychiatry and Neuropsychiatry, has strong collaborations with the Russell H. Morgan Department of Radiology and Radiological Sciences, the F. M. Kirby Research Center for Functional Brain Imaging of the Kennedy Krieger Institute, the Departments of Pathology (Neuropathology), Neurology and Neurosurgery. The fellow will have designated responsibility for specific projects, including the planning, design, execution, image processing, and analysis and will be expected to take the lead on preparing manuscripts for publication and on presentation of the results at scientific meetings. Successful applicants will have strong academic preparation (PhD, MD or MD/PhD in a relevant discipline), high motivation and enthusiasm for research, excellent written and oral communication skills including evidence of successful manuscript writing and publication productivity, strong intellectual curiosity, and ability to work independently and as part of a collaborative interdisciplinary team. Preference will be given to candidates with experience in clinical research, as well as in MRI and/or PET imaging. Applicants who plan to develop an independent research career are especially encouraged to apply. Review of applications will begin immediately and will continue until the position is filled. Applicants should send their Curriculum Vitae, a statement of academic interests and the names and addresses of four professional references to: Gwenn S. Smith, PhD, Richman Family Professor, Director, Division of Geriatric Psychiatry and Neuropsychiatry, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine 5300 Alpha Commons Drive, Baltimore, MD 21224 (gsmith95(a)jhmi.edu) The Johns Hopkins University is an equal opportunity/affirmative action employer committed to recruiting, supporting, and fostering a diverse community of outstanding faculty, staff, and students. All applicants who share this goal are encouraged to apply.

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TRACULA trac-all speed
by Mina Fakhry 12 Aug '17

12 Aug '17

I am currently using the last stable version freesurfer 6.0 I gave TRACULA a try on one subject and it took more that 2.5 days to finish the steps, with PC specs: - Processor core i7 4 GHz - VGA Nvidia GTX 980 with 1500 CUDA cores - 16 GB RAM I tried to speed it up (trac-all command) using openmp or use-gpu, but non of them worked. Is there any way to speed the TRACULA processing??

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Matlab 2016b and localGI
by Juranek, Jenifer 11 Aug '17

11 Aug '17

Hi, Hope someone can identify my user error...I've listed below key bits of info (system info, cmdline and error message, echo $PATH, cat .bashrc, cat startup.m). Really appreciate someone taking a look and walking me through a solution to my error? Many Thanks! Jenifer 1) Running Freesurfer_v6 on RHEL Centos7.3 and matlab 2016b (with imaging processing toolbox) 2) recon-all -s <FSID> -localGI returns the following: #@# Local Gyrification Index lh Thu Aug 10 15:39:03 CDT 2017 mris_compute_lgi --i lh.pial ERROR: Matlab is required to run mris_compute_lgi! Linux localhost.localdomain 3.10.0-514.el7.x86_64 #1 SMP Wed Oct 19 11:24:13 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux 3) matlab is in my path [jjuranek@localhost subjects]$ echo $PATH /home/jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/fsfast/bin:/home/jjuranek/freesurfer/tktools:/home/jjuranek/fsl/bin:/home/jjuranek/freesurfer/mni/bin:/home/jjuranek/fsl/bin:/home/jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/fsfast/bin:/home/jjuranek/freesurfer/tktools:/home/jjuranek/freesurfer/mni/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/jjuranek/.local/bin:/home/jjuranek/bin:/home/jjuranek/matlab/R2016b/bin/matlab 4) my .bashrc file is as follows # .bashrc # Source global definitions if [ -f /etc/bashrc ]; then . /etc/bashrc fi # User specific aliases and functions export FREESURFER_HOME=/home/jjuranek/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh matlab=/home/jjuranek/matlab/R2016b/bin/matlab alias matlab=$matlab export PATH=$PATH:/home/jjuranek/matlab/R2016b/bin/matlab #/home/jjuranek/matlab/R2016b/bin/matlab #MATLAB is selecting SOFTWARE OPENGL rendering. 5) my startup.m file is as follows %------------ FreeSurfer -----------------------------% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) addpath(genpath(fsmatlab)); end clear fshome fsmatlab; %-----------------------------------------------------% %------------ FreeSurfer FAST ------------------------% fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; %-----------------------------------------------------% %------------ FreeSurfer LGI ------------------------% FSH = getenv('FREESURFER_HOME'); fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab FSH;

3 2

Generating Surfaces from Labels
by Zach Humphrey 11 Aug '17

11 Aug '17

Hello All, I have been attempting to convert Label files generated using mri_annotation2label into surface files for use in external programs. In order to do this I first need to convert the label files into freesurfer binary. I have attempted to use the mri_label2vol function to generate an mgz file which could then be converted into freesurfer binary but this has resulted in mgz files which depict a solid cube rather than any brain structure. Any ideas as to why this could be? I would also prefer to avoid ever converting the label files to a volume as converting the volume file to a surface file results in a lower quality than if the file has been maintained as a surface file throughout. Is there any way to use the Desikan Atlas to "divide" say the lh.pial surface file and generate a number of .pial files each consisting of one of the regions described by the Desikan Atlas? Thanks, Zachary Humphrey

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vvol2surf flip issue
by Redwan Maatoug 11 Aug '17

11 Aug '17

Hi Doug, First of all sorry to bother you again with that. We still have an issue with the vol2surf command line and almost all the people in the lab tried without any success. We have the following nifti file attached and we tried to convert it to surface file. We used a MNI152 2mm brain template and when we look at the image with tksurfer, the image is flipped. (we have this issue with half of the data). I have attached the screenshot of the NIFTI file displayed with freeview. (file1) I have attached how we are supposed to see the MGH file (not flipped) in tksurfer I have attached how we see the MGH file (flipped) The command line we have used : *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg MNI152_T1_brain.dat --t1 --init-coreg* *mri_vol2surf --file1.nii --reg MNI152_T1_brain.dat --hemi rh --o file1.mgh* Can you try to replicate the issue or give some tips ? We have this issue with half of the data Thank you very much, I would really appreciate any help, Redwan

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Re: [Freesurfer] mri_glmfit-sim output
by Van Der Deijl, Rosanne 11 Aug '17

11 Aug '17

Thanks for the link, I hadn't seen that one indeed! However, the variable WghtVtx is not explained on this page. What is this variable? Thank you! Message: 8 Date: Mon, 7 Aug 2017 15:01:46 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_glmfit-sim output To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <0b5fc464-a5ed-cee5-e3fa-3603b99e8136(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed see here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSu… On 08/07/2017 02:40 PM, Van Der Deijl, Rosanne wrote: > Dear Freesurfer team, > > In the mri_glmfit-sim summary output file, I get a number of output > variables, and I'm not sure what some of them are. Could you explain > the ones in bold to me? > > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ *CWP > CWPLow CWPH * NVtxs *WghtVtx* Annot > 1 2.015 134872 355.89 -36.3 -9.7 -1.4 > 0.96620 0.96390 0.96850 841 1298.68 insula > 2 1.652 71259 154.25 -49.4 -52.7 39.2 > 1.00000 -0.00010 1.00000 363 526.18 supramarginal > 3 -1.521 91550 39.92 -37.1 -26.5 -23.3 > 1.00000 -0.00010 1.00000 90 -125.33 fusiform > 4 1.322 139141 0.76 -36.4 3.5 -10.7 > 1.00000 -0.00010 1.00000 2 2.62 insula > 5 1.312 73658 0.47 -36.0 -4.4 9.6 > 1.00000 -0.00010 1.00000 1 1.31 insula > 6 1.387 133422 0.44 -5.1 -17.2 51.7 > 1.00000 -0.00010 1.00000 1 1.39 paracentral > > I know CWP stands for Cluster-wise P-value. But what is the low and > the high number, a confidence interval? And isn't it odd that my > p-values are (almost) 1? > > Thank you in advance. > > Kind regards, > > Rose >

2 1

Test-retest reliability small subcortical regions
by Van Der Deijl, Rosanne 11 Aug '17

11 Aug '17

Dear Freesurfer team, I was wondering what the test-retest reliability is of comparing small regions in the subcortical volume, e.g. the amygdala. Has this improved with the 6.0 version? Thank you! Kind regards, Rose

2 1

PET surfer
by John Anderson 11 Aug '17

11 Aug '17

Hi Dr Greve, I have PET data for two groups and I used PET surfer in FSV 6.0 to run the analyses. The pipeline is straightforward and the analysis ran smoothly without any issues. Is it correct procedure to adjust PET signal to differences in gray matter volume or cortical thinness between two groups? In other words, is it correct if gray matter volume or cortical thickness for subjects be included as EVs in GLM or a nausiance factor in QDEC? Specifically, is the PET signal changeable depending on differences in cortical thickness. or differences in gray matter volume? Thank you for any clarification > Thank you ! > Jon

2 4

(no subject)
by Redwan Maatoug 10 Aug '17

10 Aug '17

Hi Doug, First of all sorry to bother you again with that. We still have an issue with the mri_convert command line and almost all the people in the lab tried without any success. We have the following nifti file attached and we tried to convert it to surface file. We used a MNI152 2mm brain template and when we look at the image with tksurfer, the image is flipped. (we have this issue with half of the data). I have attached the screenshot of the NIFTI file displayed with freeview. (file1) I have attached how we are supposed to see the MGH file (not flipped) in tksurfer I have attached how we see tne MGH file (flipped) The command line we have used : *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg MNI152_T1_brain.dat --t1 --init-coreg* *mri_vol2surf --file1.nii --reg MNI152_T1_brain.dat --hemi rh --o file1.mgh* I have attached one of the nifti file to see if you can replicate the issue. Thank you very much, I would really appreciate any help, Redwan

1 0

"failed to load mri" in terminal, not in GUI
by Z Hessam 10 Aug '17

10 Aug '17

Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards

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