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30065 discussions

Question about global mean cortical thickness
by Zhiliang Long 14 Aug '17

14 Aug '17

Dear FS experts: I am writting to ask for help about the computation of global mean thickness. On the FAQ page, one suggestion is that the global mean thickness is equal to the (lh.thickness*lh.surfarea + rh.thickness.rh.surfarea) / (lh.surfarea+rh.surfarea). I am wondering how the ?h.thickness and ?h.surfarea are calculated. Any suggestions are appreciated. Thanks for your time. Best Zhiliang Long

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Re: [Freesurfer] test-retest variability small subcortical regions
by Van Der Deijl, Rosanne 14 Aug '17

14 Aug '17

Hi Bruce, I mean for the longitudinal analysis. Forgot to mention this, sorry! Kind regards, Rose Date: Fri, 11 Aug 2017 12:39:58 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Test-retest reliability small subcortical regions To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1708111239430.24300(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Rose do you mean cross-sectional or longitudinal analysis? cheers Bruce On Fri, 11 Aug 2017, Van Der Deijl, Rosanne wrote: > 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 >

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problem with fsgd glmfit
by Kasper Jessen 14 Aug '17

14 Aug '17

Dear FreeSurfer, I would like to do the long. two stage model (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel) Study design: 2 groups (one control group, one patient group) with gender and age as covariates. Each subject was MRI scanned at baseline and 6 weeks follow-up. I would like to test the difference in structural measures between groups over time. My problem 1. Is the process and setup below correct? 2. When i pass the above command under 3) i get an error where it says: FSGDF Format Error: file = /Volumes/External/P1_FU/GroupDiffLhThickness.fsgd, tag=Input Is there anyone that can help? I have followed the tutorial: FIRST STAGE: Preparing the Data - QCACHE is done. SECOND STAGE: Option mri_glmfit: Then i would like to test the difference between groups, and this is were i have a hard time following the tutorial. I looked at the following guide: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis concerning Group Analysis using mri_glmfit and i understand that i need to use the command below creating my own fsgd file. 1) Since i have a longitudinal setup, i converted it to a cross-sectional steup as you would do if you used the QDEC option. My fsgd file looks as the one below. 1 = patients and 0 = controls. GroupDescriptorFile 1 Title GroupDiff_Lh_Thickness Class 1 Class 0 Variables age gender Input b101_base 1.0 24.0 1.0 Input b103_base 1.0 41.0 0.0 Input b105_base 1.0 22.0 1.0 Input b206_base 0.0 25.0 1.0 Input b207_base 0.0 23.0 0.0 2) To test group difference between groups regressing out the effect of age and gender i have made a .mtx file with the following input: 1 -1 0 0 0 0 3) Therenext, i ran the following but something is wrong with my fsgd file: mri_glmfit --y lh.thickness-spc.stack.fwhm15.mgh --fsgd GroupDiffLhThickness.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh_thickness_spc_fwhm15_groupdiff I hoper there is someone who can help. Best wishes Kasper Jessen

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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;

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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 >

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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

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