Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30134 discussions

setenv command not found
by pietro de rossi 27 Feb '14

27 Feb '14

Dear Freesurfers, I am using Freesurfer version 5.1 on Linux-centos4_x86_64. I am trying to set up as SUBJECTS_DIR a folder which is different from freesurfer's predetermined subjects folder..... my command line was setenv SUBJECTS_DIR /path/to/my_folder I get: bash: setenv: command not found How can I solve the problem? It never happened on the Mac I was previously working on... Thanks -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant'Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com

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questions about ROI analysis
by Rujing Zha 26 Feb '14

26 Feb '14

Hi FS experts and others, I have done two group thickness difference analysis based on whole brain. Now I want to do correlation analysis between specific ROI thickness and behavior score. I searched roi in the FS website, but I cannot distinguish the volume ROI and surface ROI very clearly. So I have some questions as below: 1,As I get some clusters in the two group t-test,I want to use one of these clusters to correlate thickness with behavior score. How to generate this mask and how to use this mask in the mri_glmfit and mri_glmfit-sim? 2,If I want to draw ROI manually or set ROI according previous studies, how to create this ROI mask. Any detailed information will be highly appreaciated. Thanks. All the best. Rujing Zha

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two labels in tksurfer/freeview?
by Yang, Daniel 26 Feb '14

26 Feb '14

Dear FreeSurfer experts, Is it possible to display two labels in tksurfer or freeview, where one label is outlined with a certain color and the other label is filled with a different color? I want to show two labels, one is within the other one. If yes, could you please tell me the specific steps..? thanks a lot! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang(a)yale.edu

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(no subject)
by Douglas Wojcik 26 Feb '14

26 Feb '14

Good afternoon; I am hoping you can help me answer a pretty quick & easy question…. I am trying to identify the best MRI protocol to use for Freesurfer analysis… When I look at the FAQ: Data Requirements The processing procedures for the creation of cortical models require good quality T1 weighted MRI data, such as a Siemens MPRAGE (examples of appropriate Siemens scanner protocols) or GE SPGR sequence with approximately 1mm3 resolution (although a variety of quality data sets can be processed with additional manual intervention). Thickness should not exceed 1.5mm (~1mm^3 is ideal). The protocols specified for the ADNI project are excellent examples to follow. The best FreeSurfer processing results come from scans having excellent gray/white matter contrast. The link to the ADNI project protocols is broken…I think that they should be here: http://adni.loni.usc.edu/methods/documents/mri-protocols/ Thanks Douglas

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No labels file in label directory?
by sabin khadka 26 Feb '14

26 Feb '14

Hi all, I ran recon-all -all and all the subjects finished without any error. However in few subjects directory, labels sub-directory only have lh.cortex.label and rh.cortex.label and not other label files like *.label and *.annot. Could anyone help me on how to fix this. -Sabin

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mris_preproc xhemi
by Daniel Carey 26 Feb '14

26 Feb '14

Dear All, We have been attempting to run a cross hemisphere analysis using .curv files, as per the wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi I have outlined the exact steps within our pipeline below. When fitting any glm to the data (simple osgm shown below), we find that across all vertices, the significance values are 0 (despite the vertex by vertex diff values appearing to be very slightly different, based on a cursory inspection of the sig.mgh file overlaid onto lh of fsaverage_sym in tksurfer). Oddly, the vertex by vertex diff values also appear to be lower than we would expect (approximately by a factor of 10). Within the terminal output from glm_fit, we see both F and sig values of 0. We are unsure as to why the analysis isn't working quite as expected. Any advice on this would be greatly appreciated. Many thanks in advance, Dan --- # register subs foreach sub (01 03 04 05 06 08 10 11 12 13 14 15 16 18 19 20 21 22 23 24 25 27 28 29 30 31 32 33 35 36 37 38 39 40) surfreg --s S$sub-synth --t fsaverage_sym --lh surfreg --s S$sub-synth --t fsaverage_sym --lh --xhemi end # mris_preproc mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff --srcsurfreg fsaverage_sym.sphere.reg --meas curv --out lh.lh-rh.curv.sm00.mgh \ --s S01-synth --s S03-synth --s S04-synth --s S05-synth --s S06-synth --s S08-synth --s S10-synth --s S11-synth --s S12-synth --s S13-synth --s S14-synth \ --s S15-synth --s S16-synth --s S18-synth --s S19-synth --s S20-synth --s S21-synth --s S22-synth --s S23-synth --s S24-synth --s S25-synth --s S27-synth \ --s S28-synth --s S29-synth --s S30-synth --s S31-synth --s S32-synth --s S33-synth --s S35-synth --s S36-synth --s S37-synth --s S38-synth --s S39-synth \ --s S40-synth # smooth mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm 5 --i lh.lh-rh.curv.sm00.mgh --o lh.lh-rh.curv.sm05.mgh # mris_glmfit mri_glmfit --y lh.lh-rh.curv.sm05.mgh --glmdir glm.lh.lh-rh.curv.sm05.osgm --osgm --surf fsaverage_sym lh --- Daniel Carey Marie Curie Ph.D. Fellow, Centre for Brain and Cognitive Development, 32 Torrington Sq., London WC1E 7HX UK email: d.carey(a)bbk.ac.uk web: http://www.cbcd.bbk.ac.uk/people/students/daniel_carey

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-noskullstrip 'directive'
by Pedro Rosa 26 Feb '14

26 Feb '14

Dear all, I have a dataset with 1.5T T1 images which have already been skullstriped. So to avoid the autorecon1 skullstrip, I ran 'recon-all -i subject.nii.gz -s subject -all -noskullstrip', but it finished with the same error for more than a dozen of images (example log attached). It says that the 'mri_em_register' could not open mask volume brainmask.mgz, which I believe is generated by the skullstrip and indeed could not be found in the 'subject/mri' folder. How should I ran the pipeline skipping the skullstrip? Thank you very much in advance. Pedro Rosa.

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Volumetric data for GM,WM,CSF.
by Saurabh Thakur 26 Feb '14

26 Feb '14

Hi Freesurfer expert, I am looking for just volumetric quantity of *GM,WM,CSF.* Can u suggest some commands tat i used or explore so that i get volumetric data. Presently value for subject* Bert i m getting:* Right now i m working on mri_segstats ---->giving me vol of white matter by using *wmparc.stats* *Total cortical white matter volume, 484479.305031, mm^3* mri_segstats-----> giving me vol of grey matter by using* aseg.stats* *Total gray matter volume, 655593.521190, mm^3* *If i wanted to have all the value in one single window/file.* cheers Saurabh Thakur

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WM segmentation question
by Moore, Matthew 26 Feb '14

26 Feb '14

Dear Freesurfer Experts, I am assessing the quality of the initial skull strip for some subject data after running autorecon1. I notice that in some cases non-brain matter near the eyes appears to remain, as well as some dura matter at the posterior of the brain. If these voxels are left untouched, or if some remain after either watershed adjustment or gcut, and autorecon2 is run, it appears that some of these voxels are identified as white matter (based on WM volume visualized in Freeview). I am wondering if the voxels are identified as white matter, but are not included in the surface reconstruction as shown by WM and pial surface outlines in Freeview, do they influence any of the measurement calculations (e.g. CorticalWhiteMatter) or segmentation accuracy downstream? In some troubleshooting pages I see examples that if they are included in the surface reconstruction, they are a problem, but if they are not, does the brainmask still require improvement? I am using Freesurfer 5.3 CentOS6 64bit. Thanks. Matt

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Postdoctoral Position within Cambridge Centre for Ageing and Neuroscience
by Kirstie Whitaker 26 Feb '14

26 Feb '14

Please accept my apologies for cross-posting. I am delighted to advertise the following postdoctoral research position on behalf of Prof Ed Bullmore at the University of Cambridge. The job posting is listed at www.jobs.cam.ac.uk/job/3229 and informal enquiries should be directed via email to Ms Karen Enright at ke242(a)cam.ac.uk. The closing date for applications is 16th March 2014. Best wishes Kirstie *Research Associate (Fixed Term)* *Copied from www.jobs.cam.ac.uk/job/3229 <http://www.jobs.cam.ac.uk/job/3229> * Applications are invited for a post-doctoral researcher to join the Cambridge Centre for Ageing and Neuroscience (Cam-CAN, www.cam-can.com) This centre brings together a large group of researchers across the University of Cambridge and at the MRC Cognition and Brain Sciences Unit (MRC-CBSU) who aim to relate brain changes to cognitive changes over the adult lifespan (covering ages 18-88). The appointee will work with a unique population-representative sample of 700 adults on whom we have collected extensive cognitive and neuroimaging measures from fMRI and MEG. The role of the post holder will be to conduct multivariate and network analyses of the Cam-CAN 700 dataset to elucidate brain systems changes associated with normal ageing and its associated changes in cognitive function. The appointee will be a physical scientist with a strong interest in neuroscience of cognitive neuroscientist with a strong background in imaging and imaging statistics, and cognitive and/or physiological ageing. Candidates should have, or be in the final stages of obtaining, a PhD in physics, cognitive neuroscience, neuroimaging methods, applied statistics or cognitive ageing. Knowledge of and experience in advanced imaging analyses, particularly brain connectivity and network analysis is essential, and it would be highly desirable to have some prior experience of MEG/EEG and/or fMRI techniques. Excellent statistical, computer programming (MATLAB and/or Python) and neuroimaging analysis (SPM, Fieldtrip) skills are essential. Candidates should be careful, efficient, be able to communicate effectively, and enjoy working as part of a diverse and energetic interdisciplinary team. Candidates should also be willing to run fMRI and MEG sessions which will require some flexible working to accommodate evening (up to three per week) and Saturday (up to two per month) sessions. The applicant will be based in the Centre for Speech and Language in the Department of Psychology but will work closely with colleagues in the Brain Mapping Unit in the Department of Psychiatry. The post will be appointed at the appropriate point on the University of Cambridge's research associate salary scale, depending on the seniority of the successful candidate. Fixed-term: The funds for this post are available until 30 September 2015 in the first instance. To apply online for this vacancy, please click on the 'Apply' button below. This will route you to the University's Web Recruitment System, where you will need to register an account (if you have not already) and log in before completing the online application form. Applicants should submit a covering letter, CV with full publication list and contact details for three referees. Informal enquiries should be directed via email to Ms Karen Enright at ke242(a)cam.ac.uk. Interviews will take place on Tuesday 25th March 2014. Please quote reference RN02762 on your application and in any correspondence about this vacancy. The University values diversity and is committed to equality of opportunity. The University has a responsibility to ensure that all employees are eligible to live and work in the UK. -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Douglas House 18b Trumpington Road Cambridge, CB2 8AH *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com

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