Freesurfer

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17 participants
30099 discussions

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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Fw: tessellate error in tksurfer
by charujing123 25 Feb '14

25 Feb '14

sorry,this e-mail has the attachment. Rujing Zha 2014-02-24 charujing123 发件人："charujing123"<charujing123(a)163.com> 发送时间：2014-02-24 11:23 主题：[Freesurfer] tessellate error in tksurfer 收件人："freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： hi all, I want to visually check the cortical reconstruction output with tksurfer, as being said in surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FinalSurfEx. It represented nothing but black in the window when I type "tksurfer CON_EIU01 lh orig". The appearance can be got in the attachment. Thanks. All the best. RujingZha 2014-02-24 charujing123

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fsgdf and contrasts
by charujing123 25 Feb '14

25 Feb '14

Hi FS experts and users, I am trying to implement independent sample t-test and correlation analysis. Here is my fsgdf design: ----------------------------- GroupDescriptorFile 1 Title lh_ttest Class CON_IA Class PAT_IA Variables score1 score2 Input CON_IA01 CON_IA 0 0 Input CON_IA03 CON_IA 0 0 Input CON_IA05 CON_IA 0 0 Input CON_IA06 CON_IA 0 0 Input CON_IA07 CON_IA 3 7 Input CON_IA09 CON_IA 0 0 Input CON_IA14 CON_IA 0 0 Input CON_IA15 CON_IA 0 0 Input CON_IA16 CON_IA 7 12 Input CON_IA19 CON_IA 6 15 Input CON_IA24 CON_IA 6 11 Input CON_IA27 CON_IA 3 3 Input CON_IA32 CON_IA 7 21 Input CON_IA33 CON_IA 7 21 Input CON_IA35 CON_IA 0 0 Input CON_IA38 CON_IA 7 15 Input CON_IA39 CON_IA 2 3 Input CON_IA40 CON_IA 6 8 Input CON_IA41 CON_IA 2 4 Input PAT_IA01 PAT_IA 8 13 Input PAT_IA02 PAT_IA 9 38 Input PAT_IA03 PAT_IA 9 33 Input PAT_IA04 PAT_IA 9 27 Input PAT_IA06 PAT_IA 9 26 Input PAT_IA08 PAT_IA 8 16 Input PAT_IA09 PAT_IA 9 33 Input PAT_IA16 PAT_IA 9 35 Input PAT_IA18 PAT_IA 9 39 Input PAT_IA21 PAT_IA 9 32 Input PAT_IA22 PAT_IA 9 31 Input PAT_IA23 PAT_IA 9 35 Input PAT_IA24 PAT_IA 9 40 Input PAT_IA25 PAT_IA 9 29 Input PAT_IA27 PAT_IA 9 30 Input PAT_IA29 PAT_IA 9 30 Input PAT_IA30 PAT_IA 8 32 Input PAT_IA33 PAT_IA 9 13 Input PAT_IA34 PAT_IA 9 21 ------------------------------------------------ Contrasts for independent sample t-test: 1,CON_IA>PAT_IA:1 -1 0 0 0 0 2,PAT_IA>CON_IA:-1 1 0 0 0 0 Contrasts for correlation analysis: 1,possitive correlation analysis between pial thickness and score1:0 0 0.5 0.5 0 0 2,negtive correlation analysis between pial thickness and score1:0 0 -0.5 -0.5 0 0 3,positive correlation analysis between pial thickness and score2:0 0 0 0 0.5 0.5 4,negtive correlation analysis between pial thickness and score2:0 0 0 0 -0.5 -0.5 Are my designs appropriate? If I want to implement regression analysis(i.e. dependent variable is thickness and independent variables are score1 and score2), how to design my contrast? Thanks. All the best. Rujing Zha 2014-02-20 charujing123

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contrast question
by dgw 25 Feb '14

25 Feb '14

Hi, I have a quick contrast question. If I don't want to regress out one of my variables for a contrast how do i set that up in a contrast file? For example fsgd: Class a Class b Class c Class d Class e Variables age mmse Input s1 a 23 30 Input s1 b 25 21 Input s1 c 29 25 Input s1 d 26 23 Input s1 e 27 22 Would I have an mtx that looked like this to contrast e from c and d ? 0 0 -.167 -.167 .333 0 0 -.167 -.167 .333 0 0 -.167 -.167 .333 Does this make sense? Would i need to setup different fsgd files? Thank You, Dan

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Group Analysis Questions
by pfotiad＠nmr.mgh.harvard.edu 25 Feb '14

25 Feb '14

Hi FS community, I had a few questions regarding my understanding of the group analysis in FS: 1) If I use an fsgd file with Two Groups (One Factor/Two Levels), No Covariates, and my contrast matrix is [1 -1], do the resulting clusters (if any) show the regional significant differences between the two groups by comparing just the means of the values that I am comparing? For instance, if I'm comparing cortical thickness between a diseased and a control group, is this going to give me the clusters where the Diseased subjects' (no age included in the fsgd file, just the two groups) mean/regional cortical thickness differs significantly from the controls'? In other words, is a 50 yo subject's mean/regional cortical thickness going to be treated the same as a 80 yo subject's? 2) Now suppose that I would like to control for age. Then I'm assuming that I need to create an fsgd file with two Groups (One Factor/Two Levels) and One Covariate (age). Similarly, if I would want to visualize the differences in the regional values of cortical thickness between the two groups but after they have been controlled/adjusted for age, what contrast matrix should I use? Normally I would use [0 0 1 -1] but this will give me the significant differences in the age slopes not the mean values, unless I am missing something here. Thanks in advance for your help and sorry for the lengthy message. Best, Panos

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Re: [Freesurfer] FsAverage
by Douglas Greve 25 Feb '14

25 Feb '14

Please post questions to the list. Thanks! You need fsaverage. What are you trying to do? Usually people point SUBJECTS_DIR to a folder in space where they have write permission, then create a symlink from fsaverage to that space. Can you not do this? doug On 2/25/14 10:04 AM, Boadu, Osei B wrote: > Apparently I don't. Is there another way to get fsaverage? > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Monday, February 24, 2014 6:39 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FsAverage > > Do you have write permission into that folder? > > > On 02/24/2014 05:28 PM, Boadu, Osei B wrote: >> Hello, >> >> When trying to either create a symbolic link or copy the fsaverage >> folder, I am told that permission has been denied. E.g.: >> ln -s $FREESURFER_HOME/subjects/fsaverage fsaverage >> ln: creating symbolic link `fsaverage/fsaverage': Permission denied >> >> I'm not sure what I should do. >> >> Thanks, >> Osei >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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