Freesurfer

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30084 discussions

can't change common-space subject in qdec
by Hubbard, Catherine 09 Nov '15

09 Nov '15

Dear Freesurfers: I've encountered the same problem as posted previously by Laura some time ago (see below), I am using qdec 1.5 with freesurfer version 5.3. freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Basically, I cannot change the common-space subject from the default fsaverage to my own custom template, which I have been able to do easily in the past. I should mention that we have recently made some changes to our server, so I'm not sure if this is related but suspect it is - I am also running Java8 also we are running ubuntu and here are some of the details regarding the environment I'm working in: CPU: 12-core Xeon E5 at 2.7 GHz GPU: 2 Radeon HD 7900 RAM: 64 GB (4x16 GB) of 1866 MHz DDR3 ECC Storage: 1 TB PCI-e Flash OS: Ubuntu Server 14.04.3 LTS Desktop Environment: Gnome 3.9.90 Java SE Runtime Environment: build 1.8.0_66-b17 GCC: 4.8.4 MATLAB: R2015a (8.5.0.197613) Freesurfer installation: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 tcsh version: 6.18.01 (Astron) libjpeg62-dev: installed Thanks for all your help!

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Re: [Freesurfer] Issues with fsgd g2v1
by Martin Reuter 09 Nov '15

09 Nov '15

Dear Heidi, 1. you need to specify --surface <subj> <hemi> for your data, subj is where the surface stack was created, usually fsaverage, and hemi is lh in your case (base on your input name for y). 2. you need to source freesurfer. The license file needs to be in FREESURFER_HOME (a file called .license). There should be lot's of comments in the archive of this mailing list about that. Best, Martin On 11/09/2015 04:49 AM, Heidi Foo wrote: > Dear Martin, > > I was trying out the mri_glmfit command. However, I have encountered > some problems with it and I was hoping that you could help me with it. > > When inputing the --y input file, it showed an error to use '--surface > subject hemi' with surface data (Attached the file). > > Also, when using tksurfer/tkmedit commands, an error that the > freesurfer license is not found. > > Would you kindly advice me on what I should do? > > Any help is very much appreciated. > > Thanks! > > Regards, > Heidi Foo -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu

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extract pial surface
by Sandy Schramm 09 Nov '15

09 Nov '15

Dear experts, how can I extract pial surface (in mm2) of all our participants? Performing aparcstats2table -meas area extracts white area. Thanks, Sandy

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Curvilinear interaction with age
by Yang, Daniel 08 Nov '15

08 Nov '15

Dear FreeSurfer experts, I have a group variable (X) with two levels and I want to test if there is a curvilinear interaction with age (Z). Can this be tested in FreeSurfer? Specifically, the model would be Y = b0 + b1X + b2Z + b3Z*Z + b4X*Z + b5X*Z*Z + error I want to test b5 while controlling for b0-b4. Many thanks! Daniel

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cannot start freesurfer from terminal
by André Schmidt 08 Nov '15

08 Nov '15

Dear FS experts, Surprisingly, I am no longer able to start freesurfer from the terminal: Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOME/SetUpFreeSurfer.sh Do you know what I am doing wrong? Thank you Andre

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Postdoctoral Position in Neuroimaging – Quantitative Neuroimaging Laboratory (QNL), Cognitive Neuroscience Division, Columbia University, NYC
by Ray Razlighi 06 Nov '15

06 Nov '15

Postdoctoral Position in Neuroimaging – Quantitative Neuroimaging Laboratory (QNL), Cognitive Neuroscience Division, Columbia University, NYC *Job Summary:* QNL invites applications for a full-time postdoctoral position to conduct processing and analyzing of PET and MRI neuroimaging data, as part of multiple research studies on aging and Alzheimer’s disease. *Principal Responsibilities:* The primary responsibility of this position includes developing novel image processing and statistical analysis methods for reconstruction of brain Beta Amyloid PET images and its accompanying structural MRI and fMRI data from healthy and diseased participants of multiple studies all focusing on aging and Alzheimer’s disease. The QNL is a new research infrastructure housed in the Cognitive Neuroscience Division of the Columbia University Medical Center Neurology Department. The main focus of the QNL is to develop techniques to quantify structural and functional brain images which allow researchers and clinicians to detect brain-based effects that are normally beyond the sensitivity and specificity of commonly-used detection methods in the field. We aim to achieve this goal by utilizing state-of-the-art signal and image processing tools as well as mathematical and statistical method. We are affiliated with Columbia’s Biomedical Engineering Department, Sergevsky Center, and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain. *Required Qualifications:* · PhD in Biomedical/Electrical Engineering, Computer Science, Medical Physics, Neuroscience or related disciplines. · Strong background in MRI analysis and related statistical methods for research (SPM, Freesurfer, FSL, AFNI or similar). · Experience with image processing and data analysis. · Strong computer programming skills (e.g., in C/C++, Matlab, R, and especially Python) are highly desirable. · Ability to think independently and work collaboratively. *Benefits* · Columbia University officers' benefits applies · Starting date: Jan 2015. · The postdoctoral position is scheduled initially for two years (open to renewal). · Salary will depend on experience. *Additional Information:* To apply, please submit a single PDF file containing the following: 1) Cover letter describing research interests and relevant background; 2) CV with list of publications; 3) The names of three individuals who could provide reference letters. All files or inquiries should be submitted electronically at: academicjobs.columbia.edu/applicants/Central?quickFind=61752 Ray Razlighi Assistant Professor in Neurology Adjunct Assistant Professor in Biomedical Engineering Email: qr2108(a)cumc.columbia.edu

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Surface-based registration
by Razlighi, Qolamreza R. 06 Nov '15

06 Nov '15

Hi Guys, I read in the sidenote here (https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) that inter-subject surface base registration using mris_register and -1 flag performs a sort of rigid registration. So I tried it between two of my subjects with the command below mris_register -1 -curv P00001639/FreeSurferClean/surf/lh.sphere P00001639/FreeSurferClean/surf/lh.sphere lh.sphere3.reg and got the results (see the attachment). It is clear that the registration output is just a shifted version of the source. Having this confirmed I want to know if there is any way to force the mris_register to perform a complete non-linear surface based registration for inter-subjects registration the same way it does for template. I have to mention that I visualize the lh.sphere3.reg using freeview and loaded the sane lh.curv on that surface. I hope I’m not doing anything stupid. [cid:AEB13CCB-455D-4591-B278-FEF31F6C0B4B@cpmc.columbia.edu] Best -- Ray Razlighi, Ph.D. Assistant Professor Quantitative Neuroimaging Laboratory Division of Cognitive Neuroscience Department of Neurology Columbia University Alt: razlighi(a)gmail.com<mailto:razlighi@gmail.com> Office Phone: 212-342-1352 Office Fax: 212-342-1838 Website: http://www.columbia.edu/cu/qnl/

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R: Re: R: Re: average z-score of each subject from a common cluster
by stdp82＠virgilio.it 06 Nov '15

06 Nov '15

I have run mri_segstats --seg .../my-glm.wls/group.diff/cache.th13.neg.sig.masked. nii.gz rh parc --i subj/fc.seed.surf.rh/R_seed/z.nii.gz --sum summaryfile and I have obtained 9 columns and 5 rows. I'm confused on results. Where is the mean z-score for cache.th13.neg. sig.masked.nii.gz? # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 -4 7 7.0 Seg-004 -2.4544 0.5023 -3.2164 -1.7619 1.4545 2 -3 153 153.0 Seg-003 -2.6662 1.4724 -6.2120 1.7587 7.9707 3 -2 848 848.0 Seg-002 -2.4930 2.0088 -6.4504 2.3528 8.8032 4 -1 1518 1518.0 Seg-001 -2.1416 1.6727 -6.4227 2.5420 8.9648 5 0 161316 161316.0 Seg0000 1.4152 1.6218 -7.0471 14.1452 21.1923 Because my data are on surface mri_surfcluster should be helpful? Thanks. Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 3-nov-2015 19.55 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: average z-score of each subject from a common cluster > >look in the summaryfile. Also, don't use --seg z.nii.gz. In the command >below, it works because you have --annot afterwards, but in general it >is not correct > >On 10/30/2015 04:22 PM, stdp82(a)virgilio.it wrote: >> Thanks. >> I have obtained: >> >> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ >> >> cwd >> >> cmdline mri_segstats --seg z.nii.gz --annot Control21_FS rh aparc -- i >> z.nii.gz --sum summaryfile >> >> sysname Darwin >> >> hostname iMac-di-Stefano.local >> >> machine x86_64 >> >> user Stefano >> >> UseRobust 0 >> >> Loading z.nii.gz >> >> Loading z.nii.gz >> >> Voxel Volume is 1 mm^3 >> >> Generating list of segmentation ids >> >> Found 22 segmentations >> >> Computing statistics for each segmentation >> >> 0 -7 2 2.000 >> >> 1 -6 110 110.000 >> >> 2 -5 255 255.000 >> >> 3 -4 518 518.000 >> >> 4 -3 1190 1190.000 >> >> 5 -2 1692 1692.000 >> >> 6 -1 4104 4104.000 >> >> 7 0 61577 61577.000 >> >> 8 1 42598 42598.000 >> >> 9 2 28146 28146.000 >> >> 10 3 14859 14859.000 >> >> 11 4 5845 5845.000 >> >> 12 5 1899 1899.000 >> >> 13 6 485 485.000 >> >> 14 7 116 116.000 >> >> 15 8 75 75.000 >> >> 16 9 74 74.000 >> >> 17 10 78 78.000 >> >> 18 11 65 65.000 >> >> 19 12 104 104.000 >> >> 20 13 45 45.000 >> >> 21 14 5 5.000 >> >> >> How I can know the meaning of this number? Where is z? >> >> I have tried also with: >> >> mri_segstats --seg z.nii.gz --annot Control_21 rh aparc --i z.nii. gz >> --sum summaryfile --mask >> .../fc.ramgseed.surf.rh/R_Amygdala/my-glm.wls/group.diff/cache.th13. neg.sig.masked.nii.gz >> --avgwfvol mrivol >> >> >> but I have problem with interpretation. >> >> >> >> Stefano >> >> >> ----Messaggio originale---- >> Da: greve(a)nmr.mgh.harvard.edu >> Data: 30-ott-2015 16.17 >> A: <freesurfer(a)nmr.mgh.harvard.edu> >> Ogg: Re: [Freesurfer] average z-score of each subject from a >> common cluster >> >> >> >> On 10/30/15 7:16 AM, stdp82(a)virgilio.it wrote: >>> Hi list, >>> I have two queries, please. >>> >>> I'd like to have the z-score from my rsfMRI data (seed- analyis). >>> >>> 1) I have extract the z-score from the Vtx Max >>> >>> In details, after groups comparison analysis, I have opened >>> the cache.th13.pos.sig.cluster.summary contained in group.diff >>> folder and I have read the Vtx Max coordinates. >>> Next, I have open the z.nii.gz of each subject and I have >>> expected the z-score from the vertex which have the Vtx Max >>> coordinates. >>> >>> Is this procedure corrected? >> Yes >>> >>> 2) z-score of each subject from a common cluster >>> >>> I would like to use the cluster which shows the group difference >>> (cache.th13.pos.sig.cluster.nii.gz) as ROI mask. Thus, I would >>> extract from it the average of the z-score which is contained in >>> each subject. >>> How should I do? >> Use mri_segstats passing the z map as the input (--i) and the >> cluster map as the seg. The output will be --sum. Run with -- help >> for more info >>> >>> Thanks. >>> >>> >>> Stefano >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> _______________________________________________ >> 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 > > >The information in this e-mail is intended only for the person to whom it is >addressed. If you believe this e-mail was sent to you in error and the e-mail >contains patient information, please contact the Partners Compliance HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in error >but does not contain patient information, please contact the sender and properly >dispose of the e-mail. > >

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mri_convert and large values
by McMains, Stephanie 06 Nov '15

06 Nov '15

We are finding a conversion problem with our latest multiband/SMS data (Using a sequence from Minnesota). The values can be very large, greater than 53,000. These large voxels get turned into very large negative numbers when converting to nii. This happens even if we use the flag –odt float and/or –ns 1. When we use the –odt flag, it does set the output data type to float32, but the values are still wrong. We're using FreeSurfrer 5.3.0 on CentOS 6.5 x86_64. Thanks, Stephanie +++++++++++++++++++++++++ Stephanie McMains Neuroimaging Staff Scientist Center for Brain Science Harvard University 52 Oxford Street Cambridge, MA 02138 +++++++++++++++++++++++++ For answers to frequently asked questions: http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/information…

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Re: [Freesurfer] Recon-all with lower resolution T2 / Proton Density reconstructions and higher res T1
by Ajay Kurani 06 Nov '15

06 Nov '15

Hi Bruce, 1) I was also concerned 3mm may be too thick but I will try a few subjects to see how it goes. 2) Hi Eugenio I wanted to see if you can give a bit of insight into the hippocampal issue. 3) Bruce, sorry for the confusion. I was referring to sqrt(T1w*B1 x T2w*B1) ~ B1 bias field estimate not the T1/T2 myelin mapping. Do you see any forseeable issues of correcting the T1w and T2w image with the B1 estimate prior to running myelin mapping (T1/T2)? Essentially if we remove B1 already then there should not be any additional B1 cancellation when dividing the images. Do you see any issue with using the same B1 bias field to correct resting state data after motion correction is performed? Thanks, Ajay

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