Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

use manually defined talairach.xfm
by clemens.schroeder＠uzh.ch 15 Aug '17

15 Aug '17

Hi I got a Talairach Failure Detection Error and therefore did manual registration using tkregister2 following the advice at: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview Again following the advice on the site, I re-ran recon-all just to run into the identical error. When I checked talairach.xfm it was the same as BEFORE I did manual registration in tkregister2. The above site states: Because the talairach transformation affects everything in the stream it is necessary to rerun the whole process using your new talairach, which is a default. However, it seems this is not the default since recon-all comes up with its own talairach.xfm and overwrites my manual version, after which recon-all fails. How can I make recon-all use my manual registration?

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mri_glmfit long_stats_slopes with group
by Kasper Jessen 15 Aug '17

15 Aug '17

Dear Freesurfer, I would like to test if the percentage change (two time points) of cortical thickness is different between two groups. What i have done: FIRST: long_stats_slopes --qdec ./qdec/long.qdec.table.dat --stats lh.aparc.stats --meas thickness --sd $SUBJECTS_DIR --do-spc --generic-time --stack-spc ./qdec/long.lh.aparc.stats.stack.txt SECOND: mri_glmfit --osgm --glmdir lh_thickness.aparc-spc --table long.lh.aparc_thickness.stats.stack.txt THIRD: cat lh_thickness.aparc-spc/sig.table.dat Qesteions: 1. How do i test if there is a significant difference between the two groups? 2. How do i visualise this difference in FreeView? Best regards Kasper Jessen

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recon-all error
by Yeseul Kim 14 Aug '17

14 Aug '17

Hi I'm beginner of freesurfer and have an error while using recon-all. I'm Mac (Sierra) user. My subject's data is under: /Applications/freesurfer/subjects/yeseul_data After open terminal, I put commands like: export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=/Applications/freesurfer/subjects/yeseul_data/sbj1 recon-all –i $SUBJECTS_DIR/20170720_LHS.MR.HEAD_CNIR_IBS.0017.0001.2017. 07.20.16.26.07.667681.198987303.IMA –subject $SUBJECTS_DIR/sbj1_rec -all (My subjects' data is *.IMA format. Filenames are like "20170720_LHS.MR_HEAR_CNIR_IBS.0017.0001......198987303.IMA". I don't think I need to convert IMA format to another, right? Each subject has 192 IMA files and I want to apply recon-all to all of these files.) When I run these commands, I get a messages like: -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni Yeseului-MacBook-Pro:~ yeseulkim$ Yeseului-MacBook-Pro:~ yeseulkim$ export SUBJECTS_DIR=/Applications/ freesurfer/subjects/yeseul_data/sbj1 Yeseului-MacBook-Pro:~ yeseulkim$ Yeseului-MacBook-Pro:~ yeseulkim$ recon-all –i $SUBJECTS_DIR/20170720_LHS.MR .HEAD_CNIR_IBS.0017.0001.2017.07.20.16.26.07.667681.198987303 –subject $SUBJECTS_DIR/sbj1_rec -all ERROR: Flag i unrecognized. i /Applications/freesurfer/subjects/yeseul_data/sbj1/ 20170720_LHS.MR.HEAD_CNIR_IBS.0017.0001.2017.07.20.16.26.07.667681.198987303 subject /Applications/freesurfer/subjects/yeseul_data/sbj1/sbj1_rec -all Darwin Yeseului-MacBook-Pro.local 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Tue Aug 15 01:08:53 KST 2017 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting Does it matter with the format of my data files? Or did I set variables incorrectly? Thank you in advance! Best wishes, Yeseul -- Yeseul Kim Visual Cognitive Neuroscience Lab Department of Psychology Korea University Seoul, Korea

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obtaining the most recent build of FreeSurfer development version
by Antonin Skoch 14 Aug '17

14 Aug '17

Dear experts, I would like to download the most recent build of FreeSurfer development version (linux 64 bit). The origin/dev git repository contains commit up to today (14.8.17), but last change of "daily build" of dev version is 28.7.17. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Linux-c… How is the build of dev version sheduled? Antonin Skoch

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mri_binarize/mri_mask command help
by Yagmur Ozdemir 19 14 Aug '17

14 Aug '17

Dear FreeSurfer experts, I am trying to use the following command to merge the volume file of a template with original T1 orientation*, with a file like rawavg to get the full brain volume, but the following attached image gets produced and I am pretty sure, as a freesurfer novice, I am using a wrong command line. I have tried mri_mask as well but do not think it is the command to go. I also checked if two volumes are in the same orientation using mri_orient. mri_binarize --i rawavg.mgz --o scanner.template_angle.mgz --wm+vcsf * (I have the native oriented version of this volume template as well, and I attached a photo of the template as well) I would deeply appreciate if someone could help me correct my command line. Thank you all for the time and help Idil

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Developmental Neuroimaging Postdoc
by emma jane 14 Aug '17

14 Aug '17

The Program for Translational Research on Adversity and Neurodevelopment (P-TRAN) at The Pennsylvania State University is seeking a qualified postdoctoral researcher with expertise in human brain imaging, specifically magnetic resonance imaging (MRI)) with children and adolescents. This position is supported by a recently awarded NICHD Center Grant (i.e., a CAPSTONE Center for Multidisciplinary Research in Child Abuse and Neglect; PI: Dr. Jennie Noll) and will be based in the Child Maltreatment Solutions Network (http://solutionsnetwork.psu.edu/) and the Prevention Research Center (www.prevention.psu.edu) both of which are located on the University Park campus in State College, PA. The primary responsibility of this position will be to provide neuroimaging research support (e.g., experimental design, implementation and data analysis) to a longitudinal project that will consider the biological embedding of child maltreatment in multiple biologic systems (e.g., neuroendocrine, autonomic, genetic, epigenetic, immunologic) and the impact of embedding on health outcomes, including neurodevelopmental trajectories. Candidates must have a PhD in psychology, neuroscience, or an allied field, or have completed all requirements for a PhD by the time of appointment. Applicants must have expertise in human subjects MRI, preferably with developmental cohorts. Preference will be given to those candidates with experience working with children who have experienced maltreatment or other high-risk groups. The successful candidate will be expected to contribute to experimental design and co-ordination of the neuroimaging aspects of the project and data analysis. Candidates must demonstrate expertise in functional and structural MRI analysis methods using standard processing packages (e.g., SPM, AFNI, FSL, Freesurfer etc.) and experience with longitudinal and complex datasets would be advantageous. The postdoctoral researcher will also be expected to contribute to manuscript preparation and presentation of study-related outcomes at key scientific meetings. Extensive mentorship will be provided to the successful candidate in order to facilitate transition to an independent research career. This position will provide an opportunity to interact with several vibrant research communities at Penn State, including the Social Sciences Research Institute (www.ssri.psu.edu) and the Social, Life and Engineering Science Imaging Center (www.imaging.psu.edu) among others. The initial appointment will be for one year, with the possibility of renewal in subsequent years. Salary and benefits are based on NIH guidelines, commensurate with experience and qualifications. Interested candidates should upload a CV, cover letter, statement of research interests, and 2-3 relevant publications. In addition, applicants should arrange for 3 professional references to be submitted separately to Dr. Emma Jane Rose (Associate Director for P-TRAN) at emmajanerose(a)psu.edu. Review of applications will begin immediately and will continue until the position is filled. For further information about this appointment, please contact Dr. Emma Jane Rose at emmajanerose(a)psu.edu or 814-865-0114. Apply online at https://psu.jobs/job/69051 CAMPUS SECURITY CRIME STATISTICS: For more about safety at Penn State, and to review the Annual Security Report which contains information about crime statistics and other safety and security matters, please go to http://www.police.psu.edu/clery/, which will also provide you with detail on how to request a hard copy of the Annual Security Report. Penn State is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, color, religion, age, sex, sexual orientation, gender identity, national origin, disability or protected veteran status. -- *Emma Jane Rose PhD.* *Assistant Research Professor & * *Associate Director for the **Program for Translational Research on Adversity and Neurodevelopment (P-TRAN)* *Edna Bennett Pierce Prevention Research Center* *The Pennsylvania State University* *308 Biobehavioral Health Building* *University Park, PA 16802* *www.prevention.psu.edu <http://www.prevention.psu.edu/>* *www.npscoalition.org <http://www.npscoalition.org/>*

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Neuroimaging Postdoc at Penn State
by emma jane 14 Aug '17

14 Aug '17

[image: image.png] -- *Emma Jane Rose PhD.* *Assistant Research Professor & * *Associate Director for the **Program for Translational Research on Adversity and Neurodevelopment (P-TRAN)* *Edna Bennett Pierce Prevention Research Center* *The Pennsylvania State University* *308 Biobehavioral Health Building* *University Park, PA 16802* *www.prevention.psu.edu <http://www.prevention.psu.edu/>* *www.npscoalition.org <http://www.npscoalition.org/>*

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white matter ROI mask using an fsaverage label
by Eryilmaz, H. Hamdi 14 Aug '17

14 Aug '17

Hi Anastasia and FS experts, I am trying to create a white matter ROI mask underneath a cortical ROI label (e.g., 2 mm into the white matter) created in fsaverage space. I will then use this mask to extract values from individual dtifit_FA and dtifit_MD maps generated by trac-all. What would be the easiest way to do this? I thought about using mri_aparc2aseg but I am not quite sure about how to specify a label with this command. Thanks so much for your help! Best, Hamdi

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Combining Results of Per-Run GLM?
by Taylor, Johnmark 14 Aug '17

14 Aug '17

Hello, I am trying to do a GLM analysis for a study in which I scanned each participant twice. Currently, to combine the two scanning sessions I am combining the runs from the two sessions into a single session directory and applying per-session motion correction, essentially treating all the data as though it came from a single session. The issue is that when I do this, the GLM analysis takes prohibitively long (with just 8 subjects, the analysis has already been running for two weeks). To speed things up, I had the idea of doing the runwise GLM (getting the betas and contrast values for each run), then combining the runwise results to get t-values and p-values for the whole session. However, I am not entirely sure how to do this last bit; is there some kind of function that can be used to take all the per-run t-values or effect sizes in a session and combine them to get an aggregate t-value and p-value for the whole session, for a given contrast? I believe FSL follows this analysis strategy (doing runwise analyses then combining them into the whole session), so I was wondering whether FSFAST had a way of doing the same. Thank you very much, JohnMark

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Error when trying to compile the code
by Aziz Nanthaamornphong 14 Aug '17

14 Aug '17

Dear FreeSurfer Experts, I was trying to compile the FreeSurfer code by following steps shown in https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page However, I got this error message after I ran ./configure configure: error: FATAL: netcdf lib not found. Set LDFLAGS or --with-mni-dir. I currently use OS X El Capitan as the OS. How can I solve this problem? Thank you in advance. Aziz.

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