Freesurfer June 2017

freesurfer@nmr.mgh.harvard.edu

116 participants
186 discussions

question in using qdec
by 王梓良 04 Jun '17

04 Jun '17

Dear FS experts I have two questions when I use qdec in group analysis. Firstly , when I press the button of ‘ set using FDR ’, there is no result left no matter how big the threshold is. But I notice the value in the color bar changes, the value is not consistent with the terminal. I don’t know whether there is something wrong. Besides, after pressFindClustersAndGotoMax button, we can get a Scatter plot, Can I calculate it correlation coefficient and p value in freesurfer. Thanks in advance Regards Ziliang Wang

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Label numbers aparc.a2009s
by Juergen Haenggi 03 Jun '17

03 Jun '17

Dear FS experts I have a question wrt the label numbers in FreeSurferColorLUT.txt compared with those in aparc.a2009s+aseg.mgz. I noticed that the last ctx (GM) label in FreeSurferColorLUT.txt file is 12175 ctx_rh_S_temporal_transverse whereas in the aparc.a2009s+aseg.mgz file, the highest intensity (label number) is 12138. Where this difference come from? Thanks in advance Regards Jürgen Hänggi ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. -----------------------------------------------------------------------------------------------------

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running hippocampal segmentation on PING
by Anthony Dick 02 Jun '17

02 Jun '17

Hello, Our group is interested in running the hippocampal segmentation on the PING dataset. That dataset was already Freesurfed, v4.5. When we try to just run the –hippocampal-subfields flag (i.e., recon-all -s bert -hippocampal-subfields-T1) it dies looking for a number of files that were not a part of v.4.5. One option is to start from scratch with v6: recon-all -all -s bert -hippocampal-subfields-T1 However, this seems to be a bad option because the quality control on the ~1500 brains is already completed for the original FS run. My question is, are there certain flags from –autorecon2 and –autorecon3 that we could run so we don’t have to re-freesurf everything, or would it be better to just run –all? In other words, what are the minimum files needed to get hippocampal-subfields-T1 to run? Thanks for any suggestions! Anthony — Anthony Steven Dick, Ph.D. Associate Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://myweb.fiu.edu/adick Join the Society for the Study of Human Development: http://www.sshdonline.org

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02 Jun '17

Dear Freesurfer experts, I have used fslregister to register fMRI data to anatomical data. However, now I would like to register all fMRI runs to the fMRI run that I have registered to the anatomical data. Could someone please let me know how to get a register.dat file between fMRI runs? Many thanks already in advance! Best, Maria

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Creating age-adjusted z score maps against a control group
by Elijah Mak 02 Jun '17

02 Jun '17

Hi Doug, I have used fscalc to create subject-level Z score maps of cortical thickness against a set of healthy controls. fscalc $i/surf/lh.fsaverage.mgh sub group_mean_control_lh.mgh div group_std_control_lh.mgh --o $i/surf/lh.Z.thickness.fsaverage.mgh; done Beyond this, is there a way to adjust the Z score maps for age, and then produce an age-adjusted Z score map? Thanks for your help. Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry, Old Age Psychiatry Group University of Cambridge Trinity College, CB21TQ, UK http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24

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question about recon-all
by Jasmin Alves 01 Jun '17

01 Jun '17

Hello, I have used FS6.0 to do recon-all on about 57 brains, but for some reason, recon-all is not working on some brains, recon-all is not able to get past "Automatic topology fixer", after the command has been running for 24 hours. Is it possible there is too much motion in the image? Or does FS6.0 possibly take longer to complete for some brains? Thanks, Jasmin -- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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Monte Carlo error (fwhm4 vs. fwhm04)
by Rockers, Elijah D. 01 Jun '17

01 Jun '17

Hello FS, I am attempting to run a monte carlo simulation on some cortical thickness data in Qdec 1.5, but I get the following error: ERROR: CSDread(): could not open ....../freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm4/abs/th40/mc-z.csd I thought it might be a permissions issue since the installation is on an NFS share, but in fact the ......./lh/cortex/fwhm4/.... directory does not exist. There is a fwhm04, but not fwhm4. I have two versions of FS installed (5.3 and 6) so I thought it might be referencing the wrong version, but in fact both versions have the same directory structure anyway... Any ideas what is going on? Thanks, - Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Post Doc Job Posting
by O'Shea,Andrew 01 Jun '17

01 Jun '17

Hello, We are looking for a Post-doctoral associate with experience and skills in multimodal neuroimaging. See below for the posting. Post-doctoral Associate Woods Lab, Center for Cognitive Aging and Memory Description: The Department of Clinical and Health Psychology and Center for Cognitive Aging and Memory are searching for a highly qualified post-doctoral associate candidate to join the research team of Dr. Adam Woods to study the benefits of transcranial direct current stimulation (tDCS) for enhancing cognitive training effects in older adults. The Woods lab focuses on discovering and implementing novel interventions aimed at combating cognitive aging and slowing the onset of dementia in older adults, with a special interest in understanding the neural mechanisms of intervention effects. This position will work on Dr. Woods NIA funded clinical trials using transcranial direct current stimulation paired with cognitive training. The ACT study (R01) is a Phase III randomized clinical trial, while the Stimulated Brain study (K01) is a phase II RCT. These studies use comprehensive neurocognitive assessment and multimodal neuroimaging/spectroscopy to investigate the impact of tDCS and cognitive training on the brain and cognitive function in older adults. The post-doctoral trainee will have the opportunity to learn or enhance their skills in 1) multimodal neuroimaging/spectroscopy [including structural (T1 and FLAIR), functional MRI (active and resting BOLD), and GABA MEGA-PRESS magnetic resonance spectroscopy], 2) neurocognitive assessment, 3) non-invasive brain stimulation (tDCS/tACS/TMS), and/or clinical trials. In addition, the post-doctoral associate will have the opportunity to develop his or her own novel tDCS based research projects. Dr. Woods’ lab consists of 4 full time research coordinators, 2 graduate students, and administrative staff. In working in Dr. Woods’ lab, this position will join the Center for Cognitive Aging and Memory, which consists of 3 primary faculty, 12 affiliate faculty, 16 graduate students and research assistants, and two post-doctoral fellows. The Center and Dr. Woods’ lab maintains a 1000 square foot research space with dedicated parking. This facility houses Dr. Woods’ electrophysiology lab, tDCS lab, TMS lab, and 5 dedicated testing rooms in the McKnight Brain Institute. The lab is directly adjacent to both 3T research MRI systems (Siemens Prisma and Philips Achieva) and the CAM phlebotomy lab at the University of Florida. Preferred start date is July or August 1, 2017, but negotiable. The position will involve conducting assessment and intervention visits on tDCS studies, analyzing data (neuroimaging and behavioral), supervision of graduate students and staff, and writing manuscripts and grants. The post-doctoral associate is expected to possess good written and oral English language skills to present research updates at weekly lab meetings, seminars and conferences as well as to assist in writing manuscripts and grants related to the project. Advertised Salary: Salary will be in line with NIH Policy for post-doctoral positions. Minimum Requirements: The position requires a PhD or MD/PhD. Applicants should have good communication, problem-solving skills, and ability to work flexible hours depending on specific experiments. Preferred Qualifications: Neuroimaging tDCS or other non-invasive brain stimulation method Cognitive Neuroscience, Neuropsychology, or Psychology Excellent written and oral communication skills Special Instructions to Applicants: Please attach curriculum vitae and 3 reference letters and cover letter articulating your interests in the lab. Final candidate will be required to provide official transcript to the hiring department upon hire. A transcript will not be considered "official" if a designation of "Issued to Student" is visible. Degrees earned from an education institution outside of the United States are required to be evaluated by a professional credentialing service provider approved by the National Association of Credential Evaluation Services (NACES), which can be found at http://www.naces.org/. The University of Florida is an equal opportunity institution dedicated to building a broadly diverse and inclusive faculty and staff. For additional information, please contact Dr. Adam Woods at ajwoods(a)phhp.ufl.edu<mailto:ajwoods@phhp.ufl.edu>

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Separating Regions of the Brain from Choi and Yeo Loose and Tight Atlases
by Thomas DeRamus 01 Jun '17

01 Jun '17

Hi Freesurfer Mailing list, I'm examining striatal-to-cortical connections using resting state MRI and diffusion weighted imaging with tractography. I figured the Choi and Yeo atlases in Freesurfer would be the best choice for this but I'm having some difficulties implementing them. Since I'm curious about the anatomical specificity of FC and tracts grown, I took the conservative versions of the Choi and Yeo atlases and split them into left-and right hemispheres, and also separated those with multiple regions in a network (i.e. head of caudate and putamen tail in Choi or MFG, IPL, and SMA in one network in Yeo) with some clustering software. The clusters match up the to original version of the conservative (Tight on the website) well and I intend to use that for FC analyses, but I would prefer to use the liberal mask for tractography. Problematically, I've noticed that trying to separate the regions with the same clustering software on the liberal mask does not separate the regions the same way it did in the conservative mask (i.e. one cluster may contain the head of the caudate and part of the putamen). I probably shouldn't be surprised by this, but I was wondering if you would mind explaining the way the liberal versions of these masks were created. or a reasonable alternative, so that I might be able to do the same on the parcellations I've separated out into ROIs? I could do simple dilation I suppose, but I would like it to be as close to the original liberal mask as possible. -- *Thomas DeRamus* UAB Department of Psychology, Behavioral Neuroscience Graduate Research Trainee Civitan International Research Center 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 *Phone*: 205-934-0971 *Email:* tpderamus(a)gmail.com, faustus(a)uab.edu

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Talairach transform QA on pre-defaced subjects
by Giuseppe Cabras 01 Jun '17

01 Jun '17

Dear FS developers and expert users, I am preprocessing with freesurfer 6.0 recon-all a set of pre defaced subjects and the results are generally good, but the Talairach transform QA measure are terribly bad and exactly the same on all defaced: #----------------------------------------------------- TalAviQA: 0.00000 z-score: -222 WARNING: Talairach QA check failed! z-score of -222 is <= threshold of -9 #---------------------------------------------------- I have tried a few local subject of the set with face and the QA is acceptable (z-score=-2) and is the same if I pre-deface the subject with mri_deface in FS6.0 with the correct parameters. I don't know how the original datasets were defaced, but I suppose with mri_deface in an unknown older version. I need to process the defaced datasets, but I am warring about the recon-all output measure, in fact I found a thickness error of 28% between deface and face temporal lobe of the same subject. How do you suggest to proceed? Thanks in advance, cheers, Giuseppe

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Freesurfer June 2017