Freesurfer December 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
175 discussions

Power analysis
by Laura Ferrero 12 Dec '18

12 Dec '18

External Email - Use Caution Hi, I want to perform a power analysis and I read that I need 3 of 4 things: 1. Effect size (mean/std) 2. False positive rate 3. Number of subjects 4. True positive rate I also read that the effect size can be calculated using gamma.mgh and gammavar.mgh files but I do not know how to open them in order to get the numbers. Thank you, Laura

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Job ad: small animal MRI faculty position
by Keith Schneider 12 Dec '18

12 Dec '18

External Email - Use Caution Associate Professor, Behavioral Neuroscience University of Delaware: College of Arts & Sciences: Psychological & Brain Sciences Location: Newark, DE The University of Delaware invites applications for a tenured associate professor (or assistant professor nearing tenure) in behavioral neuroscience to begin September 1, 2019. We are seeking to hire a scholar with a solid background in small animal fMRI and/or DTI at ultrahigh fields for linking systems neuroscience and brain MR imaging (the university has a 9.4T/30cm Bruker MRI for animal research). The exact discipline area is open for this position as scholarly excellence will be the primary consideration. Ideal candidates will have extensive experience in brain science-oriented MR research, demonstrate outstanding and innovative scholarship, and have collaborative and synergistic possibilities with existing researchers at UD. The candidate should enjoy collaborating with researchers from various disciplines (e.g., medical engineering, biochemistry) and helping researchers new to MRI. This is an outstanding opportunity for a scholar to join and strengthen the growing Department of Psychological and Brain Sciences (https://www.psych.udel.edu <https://www.psych.udel.edu/>) and University of Delaware (https://www.udel.edu <https://www.udel.edu/>) that already has a promising core of interdisciplinary researchers utilizing cutting edge methodologies. An innovative leader in research and teaching, the University of Delaware combines a rich historic legacy with a commitment to education and the latest in advanced technology. With external funding exceeding $200 million per year, the University ranks among the top 100 universities in federal R&D support for science and engineering. Enhanced by state-of-the-art facilities, research is conducted across all seven colleges and numerous interdisciplinary institutes and centers. Relevant facilities on campus include the new 11,600 square foot Center for Biomedical and Brain Imaging, housing the 9.4T/30cm Bruker MRI, a 3T Siemens Magnetom Prisma, and transcranial magnetic stimulation machine; a 103,000 square foot Health Sciences Complex, a facility that includes labs for small animal and human-based studies, and an active outpatient clinic; a 194,000 square foot Interdisciplinary Science and Engineering Laboratory; and the Delaware Technology Park, where entrepreneurial and academic research labs are co-located. The Delaware Health Sciences Alliance (DHSA), a partnership among the University of Delaware, Christiana Care Health System <http://www.christianacare.org/>, Nemours/Alfred I. du Pont Hospital for Children <http://www.nemours.org/welcome.html>, and Thomas Jefferson University <http://www.tju.edu/>, provides infrastructure and opportunity for innovative clinical and translational collaborations. The University of Delaware is located in Newark, Delaware, which is only a short drive or train commute from Philadelphia, PA. UD is also within driving distance of New York City, Baltimore, Washington DC, the Poconos and some of the finest beaches in the country, making it an ideal location for day or weekend trips. QUALIFICATIONS Applicants for this position must have earned a Ph.D., tenure (or be nearing tenure), have a history of high-level publications in behavioral neuroscience or related fields, and conduct fundable research. APPLICATION INSTRUCTIONS Using the Interfolio system at UD, http://apply.interfolio.com/58701 <http://apply.interfolio.com/58701>, applicants submit a cover letter, a statement of research, a current curriculum vitae, three representative publications, and three confidential letters of reference. Inquiries, but not application materials, should be emailed to Jeffrey Rosen, Chair of the small animal MRI Faculty Search committee, jrosen(a)psych.udel.edu. Review of applications will begin on January 15, 2019 and will continue until the position is filled. The University of Delaware is an Equal Opportunity Employer which encourages applications from minority group members and women. The University's Notice of Non-Discrimination can be found at http://www.udel.edu/aboutus/legalnotices.html. ----- Keith Schneider Director, Center for Biomedical and Brain Imaging Associate Professor Department of Psychological and Brain Sciences University of Delaware

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recon-all ERROR: killed
by 张亮军 12 Dec '18

12 Dec '18

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to use "recon-all -i T1.nii.gz -s zhang -all", but there is a ERROR: saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt Killed Linux ubuntu 4.10.0-37-generic #41~16.04.1-Ubuntu SMP Fri Oct 6 22:42:59 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s zhang exited with ERRORS at Wed Dec 12 22:18:35 CST 2018 For more details, see the log file /usr/local/freesurfer/subjects/zhang/scripts/recon-all.log I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu16.04 LTS(VMware Workstations pro) 3) uname -a: Linux ubuntu 4.10.0-37-generic #41~16.04.1-Ubuntu SMP Fri Oct 6 22:42:59 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: killed Best, Liangjun.

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Beta series method in FS?
by Hahn, Emily M. 12 Dec '18

12 Dec '18

Hi, I am interested in using the beta series method (https://neuroscape.ucsf.edu/wp-content/uploads/publications/Rissman2004-Mea…) for intra-subject analysis. Is there a straightforward way to do this in FreeSurfer? I attempted and the following analysis (code starting @ foreach) and an error appeared at the selxavg3-sess step: ERROR: condition ids are not contiguous Should I include a positive contrast for each condition (i.e. instead of '-no-con-ok', use 'mkcontrast-sess -analysis $analysis -contrast $contrast -a $1_to_194') or is something else about the design erroneous? Thank you in advance for feedback. Notes regarding the paradigm file: (1) treats each condition type as a unique event (i.e. second column consists of numbers 1:194; $Nconditions = 194) (2) stim weight == 1 (i.e. third column all ones) foreach cortices ( lh rh ) mkanalysis-sess \ -fsd $fsd \ -surface fsaverage $cortices \ -fwhm $FWHM \ -event-related \ -paradigm $paradigm \ -nconditions $Nconditions \ -spmhrf 0 \ -TR $TR \ -refeventdur $EVENT_DUR \ -nskip $Nskip \ -hpf $HPF \ -analysis bsm.analyses.$cortices \ -per-run \ -nuisreg $MC_nuis -1 \ -tpexclude $MCR_censor \ -force end foreach cortices ( lh rh ) selxavg3-sess \ -s $SUBJECT \ -analysis bsm.analyses.$cortices \ -no-con-ok end ------ Emily M. Hahn | Clinical-Computational Research Coordinator Division of Neurotherapeutics | A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital/Harvard Medical School

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Download link for Matlab runtime broken?
by raul perez moraga 12 Dec '18

12 Dec '18

External Email - Use Caution Hello! I tried to download the Matlab runtime for Linux to use FSFAST but the link is broken. https://surfer.nmr.mgh.harvard.edu/pub/dist/mcr/MCRv83_linux.tar.gz Not Found The requested URL /pub/dist/mcr/MCRv83_linux.tar.gz was not found on this server. ------------------------------ Apache/2.2.15 (CentOS) Server at surfer.nmr.mgh.harvard.edu Port 443 Thanks in advance Raúl

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Problems with GM segmentation -- How to solve it
by Rosalia Dacosta Aguayo 12 Dec '18

12 Dec '18

External Email - Use Caution Dear Free Surfer team and Bruce, I have been doing well editing the skull stripping, and using control points to improve white matter segmentation. Furthermore, the few participants I had problems with due to large ventricles were solved using the flag you recommended me to use. I am very grateful for all your help. However, I am facing another problem I thought I could solve using control points as well but this is worsening things instead of improving them. I refer to grey matter segmentation. I have found that several participants, more than I would like, are having problems with grey matter segmentation in the ventral temporal lobes and in the occipital lobe as well. I wonder if you could kindly help me with this, telling me how I could solve this problem so GM and WM segmentation are fine. Yours sincerely, Rosalia

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aparc regions misclassified
by Simon Jones 11 Dec '18

11 Dec '18

External Email - Use Caution Hi all, I have some participants whose recons look OK except the parcellations are incorrect. For instance the right precentral gyrus should be postcentral in three people. This appears as a shifting of multiple regions posteriorly. Is there a way to fix this? Thanks for your help, Simon

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Classification of amygdala subregions using Freesurfers new Algorithm
by Sally Grace 11 Dec '18

11 Dec '18

External Email - Use Caution Dear Eugenio and experts, I have run the segmentation of the hippocampus subfields and nuclei of the amygdala using the latest algorithm implemented in the development version of Freesurfer. We have a priori hypotheses regarding the basolateral amygdala. I understand that you have broken the amygdala output down into the distinct subregions, e.g., the basal, lateral and accessory basal amygdala nuclei. Based on this reference https://www.physiology.org/doi/pdf/10.1152/physrev.00002.2003, my understanding is that the "basolateral nucleus" is comprised of the basal and lateral nucleus of the amygdala and the "basolateral nuclei" (aka. basolateral complex) comprises basal, lateral and accessory basal nuclei. So, I can create a variable called the "basolateral nucleus" (by adding together the basal + lateral) and the "basolateral complex" (by adding together basal + lateral + accessory basal). Is this assumption correct? Kind regards, Sally.

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Fwd: fcseedcor output
by Sara Jafakesh 11 Dec '18

11 Dec '18

External Email - Use Caution -----Original Message----- From: "Sara Jafakesh" <S.Jafakesh(a)sutech.ac.ir> To: freesurfer(a)nmr.mgh.harvard.edu Cc: DGREVE(a)mgh.harvard.edu Date: Sat, 08 Dec 2018 22:25:20 +0330 Subject: Fwd: fcseedcor output -----Original Message----- From: "Sara Jafakesh" <S.Jafakesh(a)sutech.ac.ir> To: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Date: Sat, 08 Dec 2018 12:21:06 +0330 Subject: Re: fcseedcor output Dear Greve I send the entire email chain: I think some thing wrong with my matlab setting, It is not compatible with my freesurfer I guess, but I dont know how can I compatible matlab with freesurfer. best.. Can? you send the full terminal output? On 12/05/2018 01:25 AM, Sara Jafakesh wrote: > > ????????External Email - Use Caution > > > Dear freesurfer experts, > I want to calculate corrolation between two seeds with > freesurfer-linux-centos6_x86_64_stable_pub-v6 .after using > fcseed-config and fcseed-sess, I used fcseedcor. the command > that I trying to run is as follow: > fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed > lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg > 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat > but the output of fcseedcor is not dat file ( the > connectivity matrix for my result 2*2 matrix) as it has been > explained in the fcssedcor help. the output is just the log > file named seedcor2.dat.log. although it has been done > without error. > I really dont know what is the problem. > I would be grateful if you could help me. > best regards, > sara hi sara, can you include the entire email chain so that I can see the context? On 12/7/18 4:19 PM, Sara Jafakesh wrote: External Email - Use Caution Dear Dr.GREVE , thank you for your reply my full terminal output is: [user at localhost subjects]$ fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat Sat Dec 1 18:05:11 IRST 2018 setenv SUBJECTS_DIR /home/user/freesurfer/subjects cd /home/user/freesurfer/subjects /home/user/freesurfer/fsfast/bin/fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: fcseedcor,v 1.3 2015/12/10 22:51:29 zkaufman Exp $ Linux localhost.localdomain 2.6.32-642.el6.x86_64 #1 SMP Tue May 10 17:27:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux ------- matlab output -------------------- matlab: Command not found. Started at Sat Dec 1 18:05:11 IRST 2018 Ended at Sat Dec 1 18:05:12 IRST 2018 Fcseedcor-Run-Time-Sec 1 Fcseedcor-Run-Time-Hours 0.00 fcseedcor Done best, sara -----Original Message----- From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> To: Sara Jafakesh <S.Jafakesh(a)sutech.ac.ir>, "87fc6eef-18d0-2f7d-99f5-eb8a79707c5c(a)mgh.harvard.edu" <87fc6eef-18d0-2f7d-99f5-eb8a79707c5c(a)mgh.harvard.edu> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Date: Fri, 7 Dec 2018 22:33:49 +0000 Subject: Re: fcseedcor output hi sara, can you include the entire email chain so that I can see the context? On 12/7/18 4:19 PM, Sara Jafakesh wrote: External Email - Use Caution Dear Dr.GREVE , thank you for your reply my full terminal outpou is : [user@localhost subjects]$ fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat Sat Dec 1 18:05:11 IRST 2018 setenv SUBJECTS_DIR /home/user/freesurfer/subjects cd /home/user/freesurfer/subjects /home/user/freesurfer/fsfast/bin/fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: fcseedcor,v 1.3 2015/12/10 22:51:29 zkaufman Exp $ Linux localhost.localdomain 2.6.32-642.el6.x86_64 #1 SMP Tue May 10 17:27:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux ------- matlab output -------------------- matlab: Command not found. Started at Sat Dec 1 18:05:11 IRST 2018 Ended at Sat Dec 1 18:05:12 IRST 2018 Fcseedcor-Run-Time-Sec 1 Fcseedcor-Run-Time-Hours 0.00 fcseedcor Done best, sara 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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Conversion of registration files
by Jane Tseng 11 Dec '18

11 Dec '18

External Email - Use Caution Dear Freesurfer experts, I was wondering if there is any way to convert the .dat file output from spmregister (generated using Freesurfer version 5.3) to a .lta file? Thank you! Best wishes, Jane

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Freesurfer December 2018