Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

error during longitudinal -long stream
by Jinsong Tang 30 Jul '16

30 Jul '16

Hi all, I found an error during the longitudinal -long stream: recon-all -long P1001-2 P1001 -all ...... FREESURFER_HOME /space/raid/fmri/freesurfer Actual FREESURFER_HOME /space/raid/fmri/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21 UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux ...... mris_spherical_average -erode 1 -orig white -t 0.4 -o P1001-2.long.P1001 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject P1001-2.long.P1001. processing subject lh.EC_average... MRISread(/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Not a directory mris_spherical_average: could not read surface file /space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg Not a directory Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21 UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux recon-all -s P1001-2.long.P1001 exited with ERRORS at Fri Jul 8 21:33:02 PDT 2016 Please help me fix this error! Thanks and best regards, Jinsong

2 6

Re: [Freesurfer] significance overlay in freeview
by Caroline Beelen 30 Jul '16

30 Jul '16

Dear Ruopeng, Yes, I'm running FS 5.3. :) But then how can I see the correct significance overlay? Cause even when leaving out some commands (which may or may not work in 5.3), freeview does load, but seems to only display the DK-atlas on fs average (... and gets stuck sometimes too), as I described below. I cant find the right command ... So I guess my actual question is: Which command should i use to view a (correct) significance overlay in FS 5.3? Thank you very much for your help! Regards, Caroline Hi Caroline, Are you running FS 5.3? The command on the webpage is based on the upcoming 6.0, I believe. So some of the command line options are not available in 5.3. Best, Ruopeng > On Jul 29, 2016, at 9:11 AM, Caroline Beelen <caroline.beelen(a)kuleuven.be> wrote: > > Dear FS team, > > Apologies in advance for perhaps again a rather basic question. I attempted to load the aparc overlay in freeview by using the written command from the group analysis page, however it failed to load correctly. > > I used the following command: > freeview -f fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=roi.lh.area.dyslect_basic.glmdir/dyslect/sig.mgh:overlay_threshold=4,5 -viewport 3d > ? roi.lh.area.dyslect_basic.glmdir is the file obtained from the GLM-analysis and dyslect is the contrast folder within this file (main effect of dyslexia), containing a sig.mgh file (all seems fine) > > Unfortunately, I got an error that it does not recognize ?overlay_treshold=4,5?. I used freeview ?h and tried certain commands alike, but they didn?t work. When leaving out this part, I got another error that it failed to recognize ?annot_outline=1?. Again, leaving this out too, freeview loads itself and the DK-regions become visible. However, nothing else seems to get activated, and even not when putting ?configure overlay? (which is set to sig.mgh) to 1.3 as minimum and 3 as maximum. So basically nothing happens. > When looking at the command line it says that it implemented the colortable of DK-atlas (even twice), but it tells me nothing else. Also, after closing and reloading Freeview by using the similar command and then clicking on ?configure overlay? the screen sometimes gets stuck, giving me the impression that something must be wrong with the command. > > Could you please help me out and provide me the right command-line for loading the overlay of the significance map of ?roi.lh.area.dyslect_basic.glmdir/dyslect?? > > Thanks in advance! > > Kind regards, Caroline

1 0

brain mask and T1 are not the same size
by Isabelle Deschamps 29 Jul '16

29 Jul '16

2 1

Research Assistants needed for longitudinal brain development study at Boston Children's Hospital
by Gaab, Nadine 29 Jul '16

29 Jul '16

The Gaab Lab<http://www.thegaablab.com/> in collaboration with the Fetal-Neonatal Neuroimaging and Developmental Science Center<https://fnndsc.babymri.org/> at Boston Children's Hospital is looking for two Research Assistants to assist with all study phases of a new NICHD funded longitudinal project which assesses functional and structural brain development from infancy to early elementary school age. This includes subject recruitment for pediatric research studies which will include close interaction with nurseries, child care centers and elementary schools in the Boston area, scheduling of pediatric research subjects, database maintenance, implementation and maintenance of analysis software; pediatric testing (including MRI/fMRI scanning of young children and infants<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.babymri.org_&d=BQMF…>) and data analyses (psychometrics, psychophysics and structural/functional magnetic imaging), stimuli design and administrative work (e.g., preparation of internal review board proposals). These positions are ideal for anyone considering future graduate study in cognitive (developmental) neuroscience, developmental psychology, computer science, cognitive science or neuroscience. Bachelor's Degree in computer science, psychology, cognitive science, neuroscience, math, or related field required. Comfort with a heterogeneous computing environment (Linux/Unix, Mac, and Windows) as well as some programming experience preferred; knowledge of psychological experiment software (E Prime, Presentation, etc.) and/or fMRI analyses software helpful. Prior experience with infants and children would be very helpful. Demonstrable pre-existing interest in developmental psychology/ cognitive neuroscience desired; knowledge of neuroanatomy, statistics or machine learning helpful. Must be self-motivated and able to work in a fast-paced, changing environment and must like working with infants, children and families. Start date September or October 2016. Please first apply to Nadine.gaab(a)childrens.harvard.edu<mailto:Nadine.gaab@childrens.harvard.edu> with a cover letter and CV. "If we knew what it was we were doing, it would not be called research, would it?" A. Einstein (1879-1955) Nadine Gaab, PhD Associate Professor of Pediatrics Boston Children's Hospital/Harvard Medical School Department of Medicine/Division of Developmental Medicine Laboratories of Cognitive Neuroscience Mail stop code: BCH3178 1 Autumn Street (Office 643); Boston, MA 02115 nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu> phone: 857-218-3021 www.gaablab.com<http://www.gaablab.com>

1 0

How does Optseq2 arrange order of conditions?
by 連志浩 29 Jul '16

29 Jul '16

Hello all, I'm a new user of Optseq2, and I have 2 questions about optseq2 after I got some sequences and read Dale (1999). I'll be grateful to anyone can provide help. 1. I'm curious about why optseq2 arranged the order of conditions, does anyone can provided some references to me? Dale (1999) just discussed about mean ISI and fixed/randomizes ISI design, I wonder what's the difference if I just keep the duration order of null condition (jitter) and randomly present different conditions. 2. This question is about the total duration of experiments. I'm used to execute experiments by E-Prime 2.0, and the presentation may delay in E-Prime (I know this situation can be deal with "Pre-release"). If there's a fixation period (15s) after my trials is over (but participants are still scanned), and the delay just affect the duration of the fixation period. Should I reduce the duration of delayed stimulus in terms of the delayed time? Or I don't need to care about the delay, because the key point is the order of conditions and null/jitter? Thanks for your reading. Best regards, Chih-Hao

2 1

significance overlay in freeview
by Caroline Beelen 29 Jul '16

29 Jul '16

Dear FS team, Apologies in advance for perhaps again a rather basic question. I attempted to load the aparc overlay in freeview by using the written command from the group analysis page, however it failed to load correctly. I used the following command: freeview -f fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=roi.lh.area.dyslect_basic.glmdir/dyslect/sig.mgh:overlay_threshold=4,5 -viewport 3d ? roi.lh.area.dyslect_basic.glmdir is the file obtained from the GLM-analysis and dyslect is the contrast folder within this file (main effect of dyslexia), containing a sig.mgh file (all seems fine) Unfortunately, I got an error that it does not recognize "overlay_treshold=4,5". I used freeview -h and tried certain commands alike, but they didn't work. When leaving out this part, I got another error that it failed to recognize "annot_outline=1". Again, leaving this out too, freeview loads itself and the DK-regions become visible. However, nothing else seems to get activated, and even not when putting "configure overlay" (which is set to sig.mgh) to 1.3 as minimum and 3 as maximum. So basically nothing happens. When looking at the command line it says that it implemented the colortable of DK-atlas (even twice), but it tells me nothing else. Also, after closing and reloading Freeview by using the similar command and then clicking on "configure overlay" the screen sometimes gets stuck, giving me the impression that something must be wrong with the command. Could you please help me out and provide me the right command-line for loading the overlay of the significance map of "roi.lh.area.dyslect_basic.glmdir/dyslect"? Thanks in advance! Kind regards, Caroline

2 1

28 Jul '16

The 2016 HCP Course: “Exploring the Human Connectome” <http://humanconnectome.org/courses/2016/exploring-the-human-connectome.php> starts in one month: August 28-September 1 in Boston! There are still some open slots, but we encourage you to Register <https://www.humanconnectome.org/courses/course-registration.php> today! The HCP Course is the best place to learn directly from HCP investigators and to explore HCP data and methods. This year's course will provide hands-on experience in working with the new, multi-modal human cortical parcellation (Glasser et al., Nature, July 20, http://www.ncbi.nlm.nih.gov/pubmed/27437579) and with the “HCP-Style” paradigm for data acquisition, analysis, and sharing (Glasser et al., Nature Neuroscience, in press). The 2016 HCP Course curriculum (see the full Course Schedule <https://www.humanconnectome.org/courses/2016/exploring-the-human-connectome…>) includes over *20 Lectures and 15 Practicals* and will be presented by 19 HCP investigators and staff <https://www.humanconnectome.org/courses/2016/exploring-the-human-connectome…> and and will be held over *five full days: August 28-September 1 (Sunday-Thursday) *at the Joseph B. Martin Conference Center at Harvard Medical School <http://www.theconfcenter.hms.harvard.edu/>, in Boston, Massachusetts, USA. If you have any questions, please contact us at hcpcourse(a)humanconnectome.org Hope to see you in Boston! Best, 2016 HCP Course Staff Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam(a)wustl.edu www.humanconnectome.org

1 0

question about mask coordinates
by Dorsa Haji Ghaffari 28 Jul '16

28 Jul '16

Hi all, I have done segmentation with Freesurfer but when I create a mask for the left thalamus and import it to CAD software it doesn't seem to be at the right coordinates. This may be due to the change in the mask volume(256x256x256) from the original MRI volume(512x512x288). I did re-slice the mask to get the original volume but it gives me an additional piece of cube at the bottom of the image. Does anyone know how to get the authentic coordinates for the mask? Thank you Dorsa

1 0

Re: [Freesurfer] FreeSurfer 6.0
by elisabetta_delre＠hms.harvard.edu 28 Jul '16

28 Jul '16

> > Dear FreeSurfer team, > we are trying to find a downloadable version of FS6.0 to use on our data. > We can not find it on the web. > Could you help us with that? > Thank you, > best regards, > Elisabetta > > -- > *Elisabetta C. del Re, Ph.D.* > > *Instructor,* > *Department of Psychiatry* > *Harvard Medical School* > *phone 617 9675569 <617%209675569>* > *mail elisabetta_delre(a)hms.harvard.edu <elisabetta_delre(a)hms.harvard.edu>* > -- *Elisabetta C. del Re, Ph.D.* *Instructor,* *Department of Psychiatry* *Harvard Medical School* *phone 617 9675569* *mail elisabetta_delre(a)hms.harvard.edu <elisabetta_delre(a)hms.harvard.edu>*

3 2

V6.0 Hippocampal subfield segmentation
by Zhuang, Xiaowei 28 Jul '16

28 Jul '16

Hi everyone, I am running the new hippocampal subfield segmentation with a V6.0 beta version released last year on 20150724. There is only 1 subject (out of about 40 total) exit with an ERROR during segmentation with T1 input. All others subjects ran through the hippocampal segmentation and gives me reasonable results. And the same T1 image ran through the V5.3 old hippocampal segmentation so I believe there is nothing wrong with image itself. I am wondering is this a bug in the beta version of V6.0 I am having? And I have attached the two ERROR log files. Any response will be appreciated. Thanks, Xiaowei. [Cleveland Clinic logo] Xiaowei Zhuang | Research Engineer | Lou Ruvo Center for Brain Health Cleveland Clinic | 888 W Bonneville Ave. | Las Vegas, NV 89106 | (702) 685-6051 =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Freesurfer