Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

Is longitudinal lme analysis invalid when it doesn't converge?
by Knut J Bjuland 14 Jun '18

14 Jun '18

External Email - Use Caution Dear FreeSurfer experts I ran the lme scripts in FreeSurfer on FA-data (dMRI). The script doesn't crash but 70% of the models yield this message: "Algorithm does not converge after 50 iterations!!!" Does that mean the results (pvalues) are invalid? I would appreciate any input on this topic. Thank you! Best regards Knut Jørgen Bjuland

1 0

Post-doc position in neuroimaging pain research
by Lussier,Desiree 13 Jun '18

13 Jun '18

External Email - Use Caution Postdoctoral Research Positions in Neuroimaging Pain Research Pain Research & Intervention Center of Excellence University of Florida, Gainesville, Florida Dr. Yenisel Cruz-Almeida and Dr. Natalie Ebner are currently accepting applications for postdoctoral research fellows and/or research associates to advance research on cognitive neuroscience and chronic pain using multi-modal brain neuroimaging. While the primary candidate will work on an NIH funded position to support neuroimaging aspects of characterizing chronic pain and treatment effects in older individuals, the candidate will be directly interacting with a large group of interdisciplinary UF researchers involved with multiple studies involving acute and chronic pain including: real-time fMRI control of brain activity, neuroimaging-based pain biomarkers, individual difference in pain and cognitive/affective dimensions of pain across a number of departments and institutes. Qualifications: Applicants should have (or anticipate having) a Ph.D. and research background in Cognitive Neuroscience, Neurophysiology, Neuropsychology, or related fields. Individuals with backgrounds in Electrical Engineering, Physics, Mathematics, Computer Science or similar fields and a strong interest/background in Psychology and human neuroimaging are also encouraged to apply. Applicants should be experienced at designing and implementing cognitive neuroscience experiments. Preference will be given to candidates who have experience with conducting fMRI studies, working with MRI scanners, processing MRI and fMRI datasets, and running neuroimaging data analysis using software packages, such as Matlab, SPM, FSL EPrime, and AFNI. Applicants should also possess strong interpersonal skills and be able to work independently and in groups. Application Process: Applications are accepted on an ongoing basis. To apply, potential candidates should submit: - Curriculum Vitae - Personal Statement describing research interests and goals - Three letters of recommendation Address applications or inquiries to: Yenisel Cruz-Almeida, M.S.P.H., Ph.D.; cryeni(a)ufl.edu And Natalie Ebner, Ph.D.; natalie.ebner(a)ufl.edu Thank you, Désirée Lussier, MS Graduate Student Department of Psychology University of Florida [1509730522218_github]<https://github.com/dllussier> [1509730529145_linkedin-icon-14small.png] <https://www.linkedin.com/in/desiree-lussier/> [1509730538655_twitter-icon] <https://twitter.com/desiree_lussier> <http://www.psych.ufl.edu/ebnerlab/> <https://people.clas.ufl.edu/desireelussier/> [1509730546740_website] <https://people.clas.ufl.edu/desireelussier/>

1 0

Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 13 Jun '18

13 Jun '18

External Email - Use Caution Thank you for your response! Just to clarify: if my input is volume, does the cache.th20.abs.sig.y.ocn.dat contain the average unadjusted volume values for each participant in each significant cluster? Since the file I just mentioned contains the average values, I used mri_segstats to calculate total volume for the cluster. mri_segstats --i <pathway to rh.volume.Study.10.mgh> --seg cache.th20.abs.sig.ocn.mgh --excludeid 0 --sumwf ClusterVolumeValues.dat However, this just calculates the sum of the unadjusted values in the cluster. I guess my main question is, is there a way to extract or calculate the adjusted values for each participant in each cluster after accounting for covariates (age, sex, and ICV)? --- Jessica ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Wednesday, June 13, 2018 11:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 172, Issue 21 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: crypt_gkey = (null) (Dicamillo, Robert) 2. tractstats2table - all tracts for multiple subjects (Alexopoulos, Dimitrios) 3. Re: tractstats2table - all tracts for multiple subjects (Yendiki, Anastasia) 4. dwi.ecclog file (Daumail, Loic Jean) 5. Re: dwi.ecclog file (Yendiki, Anastasia) 6. Re: tractstats2table - all tracts for multiple subjects (Alexopoulos, Dimitrios) 7. Re: Missing Control Points and QATools (Matthew Peverill) 8. Re: Missing Control Points and QATools (Bruce Fischl) 9. Re: Extract the entorhinal cortex as a mask (Erik O'Hanlon) 10. PREDOCTORAL POSITION at King's College London (Walter Hugo Lopez Pinaya) 11. Re: Extract the entorhinal cortex as a mask (Bruce Fischl) 12. Re: "WARNING: Image geometries differ across time" upon running base step of longitudinal pipeline (Tudor Popescu) 13. Re: dwi.ecclog file (Daumail, Loic Jean) 14. Re: Running qcache on old FS data (Douglas N. Greve) 15. Re: Group Analysis Covariates (Douglas N. Greve) 16. Re: Error during QDEC (Douglas N. Greve) ---------------------------------------------------------------------- Message: 1 Date: Tue, 12 Jun 2018 19:52:52 +0000 From: "Dicamillo, Robert" <RDICAMILLO(a)mgh.harvard.edu> Subject: Re: [Freesurfer] crypt_gkey = (null) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <5024346D-6C53-4E0F-8189-FAAE089D2108(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hello Aaron, The build timestamp from the output below shows mri_convert is from 8/2014. When I look at the build timestamp on our stable 5.3 version of mri_convert I see it is from 5/2013. So the version that you listed is about 1 year newer than the 5.3 release I can see. It is possible that someone downloaded a daily/dev build of freesurfer at that time. You might want to consider running the latest 6.0 release of Freesurfer (released in January 2017), which should be fine on CentOS 7. It can be downloaded from, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall I also suggest that you start out in a default/clean shell, set FREESURFER_HOME, and then source the setup script for linux, You can see the instructions on that same web page under ?Setup and Configuration?. The setup steps should work for version 5 or 6. - rob On Jun 12, 2018, at 2:43 PM, Aaron Tanenbaum <aaron.b.tanenbaum(a)gmail.com<mailto:aaron.b.tanenbaum@gmail.com>> wrote: External Email - Use Caution I checked my system is not encrypted. I had someone else run the command on the same machine. It worked for them. So I changed my BASH environment to a default environment. I still get the same error. I tried this again but with a different FreeSurfer 5.3. turns out the one I was using has been altered version of FreeSurfer. I do not know how it was altered. It worked. so it has to do with the altered FreeSurfer. I ran the command mri_convert -version on both FreeSurfer. for the unaltered i get the out put mri_convert -version stable5 altered version i get mri_convert -version dev build (use --all-info flag for full version info) with this output i type in mri_convert --all-info mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/12-18:32:17-GMT BuildTimeStamp: Aug 22 2014 21:04:47 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: tanenbauma Machine: rocky Platform: Linux PlatformVersion: 3.10.0-862.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Wondering is this version of mri_convert a developmental version? Also both version are the CentOS 6 build. On Tue, Jun 12, 2018 at 1:01 PM Dicamillo, Robert <RDICAMILLO(a)mgh.harvard.edu<mailto:RDICAMILLO@mgh.harvard.edu>> wrote: Hello Aaron, You could check to see if the CentOS 7 system is using disk encryption, e.g., if the following command return 1, then it would mean encryption is in use (which can be an issue with FreeSurfer). $ cat /proc/sys/crypto/fips_enabled If it returns zero, it could be an issue with a system library like glibc on CentOS 7.5 (that does not happen on older versions of CentOS). Either way, this is not your doing ;-) On Jun 12, 2018, at 11:51 AM, Aaron Tanenbaum <aaron.b.tanenbaum(a)gmail.com<mailto:aaron.b.tanenbaum@gmail.com>> wrote: External Email - Use Caution I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3. When i get to the part where MRI_convert is creating the the orig001.mgz its gives me a segmentation fault. if i run this on a centos 6 system it works fine. below is the output of the program. /data/gizmo/data1/freesurfer5.3/bin/mri_convert /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm /data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm... crypt_gkey = (null) Segmentation fault (core dumped) Did I do anything wrong? _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Postdoctoral Fellowship in Spinal Cord and Parkinson's Disease
by Arnaud Boré 13 Jun '18

13 Jun '18

External Email - Use Caution *Postdoctoral Fellowship in Spinal Cord and Parkinson's Disease* We are looking to recruit a post-doctoral fellow in Dr. Julien Doyon’s *Motor Learning and Plasticity Laboratory*, at McGill University. The suitable candidate will join a team of post-doctoral fellows and PhD students who are conducting neuroimaging research in motor learning, both fundamental and clinical. For the current job opening, we seek to recruit a post-doctoral fellow who will *conduct neuroimaging and behavioral studies on healthy individuals and Parkinson’s Disease (PD) patients*. These studies are part of a research program aiming to characterize motor learning related plasticity in both brain and spinal cord, as well as to identify neuronal correlates of early stages of PD at both spinal and supra-spinal levels. The position is based at the Montreal Neurological Institute (MNI). The ideal candidate is expected to take the lead in regards to the methodological aspects of the study, addressing specifically the challenges related to the functional neuroimaging of the spinal cord, and to the analysis of complex data sets. The fellow will be involved in all stages of the research projects, from experimental design to data analysis and manuscript writing. The following requirements are mandatory: - PhD degree in neuroscience or a related field; - Experience with functional neuroimaging in human participants and with neuroimaging data analysis techniques and software (i.e. SPM, FSL or similar); - Ability to work independently and to collaborate with other team members; - Excellent organizational and social skills, especially when dealing with patient participants; - Established publication record attesting the above-mentioned requirements; - Good English proficiency (especially scientific writing and oral communication). The following requirements are assets: - Experience with spinal cord imaging; - Experience with multivariate data analysis approaches as implemented in established neuroimaging data analysis software; - Good proficiency with programming (such as Python or Matlab); - French proficiency; - Research experience with PD patients (or other movement-related disorders); - Availability to start as soon as possible. If you are interested in this position, please send your CV, a cover letter and the contact information of two individuals who can provide references at the following e-mail address: *francine.belanger(a)mcgill.ca <francine.belanger(a)criugm.qc.ca>*

1 0

Re: [Freesurfer] hippocampus subfields and manual editing
by Iglesias Gonzalez, Eugenio 13 Jun '18

13 Jun '18

External Email - Use Caution Hi Lara, A little trick you can do (it shouldn’t be too hard to implement in Matlab with the functions in $FREESURFER_HOME/matlab) For each subject: 1. make a copy of aseg.mgz 2. create a binary mask for your edited hippocampi. 3. in aseg.mgz, replace each voxel labeled as hippo by the label of the closest, non-hippocampal structure. 4. Paint your hippocampi from step 2 on the hippocampal-less aseg. I hope this helps, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 13/06/2018, 17:18, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Lara Foland-Ross" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of lfoland(a)stanford.edu> wrote: External Email - Use Caution Hello, I am running an analysis of hippocampus volume on a set of T1-weighted scans with 1mm^3 isotropic resolution. Due to flow and other artifacts, a moderate degree of manual editing was required to correct the boundaries of each subject's hippocampus. Final volumes of manually edited hippocampi were submitted to a repeated measures ANOVA which showed a significant main effect of diagnosis on the overall size of this structure (controlling for age and TBV). We recently submitted this paper and just received a request from a reviewer that asked that we run a subfield analysis on these data to better understand the regions driving this overall effect. What I'd like to know is: would the subfield approach *not* be recommended on this dataset considering that artifacts necessitated a good deal of manual intervention for the entire region? Second, if it a subfield approach *is* okay to run on these data, how can I feed in my manually edited volumes to ensure that the corrected segmentations of the entire hippocampus is used during subfield creation? thanks very much in advance! Lara Lara Foland-Ross, Ph.D. Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 _______________________________________________ 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.

1 0

hippocampus subfields and manual editing
by Lara Foland-Ross 13 Jun '18

13 Jun '18

External Email - Use Caution Hello, I am running an analysis of hippocampus volume on a set of T1-weighted scans with 1mm^3 isotropic resolution. Due to flow and other artifacts, a moderate degree of manual editing was required to correct the boundaries of each subject's hippocampus. Final volumes of manually edited hippocampi were submitted to a repeated measures ANOVA which showed a significant main effect of diagnosis on the overall size of this structure (controlling for age and TBV). We recently submitted this paper and just received a request from a reviewer that asked that we run a subfield analysis on these data to better understand the regions driving this overall effect. What I'd like to know is: would the subfield approach *not* be recommended on this dataset considering that artifacts necessitated a good deal of manual intervention for the entire region? Second, if it a subfield approach *is* okay to run on these data, how can I feed in my manually edited volumes to ensure that the corrected segmentations of the entire hippocampus is used during subfield creation? thanks very much in advance! Lara Lara Foland-Ross, Ph.D. Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

1 0

Group Analysis Covariates
by Hua, Jessica 13 Jun '18

13 Jun '18

External Email - Use Caution Dear Freesurfer Experts: I analyzed my data following the guidelines on the FSL Tutorial/Group Analysis page . I am trying to plot the adjusted values (covariates: age, sex, and ICV) for the significant clusters for each of my participants. I set up the contrast to test group differences. So testing whether there is a difference between groups regressing out the effects of sex, age, and ICV. Contrasts created were [1 -1 0 0 0 0 0 0] and [-1 1 0 0 0 0 0 0]. I then extracted values from this file (cache.th20.abs.sig.y.ocn.dat; i.e., the average value of each subject in each cluster) into my dataset. I believe these are the unadjusted values, correct? I calculated total volume and total surface area by multiplying these values by the total number of vertices in each cluster. To adjust for covariates, I ran a regression with the ExtractedClusterValues as the DV and Group, Sex, Age, and ICV as predictors. Looking at the output, there was no significant effect of group (p = .769; whereas in FreeSurfer the cluster-wise p < .001). Also when I plotted the predicted values adjusting for covariates, the means between the groups were very similar. Why am I getting a p = .769 when I adjust for covariates, but FreeSurfer has a cluster-wise p < .001? Or is there a way to calculate adjusted values in FreeSurfer? Best, Jessica

2 1

dwi.ecclog file
by Daumail, Loic Jean 13 Jun '18

13 Jun '18

Hello, I have several questions regarding the dwi.ecclog file data from Tracula, using the FreeSurfer version V6.0.0. 1) Does Tracula still use eddy_correct from FSL, or was it updated with the new eddy function from FSL? 2) Are the values for each slice of dwi.ecclog relative to the first slice or to the previous slice, or to another template? is it the same for both rotation and translation values? 3) What is the coordinate system for the rotation values? Is there a way to determine the total rotation from these 9 values? Thanks, Sincerely, Loic Daumail

2 2

Extract the entorhinal cortex as a mask
by Erik O'Hanlon 13 Jun '18

13 Jun '18

External Email - Use Caution Hi FS experts , I'd like to make masks for the entorhinal cortex to use for tractography. Can you advise what FS tool should be used? I've used the mri_extract_label for my hippocampal masks but not sure what files to use to extract EC ? I'm sure it's straightforward Thanks for any advice Best regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

2 5

PREDOCTORAL POSITION at King's College London
by Walter Hugo Lopez Pinaya 13 Jun '18

13 Jun '18

External Email - Use Caution Dear colleagues, We are looking for a predoctoral research assistant with knowledge of neuroimaging to work on a research project involving the application of machine learning techniques to neuroanatomical data. The project will lead to the development of a practical and flexible web-based tool for measuring neuroanatomical alterations in any brain-based disorders. The successful applicant will have previous experience in the handling of multiple structural neuroimaging datasets within the same project. Previous experience of using machine learning would be considered a strength but is not a requisite. The post holder will join a multi-disciplinary team including neuroscientists, psychologists and computer scientists. This project is a collaboration between King’s College London, UK (Dr. Andrea Mechelli), the University of New Mexico, USA (Prof. Vince Calhoun) and the Universidade Federal do ABC, Brazil (Prof João Sato) and is funded by an Innovator Award from the Wellcome Trust. The post holder will be based at the Institute of Psychiatry, Psychology & Neuroscience (King’s College London). For more information, please see https://www.hirewire.co.uk/HE/1061247/MS_JobDetails.aspx?JobID=79233 Best wishes, Walter Hugo Diaz Sanz

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer