Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Combined parcellation of the left and right hemispheres
by varshas＠cns.iisc.ernet.in 21 Jul '16

21 Jul '16

Hi, I've been working on getting a finer parcellation of the Desikan-Killiany atlas using mris_divide_parcellation. I was able to generate two annotation files; one each for the left and right hemisphere. I want to create a volume similar to aparc+aseg.mgz, containing the labels and indices of the ROIs from both hemispheres. I tried using mri_label2vol. However, this gives me two separate volumes for the left and right hemispheres. Is there a way to combine these volumes into one? Alternatively, can one generate such a volume form an annotation file that has information of both hemispheres? Any help is greatly appreciated! Regards, Varsha

2 1

tkmedit issue - image too bright in tkmedit after running gcut
by Uquillas, Federico D'Oleire 20 Jul '16

20 Jul '16

Hi fellow FreeSurfer users, I just did a gcut procedure and now that I'm opening it up again to check out how it went the brain is so bright I can't see white matter and gray matter contrast. Anybody ever experience this before? I tried exiting the terminal, and opening it again, but that doesn't do the trick. I'm opening up the image in tkmedit. If I use Freeview, the image looks fine and is not super bright as when I open it up in tkmedit. Not sure what is going on. Any thoughts? Best, Fred

2 1

Beta-Zero Correction - No Phase File
by Afzal, Afsana 20 Jul '16

20 Jul '16

Hi, I'm working with a dataset that outputs only one file (not two separate mag and phase files) for the fieldmap. The data was also collected on non-Siemens scanners: Philips Ingenia and GE SIGNA HDx (not sure if this is the reason the fieldmaps are unpacking differently). I've attached the .dat file for one of the fieldmaps in this email. If there a way to separate out the mag and phase from the single fieldmap file so I can use epidewarp.fsl? Thanks, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

3 4

Re: [Freesurfer] Fwd: question about voxel size
by Dorsa Haji Ghaffari 20 Jul '16

20 Jul '16

Hi Bruce, that is a 3TS T1 weighted image and is taken after the patients have taken the contrast medium. I have played with the intensities in Analyze and this is the best I could get. Do you have any suggestions for getting better contrast? Thank you Dorsa On Tue, Jul 19, 2016 at 4:29 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > also, please post to the list so that others can answer! > thanks > Bruce > On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: > > Here it is. Also can you explain why the algorithm works best with 1mm^3 >> voxel size? >> >> Thank you! >> >> >> >> >> >> >> > > 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. > >

2 5

Fwd: Connectome Research Coordinator (Senior), University of Pennsylvania
by Jeff Phillips 20 Jul '16

20 Jul '16

Dear colleagues, The Penn Frontotemporal Degeneration Center at the University of Pennsylvania (http://ftd.med.upenn.edu/) is seeking a research coordinator for the multi-site FTD Connectome study. Please see the details below; applications should be directed to http://jobs.hr.upenn.edu/postings/18756. Thanks, Jeff Phillips Postdoctoral Fellow Penn FTD Center University of Pennsylvania Duties: The primary responsibility of the successful candidate will be the coordination of a multi-site consortium using a novel approach to neuroimaging of neurodegenerative diseases. The lead site is Penn, and participating sites include Mayo Clinic, UCSF, MGH and Northwestern. All sites have specialized neuroimaging equipment, and we will be using advanced neuroimaging tools developed locally and in collaboration with the Human Connectome Project (HCP) to analyze the acquired data. The successful candidate also will be responsible for managing the Penn site. This project is coordinated with two other multi-site registries involving these same sites that are recruiting participants for this neuroimaging project (and other studies). Participants will include: 1. healthy control subjects; 2. individuals who have a frontotemporal degeneration (FTD) spectrum disorder such as primary progressive aphasia, progressive supranuclear palsy, or FTD with amyotrophic lateral sclerosis; and 3. individuals who are carrying a mutation that has resulted in an FTD spectrum disorder or are at risk for developing a FTD-spectrum disorder. Coordination will include weekly meetings with project coordinators at the other participating sites, developing reports for monthly meetings with NIH and principal investigators at other sites, monitoring imaging data flow to our coordinating site, monitoring the database that tracks participants, monitoring data flow from Penn to the HCP coordinating center, and managing requests for data from investigators. Other administrative responsibilities will include help managing the consortium budget. Local site responsibilities will include assistance with on-going recruitment processes, helping to collect imaging data, managing the local budget, supervising local technical and research staff, and participating in imaging analyses. Also included are implementation of Connectome imaging analysis and operation of the Prisma MRI scanner. Position is contingent on continued funding. Qualifications: A Bachelor’s degree and to 3 to 5 years of experience, or equivalent combination of education and experience, are required. Masters degree or PhD in neuroscience, psychology, linguistics, biology, biomedical engineering or related fields and 2 years to 3 years of experience strongly preferred. Past research and project coordination experience working in a similar lab setting is highly desirable. Experience with the following is preferred: Linux/Unix, brain imaging data analysis, MATLAB, computer programming, statistical analysis, research project management, or neuropsychological assessment. The candidate must be able to work independently and have strong organizational and interpersonal skills. Apply at http://jobs.hr.upenn.edu/postings/18756

1 0

reading lh.BA1_exvivo.label recon-all error
by Vaz pandolfo, Renata 20 Jul '16

20 Jul '16

Dear FreeSurfer developers, I am running recon-all on a healthy subject and I am also trying to get the hippocampal subfields segmentation. On the mri directory there is no hippocampus output, and the recon-all exited with errors. Command: recon-all -all \ -i ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz -s no_T2_20110815 \ -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/ \ -hippocampal-subfields-T1 Error: SUBJECTS_DIR /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/ T1s_and_T2s/20110815 FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/ T1s_and_T2s/20110815/fsaverage/label/lh.BA1_exvivo.label Linux lundb2 4.4.0-28-generic #47-Ubuntu SMP Fri Jun 24 10:09:13 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s no_T2_20110815 exited with ERRORS at Do 7. Jul 22:26:35 CEST 2016 Extra info: Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611 uname -a: Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux logs: recon-all and hippocampal-subfields-T1T2 attached Thank you!

2 1

Factors affect cortical thickness in normal population
by shi yao wang 20 Jul '16

20 Jul '16

Dear FS experts, We have few dataset of normal patients. They will be arranges as controls. I am wondering the factors affecting normal patients cortical thickness: Age, Sex Native Language Hand prefer IQ Any others? thanks Lawrence

1 0

PVE correction tool on Freesurfer 6
by Lee Subin Kristine 20 Jul '16

20 Jul '16

Hello, I am trying to use PVE correction on preprocessed PET data downloaded from the Alzheimer's Disease Neuroimaging Initiative(ADNI) database. I have a couple of questions: 1) I am using the co-registered, averaged image of the dynamic images, and it seems from your answers here (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html)<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html>that for static PET images, #3~5 will be different. Could you explain how I would need to enter the command differently? 2) I already have segmentations of my MRI images obtained via FreeSurfer(v.5.2)'s cortical parcellation. Would I still have to do procedure #1 (gtmeseg --s subject) ? I did try using xcerebralseg because it seemed from the help command that in my case where I already have some FS segmentations that I should use this one: You can use your own segmentation or a modified FS segmentation. It will be easiest if you modify apas+head.mgz to insert your segmentations. apas+head.mgz is created by gtmseg but you can create it with xcerebralseg --s $subject --o $SUBJECTS_DIR/$subject/mri/apas+head.mgz However when I do try I got the following error: ERROR: could not open /usr/local/freesurfer/subjects/002_S_4213/stats/002_S_4213/mri/apas+head.stats for writing Errno: No such file or directory Thanks a lot in advance, Regards, Subin

3 6

Hippocampal subfields --> Can't find a *ctf file?
by Perea Camargo, Rodrigo Dennis 20 Jul '16

20 Jul '16

Hi all, I am currently trying to run hippocampal subfields in a couple of my participants using FreeSurfer6.0 (located at *nmr*:/usr/local/freesurfer/stable6). It did run successfully for many of my subjects earlier in the year but some of them only had a let hemisphere segmentation. So I decided to re-run them using launchpad and also my local nmr computer. Now, none of the hippocampal sufields segmentations appear (no rh/lh.hippoSfLabels-T1-T2.*.mgz appears). I looked at <FSSUBJECT>/scripts/scripts/hippocampal-subfields-T1T2.log and the error I get is: Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf Could a missing *.ctf cause the error? (btw, the re-run happened after the major hardware crash). Thanks in advance for your help, Rodrigo PS: I am attaching the *log files as suggested in the bug reporting page. --- Rodrigo Dennis Perea Research Fellow Department of Radiology Athinoula A. Martinos Center Massachusetts General Hospital rpereacamargo(a)mgh.harvard.edu<mailto:rpereacamargo@mgh.harvard.edu>

3 6

FS V6.0 GTM PVC ROI definition
by Pradeep 19 Jul '16

19 Jul '16

Hello Freesrufer Team, I am trying to use the Partial volume correction procedure implemented in the freesurfer 6 beta version and have a few questions. In your recent Neuroimaging paper, the left and right hemispheres were combined by taking the average of the two as they did not show any age-by-hemisphere interaction. I might have interpreted the Supplementary figure 1 incorrectly, but the Geometric transfer matrix seem to show around 52 ROI's, So were the L and R ROIs combined for the PVC results you reported in that paper? Or were the same 52 used for the general PVC in the FS pipeline? Do you have any concrete results to examine the effects of the size variation over the ROIs used for PVC? Should a threshold be set for the sizes of these ROIs? How were the white matter hypo-intensities dealt with while generating the ROI masks? Thanks, Pradeep

3 4

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