Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Re: [Freesurfer] longitudinal process
by Martin Reuter 02 Mar '14

02 Mar '14

Hi Anna, No, you can still use links. When rerunning the base, the cross are not changed. Once the base loiks good, you also have to rerun the longs of course. Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Anna Jonsson <ajonsson09(a)gmail.com> Date:03/02/2014 5:27 AM (GMT-05:00) To: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal process Hi thank you for reply. May I ask other question; after editing the base it says to reocnstruct with recon-all -base -tp1 -tp2 etc. Does this require that all scans are located in the same directory? (Before i used symbolic links as scans are in different directories) but i am unsure whether after editing the abse anything further is actually done to the cross runs? Thank you for your help, Anna On Tue, Feb 18, 2014 at 7:58 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Anna, the linear mixed effects models can include subjects with a single time point and it would be a shame to drop that information. That is why we modified the longitudinal pipeline (use 5.3) to allow processing of subjects with a single time point. However, it is necessary that these images undergo the same processing steps as the rest of the data (to avoid bias). So you run it exactly as other subjects, with a cross sectional, -base and a -long step: recon-all -all -s <tp1id> -i path_to_tp1_dcm recon-all -base <templateid> -tp <tp1id> -all recon-all -long <tp1id> <templateid> -all Best, Martin On 02/18/2014 04:58 AM, Anna Jonsson wrote: Dear Freesurfer experts, I want to know if possible when doing longitudinal stream to put subjects with only one time-point through the processing (eg base and long runs) in order to subsequently use with the Matlab lme tools? Or better is to leave them out and only do those with 2+ times? Thank you Kind Regards, Anna _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ 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

longitudinal process
by Anna Jonsson 02 Mar '14

02 Mar '14

Dear Freesurfer experts, I want to know if possible when doing longitudinal stream to put subjects with only one time-point through the processing (eg base and long runs) in order to subsequently use with the Matlab lme tools? Or better is to leave them out and only do those with 2+ times? Thank you Kind Regards, Anna

2 2

Pb with a registration of diffusion images processed with tracula and anat images
by Celine Louapre 28 Feb '14

28 Feb '14

Hi Anastasia and freesurfer experts I am having some troubles with the registration of DTI images processed with tracula for one subject. When I load the lowb.nii.gz on freeview together with brainmask, it is not registered, but when I am loading it with the registration matrix anatorig2diff.bbr.dat, it is correctly registered. I don't have to specify the registration file for the other subjects, is that an issue of this particular subject? I am concerned because we later sampled surfaces on the DTI images, so I guess if the surf from the recon space is not correctly displayed on the DTI images, then my sampling is probably wrong too? The tracts are correctly displayed on the native DTI images, but if I want to display them on the anat space then it is not correct. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

3 4

Extracting only hippo campus volume
by Saurabh Thakur 28 Feb '14

28 Feb '14

Hello Freesurfer expert, I have done Hippo campus segmentation using Freesurfer. Can u tell me how to extract the only Hippo campus volume from nu.mgz Why only nu.mgz is used for the main volume--is there some specific reason to use? Thanks in advance , Saurabh Thakur,

3 4

Talairach failure in 5.3 but not in 5.2
by Corinna Bauer 28 Feb '14

28 Feb '14

Hello all, I have 2 subjects that failed autorecon-all at the same Talairach step. Both subjects successfully completed autorecon-all in version 5.2. Here is the output from one of the subjects. Any suggestions? Corinna #-------------------------------------------- #@# Talairach Fri Feb 28 12:39:50 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Feb 28 12:40:51 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Fri Feb 28 12:40:51 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux bauer 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Fri Feb 28 12:41:10 EST 2014 tmpdir is transforms/tmp.talairach.30730 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri mri_convert orig_nu.mgz transforms/tmp.talairach.30730/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.30730/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.13732e-09, 3.72529e-09) j_ras = (-3.72529e-09, -1.45519e-11, -1) k_ras = (2.6057e-10, 1, 1.45519e-11) writing to transforms/tmp.talairach.30730/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.30730/src.mnc transforms/talairach.auto.xfm Fri Feb 28 12:41:27 EST 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Feb 28 12:41:28 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0012, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux bauer 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s MWP_04182013 exited with ERRORS

1 0

Subcortical CVS registration
by Jennifer Eastman 28 Feb '14

28 Feb '14

Hi All, I just wanted to bump this question back up.I am interested in comparing sub-cortical volumes across subjects in my data set. I am wondering if using the CVS registration step is useful in improving the accuracy of the sub-cortical volume measurements independently. I will not be examining the cortical thickness just sub-cortical. I have combed the literature that is available and watched the training video, but I am not clear if there is benefit to using CVS registration if I am just looking at the sub cortical structures. Thank you. Jennifer Sent from my iPhone

2 4

How to clone from T1 to brainmask in freeview to amend a bad skull strip
by Emad Ahmadi 28 Feb '14

28 Feb '14

Hi! I want to know how to clone from T1.mgz to brainmask.mgz in freeview (to amend a skullstript that has removed too much). I couldn’t find the tool in freeview. Thank you very much, Emad Emad Ahmadi, MD ----------------------------------------------- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

2 1

Linear Mixed Effects Models
by Eric Cunningham 28 Feb '14

28 Feb '14

Hello Freesurfer Experts, I am currently trying to run the Linear Mixed Effects Models described in the wiki here: http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels And I am running into difficulties that are fairly well described by the last message in this previous mail thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25787.html Can you please clarify the variable "ni"? the following command: *[M,Y,ni] = sortData(M,1,Y,sID);* results in: ??? Error: File: sortData.m Line: 59 Column: 6 Expression or statement is incorrect--possibly unbalanced (, {, or [. do i need to build "ni" ahead of time? You probably don't need to know this, but I am using data generated by Freesurfer version 5.1, on matlab 7.8.0 (R2009a), which I gather will cause a few problems further down the line. Thank you for your help, -Eric

3 2

time course in mri_info lh.gender_age.thickness.10.mgh
by charujing123 27 Feb '14

27 Feb '14

Hi all, I have two questions. 1,If I want to get the value of specific voxel from the lh.gender_age.thickness.10.mgh, which code can I use to perform it? 2,How to graph the time course of specfic voxel from the lh.gender_age.thickness.10.mgh by freeview? Thanks. All the best. Rujing Zha 2014-02-24 charujing123

4 11

PostDoctoral Opportunity
by Mario Ortega 27 Feb '14

27 Feb '14

Dear Freesurfer Community, We have a post-doctoral opportunity available, please send CV and letter of interest to bances(a)wustl.edu Thanks. *Description:* Applications are invited for a post-doctoral position within the Departments of Neurology and Radiology at Washington University in St. Louis. Research focuses on the application of functional MRI methods to neurodegenerative diseases (including Alzheimer's Disease (AD) and HIV Associated Dementia (HAD)). This research investigates the use of functional neuroimaging measures (including arterial spin labeling (ASL) and resting state blood oxygen dependent (BOLD) imaging) as biomarkers for neurodegenerative diseases. Opportunities will be provided for pursuing personal research interests if applicable. Writing manuscripts and applying for independent grants will be strongly encouraged. *Requirements:* The qualified candidate should have a degree in neurosciences, psychology, biomedical engineering, physics, computer science, or other related fields. Previous experience with some of the following computational methods (e.g., linear algebra, time-series analysis, image analysis), programming (e.g., C/C++, MATLAB, R, Python) and neuroimaging programs (e.g. SPM, AFNI, Freesurfer) is preferred and would allow for more individualized studies. Strong facility with statistical analyses is also desired. To apply, please send a letter of interest and CV to bances(a)wustl.edu<https://pod51035.outlook.com/owa/redir.aspx?C=37AOPBO5HUO_j9bos9wYowoaxdzjA…>. Please arrange for three confidential letters of reference to be sent to the address below. Only applicants considered for employment will be contacted. Contact Information: Beau Ances MD, PhD Department of Neurology Washington University in Saint Louis Box 8111 660 South Euclid Ave Saint Louis, MO 63110 bances(a)wustl.edu

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