Freesurfer October 2018

freesurfer@nmr.mgh.harvard.edu

113 participants
156 discussions

Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

4 4

Correct for sulcuses & ventricles size
by John Anderson 13 Dec '20

13 Dec '20

External Email - Use Caution Dear Freesurfer experts, I have two groups of subjects (healthy and patients). The patients have different degrees of atrophy. Looking into the individual scans, the subjects are largely different in the space between the sulcuses and the size of ventricles. My questions are: 1. Is there any way to correct for these differences in the surface based analysis? 2. Including eTIV covariate does it help in this case? 3. Does the resampling to "fsaverage" overcome the challenge of these differences between the subjects? I appreciate any advice, John

3 5

group analysis of large data sets
by Wang, Xin 22 Apr '20

22 Apr '20

Hello, FreeSurfer Group, What is the maximal matrix size for glm_fit process? How to use FreeSurfer for group analyses of more than 2000 subjects, 128 variables, and 128 Classes? Thank you. Xin

4 5

Course in Advanced Neuroimaging (Barcelona)
by Erick Canales 20 Sep '19

20 Sep '19

Dear colleagues, I am pleased to announce our upcoming Course in Advanced Neuroimaging held annually in Barcelona. It takes a practical approach and does not require qualifications or previous experience in neuroimaging. It will be taught in Spanish. The multidisciplinary programme provides thorough training in the analysis of brain images from different MRI modalities and data modeling techniques, including voxel-based morphometry, cortical thickness, diffusion tensor imaging, fibre tracking, functional MRI and brain connectivity, as well as the statistical methods behind these techniques including elements of meta-analysis, and more. The course consists of a five-month online theoretical module (starting on November 6th) and a period of practical face-to-face training (split between two days in November and two weeks at the end of April) held in Barcelona. For further information, please visit the website: www.cursoneuroimagen.com Best regards, Erick J. Canales-Rodríguez Joaquim Radua Raymond Salvador Edith Pomarol-Clotet FIDMAG Research Foundation and Sociedad Española de Neuroimagen *www.fidmag.com <http://www.fidmag.com/>*

1 1

T2 seq. for hippocampus ??
by Anik Dar 25 Jun '19

25 Jun '19

External Email - Use Caution Hi All, I have 1x1x3 cubic mm T2 and 1x1x1 cubic mm FLAIR, in addition to 1x1x1 cubic mm MPRAGE. Can you please let me know whether I should use only T1 or should I use one of the additional seq. for hippocampal subfield segmentation ? cheers Nik

3 4

updateing freesurfer.
by Aaron Tanenbaum 22 Jan '19

22 Jan '19

External Email - Use Caution I tried updating freesurfer 6.0 using the command fs_update. I get the following output. > Build is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > Running this will update some of your freesurfer binaries. > > Shall I proceed? [y/n/Abort]: y > > rsync -zbrlv --progress --suffix=.1539713469_bak rsync:// > surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Linux-cen… > /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_6_0/ > receiving incremental file list > rsync: change_dir > "/dist/freesurfer/patches/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c" > (in pub) failed: No such file or directory (2) > > sent 8 bytes received 173 bytes 362.00 bytes/sec > total size is 0 speedup is 0.00 > rsync error: some files/attrs were not transferred (see previous errors) > (code 23) at main.c(1655) [Receiver=3.1.1] >

2 1

mris_apply_reg failing for area/volume
by James Michael Roe 14 Jan '19

14 Jan '19

External Email - Use Caution ? Dear freesurfer experts I'm running the following commands to register RH area and volume files per sub to both hemispheres of a symmetrical template following Xhemi routines. The commands have already worked for many subs, but are failing to write the target file for a number of others (and all run fine without the --jac flag) #right to left mris_apply_reg \ --src $SUBJECTS_DIR/$sub/surf/rh.area \ --trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \ --streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg $SUBJECTS_DIR/${template}/surf/lh.sphere.reg \ --jac #right to right mris_apply_reg \ --src $SUBJECTS_DIR/$sub/surf/rh.area \ --trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \ --streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg $SUBJECTS_DIR/${template}/surf/rh.sphere.reg \ --jac The error is not template-specific as the output is the same using fsaverage_sym Attached is the log file. Thanks in advance! ?- James

3 12

DKT vs. DK Freesurfer atlases
by Gabor Perlaki 11 Jan '19

11 Jan '19

Dear all, I've found an article comparing DK and DKT atlas based automatic segmentations to manual labels (Klein and Tourville, Front Neurosci. 2012; 6:171, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514540/) It seems that using DKT40 works better than DK in most of the cortical regions (based on Dice). Does anybody know that the DKTatlas related results created by Freesurfer (e.g. aparc.DKTatlas+aseg.mgz, lh.aparc.DKTatlas.stats) are based on the same DKT40 atlas used in the article and whether the DKT40 atlas related results were also created by Freesurfer in the article by Klein and Tourville? Are the Freesurfer created results in lh.aparc.DKTatlas.stats generally more reliable than the results in lh.aparc.stats? -- Gabor Perlaki research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-30-2084367 E-mail: petzinger.gabor(a)gmail.com

3 3

LME
by Tefera, Getaneh B 07 Jan '19

07 Jan '19

Dear Freesurfer experts, I have three groups g0, g1, and g2. I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ ... The slope of g0 : 0 1 0 0 0 0 The slope of g1: 0 1 0 1 0 0 The slope of g2: 0 1 0 0 0 1 The slope difference between g0 and g1: 0 0 0 1 0 0 The slope difference between g0 and g2: 0 0 0 0 0 1 The slope difference between g1 and g2: 0 0 0 -1 0 1 1) Is this contrast matrix correct to observe pairwise slope difference? In the tutorial the contrast matrix C = [zeros(3,3) [1 0 0 0 0; -1 0 1 0 0; 0 0 -1 0 1] zeros(3,6)] 2) Is it necessary to combine contrast matrix of the pair difference the same as the tutorial? If so, my contrast matrix can be C=[0 0 0 1 0 0; 0 0 0 -1 0 1] 3) How can we interpret the result for this contrast matrix? 4) How can I obtain B1, B2, ... ? [sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,... dr,pw,alpha,gr_pr) 5) For sample size calculation how can I get Dhat ( Estimated random effects covariance matrix) and phisqhat (Estimated intra-subject variability)? With regards Getaneh

2 9

Longitudinal stream : LME and limits of model
by Matthieu Vanhoutte 14 Dec '18

14 Dec '18

Dear Freesurfer’s experts, I would have some questions regarding the LME model to be used in longitudinal stream: 1) Which are the ratio limits or % of missing timepoints accepted ? (according time, I have less and less subjects time points) 2) Is it possible to include patients that would miss the first timepoint but got the others ? 3) Considering a group in longitudinal study, which is the number of subjects minimal of this group accepted for LME modeling ? 4) Finally, concerning quality control and among a big number of total time points, which essential controls are necessary ? (Control of norm.mgz of the base, alignment of longitudinal timepoints on base,… ?) Best regards, Matthieu

2 13

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 October 2018