Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Re: [Freesurfer] The mystery of the missing mcprextreg file
by Mcnorgan, Christopher 15 Apr '19

15 Apr '19

External Email - Use Caution Hi Doug, I attempted to send the mc-subjectname log files to the group, but they were bounced because of file size (one exceeds 1MB). I’ll try again with just the smaller of the two, and hopefully the same issue is at play in each case.

1 0

Research Assistant Position, Prakash Lab, The Ohio State University
by Salerno, Joanna M. 15 Apr '19

15 Apr '19

External Email - Use Caution Research Assistant Position Clinical Neuroscience Laboratory Department of Psychology Ohio State University Applications are being sought for a full-time research assistant position, starting May 2019 in the Clinical Neuroscience Laboratory<http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html> of Dr. Ruchika Prakash at the Ohio State University. RA responsibilities will include assisting in the general coordination and conduct of research in the Clinical Neuroscience Laboratory, including the administration of tests and/or questionnaires and the compilation of results; facilitating recruitment efforts between the laboratory and community partners; conducting neuropsychological assessment sessions with clinical populations; and assisting with data reduction and analyses, specifically analyses of neuroimaging data using openly-available software like FSL, AFNI, or SPM and programming experience in either UNIX or MATLAB. Desired qualifications include: Bachelor's degree in a psychology or neuroscience; programming experience in either UNIX or MATLAB, as well as experience in neuroimaging data analyses; knowledge of software package, such as FSL, AFNI, or SPM. If you are interested in being considered for the position, please apply online at https://www.jobsatosu.com, under job listing #448245 and submit a current CV and names of three references. If you have questions about the position or the lab, please contact Dr. Ruchika Prakash at prakash.30(a)osu.edu Lab Website: https://clinicalneurolab.org To build a diverse workforce, The Ohio State University encourages applications from all individuals. Ohio State is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to age, race, color, religion, sex, sexual orientation, gender identity, national origin, disability status, or protected veteran status.

1 0

the problem about XL defect detected...
by Abby tang 15 Apr '19

15 Apr '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon-all subjects but for some of my subjects I get the following error when I run recon-all command: CORRECTING DEFECT 0 (vertices=18460, convex hull=3400, v0=4) XL defect detected... Killed Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 10:44:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux I don't know how to check and amend ?h.orig.nofix. please give me some commands in detail. Thank you for your help.

2 4

recon-all error after maual control points definition
by Boris Rauchmann 14 Apr '19

14 Apr '19

External Email - Use Caution reading input surface xyz/fs_all_subjects/0031/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.3220 (-4.6610) -vertex loglikelihood: -6.6151 (-3.3076) -normal dot loglikelihood: -3.5637 (-3.5637) -quad curv loglikelihood: -6.1122 (-3.0561) Total Loglikelihood : -25.6131 CORRECTING DEFECT 0 (vertices=16503, convex hull=4824, v0=77) mrisAddEdge: too many edges (255) XL defect detected... Large defect found - not a problem, but a curiousity No such file or directory Linux linuxrechner 4.15.0-47-generic #50~16.04.1-Ubuntu SMP Fri Mar 15 16:06:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 0031 exited with ERRORS at Sun Apr 14 16:45:47 CEST 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any idea what causes this problem? Thank you, Boris

1 0

How to convert a functional FSL mask to an anatomical Freesurfer mask
by Jennifer Legault 12 Apr '19

12 Apr '19

External Email - Use Caution Hi Freesurfer experts, We ran a functional language localizer analysis in FSL and we want to apply the mask from this analysis to our SMRI analyses using the mri_glmfit command with the --mask option. Basically, we want to examine whether GMV within these language localizer regions is correlated with performance on various tasks. I previously used mri_convert to convert the .nii file to .mgh, and tried to run the mri_glmfit --mask command but received an error (ERROR: dimension mismatch 1 between y and mask) which I believe is linked to the fact that the previously run mris_preproc files are 4D, while our functional mask is still only 3D. When I use tksurfer and overlay the 3D mask file, it looks fine. So the question is how can we convert our 3D functional mask into a format that we can use for the mri_glmfit command (Nverteces x 1 x 1 x Nsubjects)? Thanks for all your help! Best, Jen -- Jennifer Legault PhD, Neuroscience Postdoctoral Scholar Language Acquisition and Brain Lab University of Delaware

2 2

mri_segstats
by Nasiriavanaki, Zahra 12 Apr '19

12 Apr '19

Dear Freesurferers I was trying to do a connectivity analysis using subnuclei of Amygdala. I had an Amygdala segmentation file (reg.lh.HBT.mgz for letf Amygdala) and I tried to use that in mri_segstats to extract the timeseries and then use it as a seed in my analysis. However when I looked at the results, the values are too high (around 800). Could you please let me know what I'm doing wrong? P.S: the segmentation was basically done in MNI152-1mm and I moved it to MNI305-2mm by mri_vol2vol. mri_vol2vol --mov MNI152template/MNI152_1/mri/reg.lh.HBT.mgz --targ $SUBJECTS_DIR/fsaverage/mri.2mm/mni305.cor.mgz --o $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --interp nearest --regheade mri_segstats --i $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz --seg $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt Thanks a lot MOna

2 6

Re: [Freesurfer] Hippocampal subfield version
by Iglesias Gonzalez, Eugenio 12 Apr '19

12 Apr '19

External Email - Use Caution Hi Emily, You need to download the dev version, but run the subfield/amygdala volume on cases reconned with FS6.0. Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Emily Schwartz <emily.schwartz(a)einstein.yu.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, 3 April 2019 at 15:44 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal subfield version External Email - Use Caution Hello FS experts, I was planning to use the hippocampal subfield segmentation module in FreeSurfer 6.0 on a Linux ubuntu computer. I also would like to use the nuclei of the amygdala segmentation, but realized I need to download the development version in order to do that. Is there any reason why I shouldn't use the development version over the 6.0 release? Thank you in advance. Best, Emily

2 3

Fwd: Fw: mriglmfit error
by Amrita Bedi 12 Apr '19

12 Apr '19

External Email - Use Caution ---------- Forwarded message ---------- From: *abedi000(a)citymail.cuny.edu <abedi000(a)citymail.cuny.edu>* < abedi000(a)citymail.cuny.edu> Date: Thursday, April 11, 2019 Subject: Fw: mriglmfit error To: Amrita Bedi <amibedi273(a)gmail.com> Amrita Bedi *Biomedical Engineering - Class of 2018* *The City College of New York - CUNY* ------------------------------ *From:* abedi000(a)citymail.cuny.edu *Sent:* Thursday, April 11, 2019 8:38 AM *To:* Freesurfer(a)nmr.mgh.harvard.edu *Subject:* mriglmfit error Good morning Freesurfer developers, While using the mri-glmfit command on 20 subjects. I got the following error- -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y test.10B.mgh --fsgd TEST.fsgd --C TEST.mtx --surf fsaverage lh --cortex --glmdir test.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.000000 (col 6), Max=228.790298 (col 3) The scale is much different between columns 6 and 3, you may want to normalize by subtracting the mean and dividing by the standard deviation. Column 6, all values are 0. 1. My command line used was- mri_glmfit --y test.10B.mgh --fsgd TEST.fsgd --C TEST.mtx --surf fsaverage lh --cortex --glmdir test.glmdir 2. My fsgd file and design matrix file are attached. Thank you for your help. Amrita Bedi

2 6

Labels in nii files
by Vidal Maxime 12 Apr '19

12 Apr '19

External Email - Use Caution Hello, I have a t1w.nii file and a segmentation.nii file. For the latter, I was wondering how I could join labels together and create new labels. Best, Maxime

3 2

Aparc stats files aren’t being generated
by Romella Durrani 12 Apr '19

12 Apr '19

External Email - Use Caution Hello, I am having problems generating the aparc stats files for all my scans. I have checked the surfaces for all scans and they were all generated correctly. However, when I go to generate the stats files, I am able to get all the aseg stats for all scans, but many of them are missing aparc stats, despite passing visual review of the surfaces. Is there a way to generate these files without having to reprocess all of them again? Thanks, Romella

2 1

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