Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Fwd: Manually fix FreeSurder ICV value when talairach.xfm registration is incorrect
by Gamaliz 13 Nov '18

13 Nov '18

External Email - Use Caution I have a few T1 scans that have obvious incorrect registration to mni_average_305. I opened tkregister2 --s subjid --fstal --surfs and I am able to fix the registration, but I wonder how to use the ew registration to recalculate the new ICV. I am interested in doing it with Freesurfer (as I know I could get the matrix and calculate the determinant. I guess I will have to save the transform and rerun some of Freesurfer command to overwrite the old icv value? Thanks Gabriel

2 4

Editing errors
by Rosalia Dacosta Aguayo 13 Nov '18

13 Nov '18

External Email - Use Caution Dear Free Surfer team, I am visually checking for errors in every step of the recon-all process. In the skull stripping stage, some participants have left skull behind, but the grey matter (gm) and white matter (wm) separation is right. Should I edit the brainmask image in order to make that no skull is left behind even when the gm and wm are fine? Best regards, Rosalia

1 0

freesurfer selxavg3-sess error
by Francesca Strappini 12 Nov '18

12 Nov '18

External Email - Use Caution Dear FreeSurfer experts, I'm trying to analyze some monkey functional data. I got this error message with selxavg3-sess. I run the following commands: mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast ON-vs-OFF -a 1 -c 0 mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast ON-vs-OFF -a 1 -c 0 preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s MonkeyCassis-FF -fsd bold -per-session selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF ------- matlab output -------------------- MATLAB is selecting SOFTWARE OPENGL rendering. < M A T L A B (R) > Copyright 1984-2016 The MathWorks, Inc. R2016b (9.1.0.441655) 64-bit (glnxa64) September 7, 2016 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m >> /usr/local/freesurfer/matlab/MRIread.m >> >> >> starting fast_selxavg3b #@# MonkeyCassis-FF ############################### /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF ------------------------- $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ ------------------------- outtop = /usr/local/freesurfer/fsfast/Monkeys Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 11, skipping 1 ON-vs-OFF.mat Subscripted assignment dimension mismatch. Error in fast_ldpar4 (line 97) par4(nthrow,1) = tonset; Error in flac_customize (line 121) [par partype] = fast_ldpar4(parpath); Error in fast_selxavg3b (line 129) flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Thank you! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

4 8

Transformation from original dicom to skull striped output
by Min Zhang 12 Nov '18

12 Nov '18

External Email - Use Caution Dear Freesufer team: I have marked bounding box in the original DICOM File, and applied autorecon1 to do the skull striping for the images. I want to transfer the bounding box to the skull stripped output. How can I get the coordinates transformation matrix between the input and skull stripped output. Many Thanks! Best Min

2 1

Re: [Freesurfer] Consistent volume increases for some regions when using longitudinal stream
by Pagliaccio, David (NYSPI) 11 Nov '18

11 Nov '18

External Email - Use Caution Hello, Our lab has been running a set of data from a pre/post-treatment study through the FreeSurfer v6 pipeline. I was comparing the pre-treatment structural values initially run through the cross-sectional pipeline with the same pre-treatment data later run through the longitudinal pipeline and was seeing the same issue as has been previously posted about (msg52994). Particularly, one cortical region of interest shows on average 0.24mm (8.8%) larger cortical thickness values processed in the longitudinal pipeline vs. the cross-sectional pipeline. While all participant’s data showed increased thickness in this area with the longitudinal vs. cross-sectional pipeline, this was not at all consistent across participants (ranging from 0.08 to 0.47mm differences [3-18%]). While the longitudinal pipeline would increase reliability and sensitivity comparing the pre to post-scans, we are just very concerned about these major and inconsistent differences analyzing the same baseline data with the different pipelines. Particularly, we have some attrition so most participants have 2 but some have only 1 scan and thus this feels like it could introduce systematic bias in overall thickness. Any input would be appreciated! David

2 1

Nonsensical Vertex Coordinates, please help with interpretation
by Bruss, Joel E 11 Nov '18

11 Nov '18

External Email - Use Caution I'm trying to make a surface file from a subject's head and to map coordinates to that surface. If I run: mri_seghead --invol $SUBJECTS_DIR/$sub/mri/T1.mgz --outvol $SUBJECTS_DIR/$sub/mri/seghead.mgz --fill 255 --thresh1 20 --thresh2 20 --nhitsmin 2 mri_tessellate $SUBJECTS_DIR/$sub/mri/seghead.mgz 255 $SUBJECTS_DIR/$sub/surf/lh.seghead and then load lh.seghead in FreeView, it looks as I would expect. Clicking anywhere near a vertex gives the typical output, showing the closest vertex. All fine and well. However, if I load the file in Matlab: vCoord=read_surf('$SUBJECTS_DIR/$sub/surf/lh.seghead'); my values are nothing near what I'm seeing in Freeview. For example, FreeView reports: vertex 234741 [-78.50,14.50,26.50] read_surf reports: vertex 234740 0 168.980000000000 0 Of note, an error log tells me that: MRISreadNewCurvature: incompatible vertex number in file $SUBJECTS_DIR/$sub/surf/lh.curv How do I edit, update or create a curv file to play with the new surface file, or what can I do to get sensical surface coordinates from this data? Thanks, Joel ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

3 11

Functional Connectivity in FreeSurfer
by Maedeh Khalilian 11 Nov '18

11 Nov '18

External Email - Use Caution Dear FreeSurfer experts, I have a general question, if i have a parcellation(an annotation file e.g aparc.annot which is the output of FreeSurfer) is FreeSurfer able to calculate the functional connectivity between the regions(parcels) using rs-fMRI data? I mean can I have a 68*68 matrix showing the functional connectivity between each pair of regions(parcels) at the end? I would be grateful if u could help me. best regards, Maedeh

2 1

Re: [Freesurfer] Fornix in TRACULA
by Yendiki, Anastasia 10 Nov '18

10 Nov '18

We are actively working on it, but it's a time consuming process that involves many tracts. A few months, probably. On Nov 9, 2018 4:40 AM, "Hayek, Dayana" <dayana.hayek(a)stud.uni-greifswald.de> wrote: External Email - Use Caution Dear all, In my research work, I am using Freesurfer for both grey and white matter segmentation. However, I am restricted in the white matter analysis since my studies and related to memory function and I am mainly interested in the Fornix. I read in one of the threads that TRACULA will include soon an Atlas with the Fornix. Any news regarding this issue? Do you have any timeline of the progress of this atlas? Thank you so much for your help! ------------------------------------------------------------ Dayana Hayek, MSc.-Bio, cand dr.rer.nat Universitätsmedizin Greifswald | Klinik und Poliklinik für Neurologie AG Kognitive Neurologie Ferdinand-Sauerbruch-Straße | D-17475 Greifswald [Intern: W.-Rathenau-Str. 49 | Whg. 6.5] E-Mail: dayana.hayek(a)stud.uni-greifswald.de<mailto:dayana.hayek@stud.uni-greifswald.de>

1 0

Please join us at Coastal Coding for Reproducible Neuroimaging: 10-16 Jan 2019 in Miami, FL
by Satrajit Ghosh 10 Nov '18

10 Nov '18

External Email - Use Caution ---------- Forwarded message --------- From: Angela Laird <alaird(a)fiu.edu> Date: Fri, Nov 9, 2018 at 3:42 PM Subject: Please join us at Coastal Coding for Reproducible Neuroimaging: 10-16 Jan 2019 in Miami, FL To: Dear Colleagues, Florida International University (FIU) is hosting a Miami workshop + code sprint in January 2019 called *Coastal Coding for Reproducible Neuroimaging* : *Jan 10-12: ReproNim + Nypipe 2.0 Workshop* The goals of this workshop are two-fold. First, to enable attendees to become familiar with best practices for reproducible analysis from ReproNim. Second, to learn how to create scalable and re-executable neuroimaging workflows with the upcoming Nipype 2.0 platform. This event is targeted towards novice neuroimaging users who meet the following requirements: (1) Working knowledge of Python 3; and (2) Familiarity with scripting in at least 1 neuroimaging package (e.g., AFNI, ANTS, FSL, FreeSurfer, SPM). Advanced users are welcome to learn about the changes and hack with Nipype developers. *Jan 14-16: NiMARE Code Sprint* NiMARE (Neuroimaging Meta-Analysis Research Environment) is a new Python package for performing analyses using neuroimaging meta-analytic data. Current tools for neuroimaging meta-analyses are spread out across several packages and languages. NiMARE aims to provide a standardized interface for a broad range of algorithms, along with interfaces to open meta-analytic resources like Neurosynth, NeuroVault, and brainspell. The three-day NiMARE coding sprint will occur after the Nipype workshop, with a one-day rest period between, in which participants can enjoy Miami. At the sprint, we’ll be working to design a standard for representing meta-analytic data, to add implementations for new tools, and to improve the documentation and test coverage of the existing codebase. Anyone interested in contributing to this new package is welcome to join. *Both the workshop and code sprint will be held at FIU’s scenic Biscayne Bay Campus*, conveniently located 17 miles from the Miami International Airport (MIA) or 19 miles from the Fort Lauderdale-Hollywood International Airport (FLL). Registration costs are $125 for one event or $200 for both events. Fees cover breakfast, lunch, snacks, and plenty of coffee. *Full details can be found at:* https://coastal-coding.github.io Please feel free to forward to your colleagues! Best, Angie ***** Dr. Angie Laird, Ph.D. Professor, Department of Physics Director, Center for Imaging Science Florida International University 11200 SW 8th ST Miami, FL 33199 Office: AHC-4 Room 310 Lab: AHC-4 Room 380 http://cismri.fiu.edu http://neurolab.fiu.edu Phone: (305) 348-6737 Fax: (305) 348-6700

1 0

myelin and thickness pvr
by Damien MARIE 10 Nov '18

10 Nov '18

External Email - Use Caution Dear freesurfer experts, I would like to replicate an analysis I did with qdec but regressing out thickness at the vertex level. It’s a myelin group contrast with age and left average myelin as nuisance factors. I used the mri_glmfit command line generated during that qdec analysis and added the pvr flag but I got that error message: ERROR: dimension mismatch between X and contrast /home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat X has 7 cols, C has 6 cols How can I solve that, should I modify the contrast.mat? Many thanks, Damien mri_glmfit --y /home/damien/bin/freesurfer6/subjects/qdec/10nov/y.mgh --fsgd /home/damien/bin/freesurfer6/subjects/qdec/10nov/qdec.fsgd dods --glmdir /home/damien/bin/freesurfer6/subjects/qdec/10nov --surf fsaverage lh --label /home/damien/bin/freesurfer6/subjects/fsaverage/label/lh.aparc.label --C /home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat --C /home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Diff-ct-dys-Intercept-R1projfrac0.5.mat --pvr lh.thicknessall.fsaverage.mgh

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