Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Re: [Freesurfer] Freesurfer Digest, Vol 191, Issue 29
by Devika K 19 Jan '20

19 Jan '20

External Email - Use Caution I tried by specicying the subjects name, by following the below command. aparcstats2table --hemi lh \ --subjects 004 021 040 067 080 092 \ --meas thickness \ --parc aparc.a2009s \ --tablefile lh.aparc.a2009.thickness.tabl But still I got the same error. On Sun, Jan 19, 2020, 10:30 PM <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. RES: Re: freesurfer container - freeview error > (marcosm(a)hucff.ufrj.br) > 2. registration of dwi images (Sam W) > 3. Re: registration of dwi images (Yendiki, Anastasia) > 4. Project hippocampus to inflated 3D model? (Mohammad Rashid) > 5. Re: aparcstats2table error (Devika K) > 6. Re: Project hippocampus to inflated 3D model? (Bruce Fischl) > 7. Re: aparcstats2table error (Bruce Fischl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 18 Jan 2020 15:05:15 -0300 > From: <marcosm(a)hucff.ufrj.br> > Subject: [Freesurfer] RES: Re: freesurfer container - freeview error > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <5e2383f1.1c69fb81.cfdf5.57cf(a)mx.google.com> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200118/f… > > ------------------------------ > > Message: 2 > Date: Sun, 19 Jan 2020 00:52:10 +0100 > From: Sam W <samfmri(a)gmail.com> > Subject: [Freesurfer] registration of dwi images > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > CAFYEHVvrxw-P0VWvqeiA_fMnUrMavmSb9wts3zDhLGFVZHC2ow(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hello! > I have run eddy on all my dwi images and then run bbregister using the > first b0 image as the source image. > The b0 image is now well aligned with the anatomical image but how can I > apply the same transformation to all other dwi images in my dataset? > > After eddy correction I extracted the first b0 image (nodif.nii.gz) and run > the bbregister command: > bbregister --s sub001 --mov /home/samm/nodif.nii.gz --reg > /home/samm/nodiffb2orig.dat --dti --init-fsl --o > /home/samm/registered_b0.nii.gz > > Thanks! > Sam >

2 1

Project hippocampus to inflated 3D model?
by Mohammad Rashid 19 Jan '20

19 Jan '20

External Email - Use Caution Hello, I have had success projecting regions such as the entorhinal region to an inflated 3D model. But I can't seem to do the same for hippocampi. I wouldn't need any hippocampal subfields, just projecting the hippocampus as a whole would be useful. Is there perhaps a particular file used for this that I am missing? Any help is appreciated, Mohammad Rashid

2 1

registration of dwi images
by Sam W 18 Jan '20

18 Jan '20

External Email - Use Caution Hello! I have run eddy on all my dwi images and then run bbregister using the first b0 image as the source image. The b0 image is now well aligned with the anatomical image but how can I apply the same transformation to all other dwi images in my dataset? After eddy correction I extracted the first b0 image (nodif.nii.gz) and run the bbregister command: bbregister --s sub001 --mov /home/samm/nodif.nii.gz --reg /home/samm/nodiffb2orig.dat --dti --init-fsl --o /home/samm/registered_b0.nii.gz Thanks! Sam

2 1

RES: Re: freesurfer container - freeview error
by marcosm＠hucff.ufrj.br 18 Jan '20

18 Jan '20

1 0

Results in different size
by Marina Fernández 17 Jan '20

17 Jan '20

External Email - Use Caution Dear Freesurfer team, I run statistical analysis with the files in the average subject of a dataset (created with 5th order icosahedron tesselation). In order to visualize the results, I open the inflated-surface and the pial-surface with tksurfer and I realize that inflated-surface of the average subject is smaller than the pial-surface. Is it normal? In the fsaverage5 subject these surfaces have a very similar size. Even, when I load the results as an overlay in the inflated-surface, the results are shown smaller (more than the proportional size) than if I load the results in the pial surface (see attached image). What can I do to generate an inflated figure with the results in the same size than in the pial surface? Thank you in advance. Best regards, Marina.

2 1

Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines
by Swati Rane 17 Jan '20

17 Jan '20

External Email - Use Caution Hello, I was wondering if someone could answer my question below Can I use mri_glmfit-sim after mri_glmfit on the longitudinal pc1 files. Are there any set of parameters that should be set differently when using pc1 instead of thickness files? Thanks! Swati ____________________________________________ Swati Rane Levendovszky, PhD Interim Director, Diagnostic Imaging Sciences Center Assistant Professor, Integrated Brain Imaging Center Radiology University of Washington Box 357115 | AA035 HSB | Seattle, WA 98195 srleven(a)uw.edu<mailto:srleven@uw.edu> | Ph: 206 543 6159 Web: https://sites.google.com/site/uwswatirane/ ____________________________________________ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Swati Rane <srleven(a)uw.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, January 10, 2020 at 10:06 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_glmfit-sim for longitudinal pipelines External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare longitudinal cortical thinning rates (pc1) between 3 groups using mri_glmfit using FreeSurfer 6.0. The tutorial suggests that you could use the multiple comparisons corrections that come with it but does not comment on using the mri_glmfit-sim option. I just want to confirm whether there is anything prohibiting me from using mri_glmfit-sim. Are there any set of parameters that should be set differently when using pc-1 instead of thickness files? Also, would you do a stricter correction and stick to the longitudinal model or prefer the linear mixed effects model and do a FDR? How do you decide between the two? Thanks! Swati

3 4

selxavg3-sess design ill-conditioned
by Marco Ninghetto 17 Jan '20

17 Jan '20

External Email - Use Caution Hello, I'm analyzing retinotopy data. I used expanding ring and rotating wedge. For my pilot, unfortunately, we used only 2 cycles for each stimulus and 1 cycle lasted 200 seconds (for sure I will change to more cycles lasting less). TR = 2.5. Retinotopy paradigm files are as follow: -for expanding ring (pos direction since it expands): stimtype eccen direction pos -for rotating wedge (neg direction since is counter-clockwise): stimtype polar direction neg To compute analyses, I ran the following pipeline: 1) recon-all 2) preproc-sess 3) mkanalysis-sess 4) selxavg3-sess Having only two cycles for each stimulus, in mkanalysis-sess, I used the option -hpf and lowered the filter to 0.5. In the last level (selxavg3-sess), I get the error. Basically this step runs up to when MATLAB starts to calculate. Here I get the following error: MATLAB is selecting SOFTWARE OPENGL rendering. > < M A T L A B (R) > > Copyright 1984-2019 The MathWorks, Inc. > R2019b Update 3 (9.7.0.1261785) 64-bit (glnxa64) > November 27, 2019 > > To get started, type doc. > 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 > > #@# SUBJ02 ############################### > /media/sf_w_Desktop/w_pRF/retinotopy/SUBJ02 > ------------------------- > $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ > ------------------------- > outtop = /media/sf_w_Desktop/w_pRF/retinotopy > Extension format = nii.gz > INFO: key nSliceGroups unrecognized, line 11, skipping > nruns = 2 > autostimdur = > > > outanadir = /media/sf_w_Desktop/w_pRF/retinotopy/SUBJ02/bold/retinotopy.lh > Found 118266/125623 (94.1) voxels in mask 1 > Creating Design Matrix > ... creation time = 0.008 sec > DoMCFit = 1 > ntptot = 260, nX = 158, DOF = 102 > Saving X matrix to > /media/sf_w_Desktop/w_pRF/retinotopy/SUBJ02/bold/retinotopy.lh/Xtmp.mat > XCond = 6.85663e+16 (normalized) > ERROR: design is ill-conditioned > ans = > 1 > >> ------------------------------------------ > ERROR: fast_selxavg3() failed\n I'm stuck with analyses and I cannot proceed further. Could you provide some insight on what to do? Having only two long lasting cycles, do I have to use further optional flags in my commands? Thank you for your time, Marco -- --------------------------------------------------- Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland

1 1

Calculate thickness in a ROI volume
by Karel Mauricio Lopez Vilaret 17 Jan '20

17 Jan '20

External Email - Use Caution Dear Freesurfer team, I would like to get the thickness values of a specific ROI (volume mask). Could you provide to me a function to calculate that? Thanks in advance, Karel

2 1

cannot find Matlab 2012b runtime in location
by Benjamin Ineichen 17 Jan '20

17 Jan '20

External Email - Use Caution Dear Freesurfer Experts, I ran the following command in FS: recon-all -i /Users/benine/Desktop/PVS_validation_cohort/MultipleMS_MRI_export/SW1-1875_M12/Brain/DICOM/0000D7EA/AACF54F0/AAA4DDA4/000037CC/EE021428 -subject 000037CC -qcache -hippocampal-subfields-T1 -brainstem-structures -cw256 -3T -all The command exited with error. Attached the log file. Additionally, this message shows up in the terminal output: ERROR: cannot find Matlab 2012b runtime in location: /Applications/freesurfer/MCRv80 It is looking for either: bin/glnxa64/libdctprocess.so (Linux 64b) or bin/maci64/libdctprocess.jnilib (Mac 64b) You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2012b. To do so, please run the following commands (you might need root permissions): LINUX: cd /Applications/freesurfer curl " http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do…" -o "runtime2012b.tar.gz" tar xvf runtime2012b.tar.gz MAC: cd /Applications/freesurfer curl " http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do…" -o "runtime2012b.tar.gz" tar xvf runtime2012b.tar.gz I did now download the runtime2012b according to the suggestion. The untaring created a folder called MCRv80. I moved this folder to the Freesurfer_Home. Before I run everything again: 1.) Is the correct procedure to download the Matlab runtime? 2.) Did the recon-all run everything just without hippocampal subfields and brainstem? If yes, can I just re-run these two commands or do I need to re-run everything? Many thanks for the support! /Ben ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01

1 0

Postdoctoral Fellowship
by Didenur Sahin 17 Jan '20

17 Jan '20

External Email - Use Caution Dear All, Brain Development And Psychosis Lab, is pleased to announce the opening of a postdoctoral fellowship position in clinical neuroscience and cognitive neuroimaging. Please take a look at the attached advertisement. Best, Didenur Sahin

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