Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

plotting mean T1/T2 values in the different cortical layers
by Anik Dar 31 Dec '18

31 Dec '18

External Email - Use Caution Hi All, I have created cortical surfaces corresponding to 25%, 50%, 75% of the cortex. Now I want to plot the T1/T2 values corresponding to these different layers.I believe I have to use mri_vol2surf. What options in the mri_vol2surf do I need to use to create these T1/T2 maps corresponding to these different layers of the cortex ? Please let me know. Merry christmas and a happy New Year. Thank you, Ani

2 1

Notebook specification
by mustafa amin 30 Dec '18

30 Dec '18

External Email - Use Caution Dear Freesurfer Members, First I would like to introduce myself my name is Mustafa Amin, and I’m planning to do a study to measure the volume of prefrontal cortex, hippocampus, and ventricle of patients with schizophrenia comparing them with control in Medan Indonesia. I read and saw information that freesurfer is capable in doing the measurement, however I am still not sure about what kind of notebook specification that I need to download and install it. For my knowledge, this is the first study that will be done in Indonesia so every explanation and further information about freesurfer and the notebook will make me very grateful. I’m thinking to buy an I5 intel core processor, with 8GB RAM, 1 TB HDD, and full HD Nvidia MX130 2G8 specification notebook. If there is anyone in here that can share the minimum requirements of the notebook, it will help me a lot to choose which one to buy. Thank you in advance. Yours faithfully, Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara

3 3

Errors in WM surface persistent after manual edits to wm.mgz
by Rachel Hoel 29 Dec '18

29 Dec '18

External Email - Use Caution Dear Freesurfer Developers, Our study is implementing the longitudinal processing pipeline in FS 6.0. When attempting to make manual white matter edits to our subjects, the edits save but do not appear to impact the white matter surface. We are using the voxel-edit tool in freeview and recon-editing is selected, and the edits are made on the wm.mgz volume. Below are the commands we use to make and submit the edits... Command to open and edit WM: freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red Command to submit edits: recon-all -autorecon2-wm -autorecon3 -subjid Thank you in advance, Rachel Hoel Research Assistant Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

1 0

temporal lobe errors in rh.white and lh.white surfaces but not in rh.orig and lh.orig surfaces
by Neva M Corrigan 28 Dec '18

28 Dec '18

External Email - Use Caution Hi, I am using recon-all to generate pial and white matter surfaces for MPRAGE data but am having trouble in the temporal lobes for all of my subjects. The pial surfaces look very good, but the white matter surfaces are poor. Notably, the wm.mgz volume and the lh.orig and rh.orig surfaces seem to correctly include all of the white matter in the temporal lobe. However, the rh.white and lh.white surfaces miss a substantial portion of the white matter. On the ReconAllDevTable I see that the ?.orig surfaces are generated before the ?.white surfaces. Can you suggest how I might be able to fix the ?.white surfaces? In case it is relevant, I had to create an xopts.txt file with the following options in order to obtain correct skull-stripping and pial surfaces for this data: mri_normalize -mprage -b 2 -n 5 I am using freesurfer development version with a date of 05-03-2018. I have attached an image of the ?.orig and the ?.white surfaces superimposed on the wm.mgz and brainmask.mgz volumes. Thank you, Neva

2 2

How to visualise DTI
by Renew Andrade 27 Dec '18

27 Dec '18

External Email - Use Caution Dear community! I would like to know how can I use Freeview or any tool of FreeSurfer to visualise preprocessed DTI files from a database. They are in a standard output like it appears in Tracula output page of FreeSurfer wiki. It shouldn’t be a problem to use these files in FreeSurfer. Everything (details of output and preprocessing stages) is explained in this website. https://www.nitrc.org/plugins/mwiki/index.php/neurobureau:INDIpreproc <https://www.nitrc.org/plugins/mwiki/index.php/neurobureau:INDIpreproc> Thanks for your help!

1 0

mpr2mni305 failed, during recon-all
by Shachar Gal 24 Dec '18

24 Dec '18

External Email - Use Caution hello, I'm running the hcp's FreeSurfer pipeline, and for some reason, after working successfully several times, on different subjects, im getting this error: *** /Users/georgieboy/Research/Piano/test/222/222/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin medical613-6.tau.ac.il 18.2.0 Darwin Kernel Version 18.2.0: Fri Oct 5 19:41:49 PDT 2018; root:xnu-4903.221.2~2/RELEASE_X86_64 x86_64 recon-all -s 222 exited with ERRORS at Sun Dec 23 15:50:23 IST 2018 *** the information in the talairach_avi.log is as follows: *** dyld: Symbol not found: ___keymgr_global Referenced from: /Applications/freesurfer/bin/gauss_4dfp Expected in: /usr/lib/libSystem.B.dylib in /Applications/freesurfer/bin/gauss_4dfp Abort ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134 ERROR: mpr2mni305 execution aborted *** to be clear, this - /usr/lib/libSystem.B.dylib exists exactly where is was expected... the input image, orig.mgz, looks fine and is in 1 mm res... so im having trouble getting to the bottom of the error. thanks in advance, Shachar

2 8

Project Effect Size onto Desikan-Killiany Atlas
by Taralee Hamner 24 Dec '18

24 Dec '18

External Email - Use Caution Hi all, We would like to project effect sizes on the FS average brain using Desikan-Killiany Atlas. We will then manually color code regions based on the effect size range. However, our command line is not loading the Desikan-Killiany Atlas. (Tksurfer fsaverage lh inflated -annotation aparc). See picture below. [image: Screen Shot 2018-12-11 at 10.35.40 AM.png] Please advise on 1) how to load the atlas on the FS average brain and 2) if it would be better to manually color code regions based on effect size or project the raw effect size data on the brain. I hope everyone is having a happy holiday season. Best, Taralee

1 0

Finding the surface vertex for a voxel in the cortex
by ts+ml＠rcmd.org 24 Dec '18

24 Dec '18

External Email - Use Caution Dear FreeSurfer experts, given a voxel in the cortex of the fsaverage subject, I would like to find the vertex on the surface that corresponds to the voxel (e.g., if volume data would be projected to the surface). I found the documentation at http://freesurfer.net/fswiki/CoordinateSystems, which helped me a lot, but it would be great if someone could comment on whether or not what I'm doing is correct: This seems to be use case 4 on the page (bottom), so I would: 1) get the affine matrix by running: mri_info --vox2ras-tkr $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz 2) Apply the matrix to my voxel x, y, z to get the coords At this point I'm not sure how to get the vertex. Should I just compute the distance from the coords to all vertices and pick the one with minimal Euclidian distance? Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

2 3

Re: [Freesurfer] mpr2mni305 failed, during recon-all {Disarmed}
by fsbuild 23 Dec '18

23 Dec '18

External Email - Use Caution Hello, I have not tried it, but it would not surprise me to see incomplete library references when running the old freesurfer 5 binaries on the latest version of Mac OS, i.e., Mac OS 10.14 (Mojave) I would try to use the rev 6 release binaries for MacOS from, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall I have built the latest development branch of freesurfer on Mac OS 10.14, but please be aware this has not been tested like the previous rev 6 release.  (I used the makefile.wiki to build it which you can download from https://surfer.nmr.mgh.harvard.edu/fswiki/CMake) - R. On Dec 23, 2018, at 10:00, Shachar Gal <gal.shachar(a)gmail.com> wrote:        External Email - Use Caution        Sorry, out of the office for the day. I'll get back to you about it tomorrowShacharOn Sun, Dec 23, 2018, 16:56 Glasser, Matthew <glasserm(a)wustl.edu> wrote:        External Email - Use Caution        Is that FreeSurfer 5.3?Matt.From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.com>Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Date: Sunday, December 23, 2018 at 8:35 AMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] mpr2mni305 failed, during recon-all        External Email - Use Caution        this is my Freesurfer version - freesurfer-i386-apple-darwin10.8.0-stable5-20130513and I think the update to macOS Mojave was after successfully running the pipeline.you think this could be the issue? should I just upgrade my freesurfer?thanksOn Sun, 23 Dec 2018 at 16:28, Glasser, Matthew <glasserm(a)wustl.edu> wrote:        External Email - Use Caution        Which version of FreeSurfer is this and did you do some OS upgrade in between?Matt.From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.com>Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Date: Sunday, December 23, 2018 at 8:24 AMTo: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] mpr2mni305 failed, during recon-all        External Email - Use Caution        hello,I'm running the hcp's FreeSurfer pipeline, and for some reason, after working successfully several times, on different subjects, im getting this error:***/Users/georgieboy/Research/Piano/test/222/222/mri\n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \nERROR: mpr2mni305 failed, see transforms/talairach_avi.logDarwin medical613-6.tau.ac.il 18.2.0 Darwin Kernel Version 18.2.0: Fri Oct  5 19:41:49 PDT 2018; root:xnu-4903..221.2~2/RELEASE_X86_64 x86_64recon-all -s 222 exited with ERRORS at Sun Dec 23 15:50:23 IST 2018***the information in the talairach_avi.log is as follows:***dyld: Symbol not found: ___keymgr_global  Referenced from: /Applications/freesurfer/bin/gauss_4dfp  Expected in: /usr/lib/libSystem.B.dylib in /Applications/freesurfer/bin/gauss_4dfpAbortERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134ERROR: mpr2mni305 execution aborted***to be clear, this -  /usr/lib/libSystem.B.dylib exists exactly where is was expected...the input image, orig.mgz, looks fine and is in 1 mm res...so im having trouble getting to the bottom of the error.thanks in advance,Shachar The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard..eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Error saving NPC results
by Daniel Leopold 23 Dec '18

23 Dec '18

External Email - Use Caution Dear Freesurfer Community, Drs. Winkler, Greve, Fischl, et al. *My apologies if this reposts, but this is my first time emailing the listserv, and I'm not sure if my earlier email went through* Could anyone help me understand which palm options are needed in order to produce tfce and clustere NPC results that are fwe-corrected across contrasts (i.e., npc_fisher_cfwep_)? I'm analyzing area and thickness and have four one-tailed contrasts of interest (e.g., C1+, C1-, C2+, C2-). Currently, I am only able to get the "output'_dpv_npc_fisher_cfwep_c[1234]" results, but the palm log ends abruptly after saving these files and does not save the _tfce_ or _clustere_ versions: Saving p-values for NPC between modalities (uncorrected and corrected within contrasts). Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c1 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c1 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c1 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c1 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c1 Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c2 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c2 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c2 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c2 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c2 Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c3 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c3 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c3 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c3 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c3 Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c4 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c4 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c4 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c4 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c4 Saving p-values for NPC between modalities (corrected across contrasts). Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c1 Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c2 Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c3 Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c4 >> The error log contains the following text, and my efforts to read through these source files have been in vain: {^HCell contents reference from a non-cell array object. Error in palm_saveall (line 1043) distmax(:,j) = plm.Tclumax{m}{c}; Error in palm_core (line 2489) palm_saveall(plm,opts); Error in palm (line 81) palm_core(varargin{:}); }^H ^G I have essentially permuted the various -corr(con/mod) and -npc(con/mod) options, as well as various combinations of -T & -C {z}, -Tuni & -Cuni {z}, and -Tnpc & -Cnpc {z}, using a small number of permutations to assess the number of output maps and whether jobs finish appropriately. Here's an example of one of the palm commands that resulted in these output and error logs (with line-breaks for legibility): fsl_sub -l $logdir palm -designperinput -i {area_dir}/292_${hemi}.area_stack.mgh -d {design_dir}/wordadhd_npc_areatotal.mat -t {design_dir}/wordadhd_npc_areatotal.con -i {thickness_dir}/292_${hemi}.thickness_stack.mgh -d {design_dir}/wordadhd_npc_thickmean.mat -t {design_dir}/wordadhd_npc_thickmean.con -m {base_dir}/palm/input/${hemi}mask.mgz -s ${surf_dir}/${hemi}.white ${surf_dir}/${hemi}.white.avg.area.mgh -o wordadhd_npc_${hemi} -eb ${EB} -corrcon -corrmod -logp -ise -npc -T -C 1.64485 -n 5 If knowing versions helps at all: PALM alpha109 MATLAB 8.3.0.532 (R2014a) FreeSurfer 5.3.0 FSL 5.0.8 Any advice you could provide on this particular error, why my input doesn't produce the tfce_npc_fisher_cfwep or clustere__npc_fisher_cfwep results, or other problem-solving suggestions would be greatly appreciated! With gratitude, Dan

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