Freesurfer January 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
156 discussions

Run Recon-all Parallel on Linux
by Frank Chau 03 Jan '20

03 Jan '20

External Email - Use Caution Dear Freesurfer experts, May I know how to run Recon-all in parallel on Linux? I have read some source said that can use "gnu parallel" to complete it. But they do not describe it in detail how to perform it. Regards Frank --------------------------- FRANK C Y CHAU Research assistant Division of Neurology Department of Medicine Tel: +852 6340 2553 Fax: 2872 5828 E-mail : cyfrank(a)hku.hk<mailto:cyfrank@hku.hk> Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong

2 1

Re: [Freesurfer] (no subject)
by Greve, Douglas N.,Ph.D. 03 Jan '20

03 Jan '20

Can you send me the subject data following these steps? From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file. On 12/20/2019 10:58 AM, Boris Rauchmann wrote: External Email - Use Caution I had a look at the mgz file with freeview and it actually looks fine to me. Its the subcortical segmentation of the BN atlas. Do you have any ideas what went wrong? Best, Boris On Tue, Dec 17, 2019 at 6:33 PM Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> wrote: OK, I'm still at a loss. The one suspicious thing is that it only took a few min to run. So you have never looked at that volume? What is in the atlas? On 12/16/2019 3:42 PM, Boris Rauchmann wrote: External Email - Use Caution This is the log when I´m creating this file: Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz sysname Darwin hostname MacBook.local machine x86_64 setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz /Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z /Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca /Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == reading 1 input volumes reading classifier array from /Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca reading input volume from /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz reading transform from /Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z setting orig areas to linear transform determinant scaled 4.97 Atlas used for the 3D morph was /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 10.8 using min determinant for regularization = 11.7 0 singular and 129 ill-conditioned covariance matrices regularized labeling volume... 0 gm and wm labels changed (%nan to gray, %nan to white out of all changed labels) 0 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 9576 changed. pass 2: 3286 changed. MRItoUCHAR: min=0, max=246 MRItoUCHAR: converting to UCHAR writing labeled volume to /Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz mri_ca_label utimesec 146.184667 mri_ca_label stimesec 1.040963 mri_ca_label ru_maxrss 1436573696 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 609288 mri_ca_label ru_majflt 112 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 4 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 3 mri_ca_label ru_nivcsw 36417 auto-labeling took 2 minutes and 28 seconds. This is what I get when I do mrs_info on the gas: Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_info /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca reading frame -1 of gca Volume information for /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca type: GCA dimensions: 256 x 256 x 256 x 3 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 3 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 128.0000 0.0000 0.0000 1.0000 -128.0000 0.0000 -1.0000 0.0000 128.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 128.0000 -0.0000 -0.0000 -1.0000 128.0000 -0.0000 1.0000 -0.0000 128.0000 -0.0000 -0.0000 -0.0000 1.0000 Am 16.12.2019 um 21:21 schrieb Boris Rauchmann <boris.rauchmann(a)gmail.com<mailto:boris.rauchmann@gmail.com>>: Thanks, it was created using: mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz Best, Boris Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>: There is something weird about that file. How was it created? doug ps. Please include previous correspondence in the email On 12/16/19 1:12 PM, Boris Rauchmann wrote: External Email - Use Caution Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, -1): could not open file Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu>>: mri_info N_Atlas_subcotex.mgz _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

2 1

tracula error gradient vectors too many ('s
by Renew Andrade 02 Jan '20

02 Jan '20

External Email - Use Caution Dear FreeSurfer experts: I am trying to run tracula in 4 subjects of a public dataset. I have encountered one error. I leave the output of terminal below. I also attach the configuration file. I hope you can follow from there. Sincerely, Andrade. root@andraderenew:/usr/local/freesurfer/subjects# trac-all -prep -c /usr/local/freesurfer/subjects/dmrirc.IXI Too many ('s. INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects INFO: Diffusion root is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer trac-preproc -c /usr/local/freesurfer/subjects/IXI_25_Guys_T1/scripts/dmrirc.local -log /usr/local/freesurfer/subjects/IXI_25_Guys_T1/scripts/trac-all.log -cmd /usr/local/freesurfer/subjects/IXI_25_Guys_T1/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections sáb dic 21 15:06:13 CET 2019 mri_convert --bvec-voxel /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz /usr/local/freesurfer/subjects/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz /usr/local/freesurfer/subjects/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998725, -0.0503472, 0.00377193) j_ras = (-0.0504772, 0.994141, -0.0955763) k_ras = (-0.00106217, 0.0956448, 0.995415) writing to /usr/local/freesurfer/subjects/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz... ERROR: Must specify input table of gradient vectors Linux andraderenew 5.0.0-37-generic #40~18.04.1-Ubuntu SMP Thu Nov 14 12:06:39 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at sáb dic 21 15:06:13 CET 2019

2 1

Different versions of fsaverage?
by Dorian P. 02 Jan '20

02 Jan '20

External Email - Use Caution Are the fsaverage versions coming from the following (as reported in recon-all.log within the fsaverage directory) significantly different ? freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20101225 freesurfer-x86_64-redhat-linux-gnu-dev4-20090216 freesurfer-x86_64-redhat-linux-gnu-dev4-20100112 I thought that fsaverage, being a template, does not change with time, but we are finding difference in size or binary information for certain fsaverage files on different freesurfer versions. Thank you.

2 1

Changelog between stable and dev versions?
by Dorian P. 02 Jan '20

02 Jan '20

External Email - Use Caution Hello everyone, and happy new year. I know it's never a good idea to mix versions within a study, but that's what has happened in a large study here, so I am trying to get a sense of what changes there have been. I was wondering if there is a way to see if there are major changes between a stable version and certain dev versions, specifically I am interested in finding out about these versions of freesurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a freesurfer-Linux-centos7_x86_64-dev-20180227-5e5b9aa freesurfer-linux-centos7_x86_64-dev-20190805-8b45905 Thanks!

2 1

mkanalysis-sess.new not found
by Marco Ninghetto 02 Jan '20

02 Jan '20

External Email - Use Caution Dear experts, my name is Marco and I'm using freesurfer to perform retinotopy analysis and I am having a problem with command: `mkanalysis-sess.new` after calling that command I get the following bash error: `bash: mkanalysis-sess.new: command not found` All the previous steps worked well. Why is this command unrecognized? Thank you all, Marco -- --------------------------------------------------- Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland

2 2

Unable to run recon all
by Sahil Bajaj 02 Jan '20

02 Jan '20

External Email - Use Caution Hello FS experts, I am trying to run recon all on about 100 subjects. But one out of 100 subjects finishes recon all with error, and doesn't complete the process. Here I am attaching recon all log for your reference. Also, before installing freesurfer on MAC Catalina, I ran sudo spctl - -master -disable I would really appreciate any help in resolving this. Thanks, Sahil 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 2) Platform: MACOS Catalina 3) recon-all.log: see attached

2 1

Fill holes in BOLD surface
by Marina Fernández 02 Jan '20

02 Jan '20

External Email - Use Caution Hi Freesurfer experts, I have projected 4D-preprocessed BOLD data to Freesurfer cortical surfaces. Resulting individual surfaces have many holes (see attached image) that I would like to fill with nearest neighbors values around each hole (avoiding the medial wall). Could you indicate me how to do this? Thank you in advance. Marina

2 1

mapping the reliability of separating GM/WM
by Liu Y 02 Jan '20

02 Jan '20

External Email - Use Caution Hi Freesurfers, The contrast between GM/WM may vary regions by regions. Some regions have high contrast, some regions have low contrast, is there a method can map the reliability of separating gray and subcortical white matter? Thanks in advance, Yawu

3 4

No Colortable Found
by Baptista, Paulo 02 Jan '20

02 Jan '20

External Email - Use Caution Hello FreeSurfer Developers, I'm helping researchers test Freesurfer 4.5 and Freesurfer 6. Running same code on Freesurfer4.5 environment produces no image with tksurfer. It says "No colortable found." See attached. 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 2) Platform: CentOS release 5.11 (Final) We're are running this in a Singularity container. It's getting close to working properly. It would be nice to have a way to run old code on newer Linux systems. Thanks, Paulo

2 2

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 January 2020