Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

When rerunning recon-all from a later stage, are only edited participants' reconstructions recalculated?
by Mohammad Rashid 06 Jan '20

06 Jan '20

External Email - Use Caution I recently ran this command: `recon-all -autorecon2-noaseg -autorecon3 -subjid subj507` after having edited aseg.mgz (there was too much matter labelled as right hippocampus, so my edit was simply overwriting Right-Hippocampus voxels with Right-Cerebral-White-Matter ones). After the command's error-free completion, I checked the hippocampal volume measurements of all of the participants again using asegstats2table and found that they were all unchanged, except slight changes to subject subj507's measurements. So when instructed, does freesurfer only redo the reconstruction and recalculate stats only for those subjects that you've edited? If so, is there a way to have it recalculate every subject, not just those I've edited? Thank you in advance.

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Inflation cortical hemisphere to sphere in Freesurfer !?
by Fatemeh Ahmadi 05 Jan '20

05 Jan '20

External Email - Use Caution Dear experts,May I know the brain cortical hemisphere inflation method to the sphere in Freesurfer is a conformal mapping (such as Ricci flow)!? Regards & thanks

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Getting issue in running bt_recon
by sudhakar Mishra 04 Jan '20

04 Jan '20

External Email - Use Caution Hi, Please suggest something for the following error. Cannot allocate memory unsupported matlab format 839537524 (unknown) Best, Sudhakar Mishra Research Scholar Website <https://modelingemotion.wixsite.com/emotion> *सर्वद्वारेषु देहेऽस्मिन्प्रकाश उपजायते । ज्ञानं यदा तदा विद्याद्विवृद्धं सत्त्वमित्युत ॥* *श्रद्धावाँल्लभते ज्ञानं तत्परः संयतेन्द्रियः। ज्ञानं लब्ध्वा परां शान्तिमचिरेणाधिगच्छति।।* *योगश्चित्तवृत्तिनिरोधः*

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Surface file format differences
by Joshua Jacobs 03 Jan '20

03 Jan '20

External Email - Use Caution Hello, When working with the nightly development version of FreeSurfer recon-all (freesurfer-linux-centos6_x86_64-dev.tar.gz 23-Dec-2019 06:01) The surface file format differed by one character (\n) from previous versions. What makes me suspicious of this change is the difference between output and the fsaverage subject. See head -n 3 surf/rh.white for each below. recon-all output: ��created by root on Tue Dec 31 23:05:44 2019 ��YcR@��]�zk=�}��m�K�4�F��h��{yM��Ò��0@ �(��ě��̫�VY�vտ�1G�s��@t�4�*��>��C80�d?f��5��˿O+@�H&�f޿ˍ��ο�\i�.3��I� ^��dn��ٿp�7_��:�x��)��!�o�� fsaverage: ��created by greve on Thu Jul 19 12:52:07 2018 �A�3^�f�Bp�nA� This is the case for all sample data in the FS/subjects/ directory save for "bert". The data of which had been produced on 2019-12.21. Although I have not tried freeview on these files, it fails to open in the python library nibabel.freesurfer.io.load_geometry. Is this change intended? Thank You. Josh J.

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hardware upgrade affect Freesurfer?
by Dincer, Aylin 03 Jan '20

03 Jan '20

External Email - Use Caution Hi FreeSurfer Experts, Would upgrading computer hardware affect FreeSurfer output? We are using FreeSurfer version 5.3-HCP and we are considering upgrading our server. It will have the same operating system but different computer specs (memory, cpu, graphics, etc.). Thank you! Aylin -------------------- _____________________________ Aylin Dincer Senior Research Technician NeuroImaging Laboratories Imaging Core, Benzinger Lab 314-362-3629 ________________________________ 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.

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mis-registration question
by Nasiriavanaki, Zahra 03 Jan '20

03 Jan '20

Dear Freesurfers Hi I have a subject that the registration is not done correctly in two runs (run 12 and run 15) . The tkregister-sess values for this subject is shown below. Subject 1 10 0.2628 Subject 1 11 0.3038 Subject 1 12 0.7639 Subject 1 13 0.3364 Subject 1 14 0.3346 Subject 1 15 0.9361 Subject 1 16 0.2584 Subject 1 17 0.2488 I attached the screen shots from tkregister2 to this email. The functional data is only collected in a slab of parietal and occipital lobe. I appreciate if you let me know how to fix them. Thanks Mona [cid:6833a8d0-828b-4f31-9b61-2a4a1c3a670d][cid:7d39f7e2-609a-43a5-a964-dd95f8179c30] Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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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

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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.

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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

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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.

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