Freesurfer January 2019

freesurfer@nmr.mgh.harvard.edu

119 participants
167 discussions

Hippocampal subfields
by Leire Zubiaurre Elorza 22 Jan '19

22 Jan '19

External Email - Use Caution Hello, We have tried running hippocampal subfields module and we get an error with one of the subjects analyzed. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c The error we get is the following (the log file has been attached): ransforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points numberOfLabels: 25 Rasterizing mesh...here: 25 Killed Started at Tue Jan 22 11:06:54 CET 2019 Ended at Tue Jan 22 11:25:14 CET 2019 #@#%# recon-all-run-time-hours 0.306 recon-all -s LR008 finished without error at Tue Jan 22 11:25:14 CET 2019 done Any help will be appreciated, Thank you very much, Leire -- -- Leire Zubiaurre-Elorza Assistant Professor Department of Methods and Experimental Psychology Faculty of Psychology and Education Tel.: +34 944 139 000-(ext.2299) Unibertsitateen Etorbidea, 24 48007 Bilbo-Bizkaia www.deusto.es

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回复： how to register feature maps to fsaverage6?
by 310913949 21 Jan '19

21 Jan '19

External Email - Use Caution Thanks for your reply! Actually, i first use "recon-all -s PT1_13 -i PT1_13.nii -all -qcache -target fsaverage6 " to process the subject, but i think i make some mistakes as i find there are about 110,000 vertex values in the"lh.thickness"file. and I also find that it generates a file named"recon-all.error",the context is as follows: Linux zhangjianing-Precision-Tower-7910 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $ /media/root/533b526f-751c-4a6a-a3da-11856d602f84/usr/local/freesurfer/bin/recon-all PWD /media/root/533b526f-751c-4a6a-a3da-11856d602f84/usr/local/freesurfer/subjects/PT1_1302/surf CMD mris_preproc --s PT1_1302 --hemi lh --meas thickness --target fsaverage6 --out lh.thickness.fsaverage6.mgh" I am not sure whether i misused this command and how to correct that. Besides,i tried to use these two commands after recon-all, "mris_register -curv surf/lh.sphere $SUBJECTS_DIR/fsaverage6/lh.reg.template.tif surf/lh.sphere.reg.newtemplate" and"mris_preproc --s PT1_13--hemi lh --meas thickness --target $SUBJECTS_DIR/fsaverage6 --out lh.thickness.fsaverage6.mgh",but it didn't work. I also tried to use"mris_preproc --s PT1_1302 --hemi lh --meas thickness --target fsaverage6 --out lh.thickness.fsaverage6.mgh",but it didn't work too. So do you mean that i need to use"mris_surf2surf" after recon-all ?And am i wrong that i used above command lines to register subjects to fsaverage6? Thanks for any info! ------------------ 邓刊 Kan Deng E-mail：310913949(a)qq.com TEL：13728774014 ------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; 发送时间: 2019年1月22日(星期二) 上午10:37 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer] how to register feature maps to fsaverage6? are you feature maps already on individual subject surfaces? If so, you an use mri_surf2surf with fsaverage6 as the target cheers Bruce On Tue, 22 Jan 2019, 310913949 wrote: > > External Email - Use Caution > > Dear freesurfer experts?? > I want to know how to register feature maps to an average space (fsaverage6) so that I can get an identical > number of vertices(40962) for each hemisphere. Can you tell me what is the command line? > I am looking forward to your reply!Thanks. > > ------------------ > > ???? Kan Deng > > E-mail??310913949(a)qq.com > > TEL??13728774014 > > > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_watershed Error：Problem in the COG calculation
by Abby tang 21 Jan '19

21 Jan '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon-all subjects but for some of my subjects I get the following error when I run recon-all command: *************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Linux abby-virtual-machine 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 0078 exited with ERRORS at Sun Jan 20 20:16:12 CST 2019 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. Thank you!

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consistent brain regions of Frontal_Sup_Medial_L(AAL) in freesurfer template
by charujing123 21 Jan '19

21 Jan '19

External Email - Use Caution Hi FS experts and users, I have an interested ROI Frontal_Sup_Medial_L in AAl. And I want to test the thickness or volume of this roi. I found some candidate roi in FS atlas, such as rostralanteriorcingulate, caudalanteriorcingulate, superiorfrontal. So which one is consistent with frontal_sup_medial in AAL. Thanks. rujing 2019-01-21 charujing123

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mris_anatomical_stats input image?
by Winkelbeiner, Stephanie A 18 Jan '19

18 Jan '19

External Email - Use Caution Hi Freesurfers, I'm using the below command to extract GM values: mris_anatomical_stats -mgz \ -cortex label/lh.cortex.label \ -f stats/lh.250.aparc.pial.stats \ -b -a 250.aparc \ -c label/colortable.ctab \ $subject lh pial Specifying "pial" which image does the command actually use? The mri/orig.mgz? Thanks for your help! Stephanie The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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error while running trac-preproc
by Barletta, Valeria 18 Jan '19

18 Jan '19

Dear Freesurfers, I am trying to run the command trac-all -prep -c but I'm getting this error: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory Can you help me? Thank you, Vale

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wm and vcsf nuisance regressors
by Nasiriavanaki, Zahra 18 Jan '19

18 Jan '19

Dear Freesurfers Hi I am using white matter and CSF external nuisance regressors in my mkanalysis-sess. However, when I make these regressors, I use -mean in fcseed-config command, and so the .dat files only have one column (the mean values, I assume). I looked up in the freesurfer archive and I saw that It is recommended to use -nuisreg wm.dat 5 and -nuisreg vcsf.dat 5. My question is that what difference it makes to use mean of these regressors vs using only 5 of the columns. I appreciate if you could please reply whenever you had time. Thanks Mona 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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Talairach Transform failure
by Daniel Ferreira 18 Jan '19

18 Jan '19

External Email - Use Caution Dear Bruce, Martin, and experts, I posted an issue a few days ago. I have been looking through the archives but can not figure out the solution myself. I was wondering if you would have any suggestion on how to fix the issue described further down? Thank you very much in advance Dani ---- Daniel Ferreira <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Wed, 09 Jan 2019 10:22:05 -0800 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> External Email - Use Caution Dear experts, I am processing some data and one of my cases failed. I checked the recon-all.log and found the following: *#@# Talairach Failure Detection tis 11 dec 2018 11:32:31 CET* */home/daniel/FreeSurfer/0e63e2e7-d1e1-4e78-9106-150994a32c44/mri* * talairach_afd -T 0.005 -xfm transforms/talairach.xfm * *ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)* *Manual Talairach alignment may be necessary, or* *include the -notal-check flag to skip this test,* *making sure the -notal-check flag follows -all* *or -autorecon1 in the command string.* *See:* *http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach>* *ERROR: Talairach failed!* *Linux siv 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux* *recon-all -s 0e63e2e7-d1e1-4e78-9106-150994a32c44 exited with ERRORS at tis 11 dec 2018 11:32:31 CET* Next, I tried to fix the issue by using tkregister: tkregister2 --mgz --s tal_before --fstal However, the Talairach volume does not load as a MOVEABLE volume. When I check the available recon-all output I only have: orig/001 --> looks good rawavg --> looks good orig --> its awful (it looks like millions of white tiny voxels on a black background) nu --> it is empty transforms/talairach.xfm --> is available I was wondering if you would know about any way to fix this? Thank you in advance, Dani -- *Daniel Ferreira, PhD, Assistant Professor* Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences and Society Karolinska Institutet (Sweden) *Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 | email: daniel.ferreira.padi...(a)ki.se <daniel.ferreira.padi...(a)ki.se>*

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Re: [Freesurfer] Longitudinal subfields segmentation single time point
by Iglesias Gonzalez, Eugenio 18 Jan '19

18 Jan '19

External Email - Use Caution Thanks a lot for your email, Saskia. Does this happen for more than one subject? Can you reproduce the error? Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London Research staff Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology Lecturer on Radiology Harvard Medical School http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Koch, S.B.J. (Saskia)" <S.Koch(a)donders.ru.nl> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 18 January 2019 at 09:46 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Longitudinal subfields segmentation single time point External Email - Use Caution Dear FreeSurfer Developers, I am attempting to run the longitudinal hippocampal subfields segmentation, using the development version of FreeSurfer. This works perfect for subjects with multiple data time points, but I get the following error for subjects for which I have a single data time point (see attachment for the error log): ******************* Global iteration 2 ******************* ***** Estimating subject-specific atlas ***** Error using kvlGEMSMatlab /autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/Matlab/kvlMatlabObjectArray.cxx:82: itk::ERROR: MatlabObjectArray(0x7f8686741c40): Trying to access non-existing object (25) Error in kvlGetOptimizer (line 11) Error in SegmentSubfieldsT1Longitudinal (line 1155) Is it possible to run this longitudinal module on subjects with a single time point? Any thoughts on how to troubleshoot this? FreeSurfer version: freesurfer-Linux-centos7_x86_64-dev-20180118-d073f7e Platform: CentOS Linux 7 (Core) Uname -a: Linux mentat003.dccn.nl 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Thanks for your help! Saskia

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Longitudinal subfields segmentation single time point
by Koch, S.B.J. (Saskia) 18 Jan '19

18 Jan '19

External Email - Use Caution Dear FreeSurfer Developers, I am attempting to run the longitudinal hippocampal subfields segmentation, using the development version of FreeSurfer. This works perfect for subjects with multiple data time points, but I get the following error for subjects for which I have a single data time point (see attachment for the error log): ******************* Global iteration 2 ******************* ***** Estimating subject-specific atlas ***** Error using kvlGEMSMatlab /autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/Matlab/kvlMatlabObjectArray.cxx:82: itk::ERROR: MatlabObjectArray(0x7f8686741c40): Trying to access non-existing object (25) Error in kvlGetOptimizer (line 11) Error in SegmentSubfieldsT1Longitudinal (line 1155) Is it possible to run this longitudinal module on subjects with a single time point? Any thoughts on how to troubleshoot this? FreeSurfer version: freesurfer-Linux-centos7_x86_64-dev-20180118-d073f7e Platform: CentOS Linux 7 (Core) Uname -a: Linux mentat003.dccn.nl 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Thanks for your help! Saskia

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Freesurfer January 2019