[Freesurfer] Freeview-stable4 error?
Hi, I'm trying to look at 2 connectivity files (saved in SPM) at the same time using Freeview, but how I've been doing it in the past is no longer working and I haven’t changed anything on my end. What I had been doing: 1. cd to the folder with my connectivity files and typing the shortcut command: stable4 (which does the following: setenv USE_STABLE_4_5_0; source /space/freesurfer/nmr-stable4-env) 2. typing the command: freeview ../../../../N12Trio_avg152T1.nii LSHSxAmyg.covBDI_PosCorr_p05_20vox.img LSHSxAmyg.covBDI_NegCorr_p05_20vox.img_blue.nii.gz This command used to work fine, but is now giving me the error: freeview.bin: error while loading shared libraries: libvtkverdict.so.vtk5.2.0: cannot open shared object file: No such file or directory This command DOES work if I don't type the shortcut command stable4 and instead keep using the stable53 environment I was already in (setenv FSL_DIR /usr/pubsw/packages/fsl/4.1.9; source /space/nexus/1/users/avi-tools/enable_avi.csh; setenv SUBJECTS_DIR /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53; source /usr/local/freesurfer/nmr-stable53-env). While I'm not positive it affects anything, I'd rather be consistent with the stable4 way I've been doing it in the past - is there a way to fix it and use Freeview in stable4, or does this freeview.bin error mean that I can no longer use Freeview with stable4? Thanks, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078 ___ Freesurfer mailing list 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.
Re: [Freesurfer] Freeview-stable4 error?
Thanks! Unfortunately it won't help; I need specific versions with specific compilation options etc :-( Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Stephanie N. DeCross sdecr...@mgh.harvard.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Douglas N Greve gr...@nmr.mgh.harvard.edu Sent: Wednesday, November 5, 2014 10:33:54 AM Subject: [Freesurfer] Freeview-stable4 error? Hi, I'm trying to look at 2 connectivity files (saved in SPM) at the same time using Freeview, but how I've been doing it in the past is no longer working and I haven’t changed anything on my end. What I had been doing: 1. cd to the folder with my connectivity files and typing the shortcut command: stable4 (which does the following: setenv USE_STABLE_4_5_0; source /space/freesurfer/nmr-stable4-env) 2. typing the command: freeview ../../../../N12Trio_avg152T1.nii LSHSxAmyg.covBDI_PosCorr_p05_20vox.img LSHSxAmyg.covBDI_NegCorr_p05_20vox.img_blue.nii.gz This command used to work fine, but is now giving me the error: freeview.bin: error while loading shared libraries: libvtkverdict.so.vtk5.2.0: cannot open shared object file: No such file or directory This command DOES work if I don't type the shortcut command stable4 and instead keep using the stable53 environment I was already in (setenv FSL_DIR /usr/pubsw/packages/fsl/4.1.9; source /space/nexus/1/users/avi-tools/enable_avi.csh; setenv SUBJECTS_DIR /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53; source /usr/local/freesurfer/nmr-stable53-env). While I'm not positive it affects anything, I'd rather be consistent with the stable4 way I've been doing it in the past - is there a way to fix it and use Freeview in stable4, or does this freeview.bin error mean that I can no longer use Freeview with stable4? Thanks, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078 ___ Freesurfer mailing list 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)
?Hello, I am encountering the exact same problem on Yosemite (10.10). The log file is attached. Any ideas? I am pretty stumped. Anthony From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Matthew Riddle mrid...@nyspi.columbia.edu Sent: Thursday, October 23, 2014 7:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite) Dear Freesurfer Team, I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I'm still experiencing an issue with freesurfer that I'm hoping you might have some idea about. Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal: sudo -E recon-all -s bert -all The processes crashes in a minute or two at the same place each time, and this is the last bit of output. MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz # #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014 I tried this on an almost identical machine running Mavericks, and got the exact same problem. From my bugr output: FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.0.0 x86_64 The recon-all.log file doesn't provide any additional information, it just mirrors the output from the terminal. Thanks, -Matt recon-all.error Description: recon-all.error recon-all.log Description: recon-all.log ___ Freesurfer mailing list 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.
[Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview
I'm sorry if this has been answered before, I have browsed the mailing and found nothing answering this. I need to generate three views of the T1 data superimposed with Aseg data automatically for Quality Control without using FreeView or Tkmedit (the server generating this has no X11) Is it possible to do it with the command line tools? Thanks - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ Freesurfer mailing list 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.
[Freesurfer] Infinite loop in mri_convert
Dear FreeSurfer experts, I get a new message when I use mri_convert command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I get the new message. In addition, it does not create mgz file, and goes to infinite loop. *mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz* mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /M1/t1_se_ax_5/IM-0004-0001.dcm... Getting Series No Scanning Directory INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5 INFO: Scanning for Series Number 5INFO: found 37 files in series INFO: loading series header info. I appreciate if you can advise me. Regards, Nooshin PhD Candidate Departments of Electrical Computer Engineering University of Miami Email: n.za...@miami.edu ___ Freesurfer mailing list 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.
Re: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)
Hello Martin, I did this (ran it from both the Desktop and Documents). Also tried re-installing Freesurfer. The subjects folder also has permissions: drwx--+ 1632 adick staff54K Nov 5 13:01 Desktop drwx--+ 42 adick staff 1.4K Nov 5 12:48 Documents I also set permissions for freesurfer/bin using the chmod command: chmod -R a+x freesufer/bin/* Not really sure what the issue is, but it seems to be related to the upgrade to Yosemite. Anthony On 11/5/14, 1:39 PM, Martin Reuter wrote: Hi Anthony, wasnt the answer (by Mathew Riddle 10/23) to this to move Bert to a place where you have write permissions (as User). Best, Martin On 11/05/2014 12:56 PM, Anthony Dick wrote: Hello, I am encountering the exact same problem on Yosemite (10.10). The log file is attached. Any ideas? I am pretty stumped. Anthony *From:* freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Matthew Riddle mrid...@nyspi.columbia.edu *Sent:* Thursday, October 23, 2014 7:48 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite) Dear Freesurfer Team, I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I'm still experiencing an issue with freesurfer that I'm hoping you might have some idea about. Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal: sudo --E recon-all --s bert --all The processes crashes in a minute or two at the same place each time, and this is the last bit of output. MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz # #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014 I tried this on an almost identical machine running Mavericks, and got the exact same problem. From my bugr output: FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.0.0 x86_64 The recon-all.log file doesn't provide any additional information, it just mirrors the output from the terminal. Thanks, -Matt ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web :http://reuter.mit.edu ___ Freesurfer mailing list 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. ___ Freesurfer mailing list 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.
Re: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)
Hello Anthony, The problem isnt with the location of the bert folder but rather with the permissions of the bert folder itself (and the permissions within). To run the bert case please 'cd' into the directory containing the bert folder and type the following: sudo chmod -R a+wr bert -Zeke On 11/05/2014 02:42 PM, Anthony Dick wrote: Hello Martin, I did this (ran it from both the Desktop and Documents). Also tried re-installing Freesurfer. The subjects folder also has permissions: drwx--+ 1632 adick staff54K Nov 5 13:01 Desktop drwx--+ 42 adick staff 1.4K Nov 5 12:48 Documents I also set permissions for freesurfer/bin using the chmod command: chmod -R a+x freesufer/bin/* Not really sure what the issue is, but it seems to be related to the upgrade to Yosemite. Anthony On 11/5/14, 1:39 PM, Martin Reuter wrote: Hi Anthony, wasnt the answer (by Mathew Riddle 10/23) to this to move Bert to a place where you have write permissions (as User). Best, Martin On 11/05/2014 12:56 PM, Anthony Dick wrote: Hello, I am encountering the exact same problem on Yosemite (10.10). The log file is attached. Any ideas? I am pretty stumped. Anthony *From:* freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Matthew Riddle mrid...@nyspi.columbia.edu *Sent:* Thursday, October 23, 2014 7:48 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite) Dear Freesurfer Team, I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I’m still experiencing an issue with freesurfer that I’m hoping you might have some idea about. Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal: sudo –E recon-all –s bert –all The processes crashes in a minute or two at the same place each time, and this is the last bit of output. MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz # #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014 I tried this on an almost identical machine running Mavericks, and got the exact same problem. From my bugr output: FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.0.0 x86_64 The recon-all.log file doesn’t provide any additional information, it just mirrors the output from the terminal. Thanks, -Matt ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web :http://reuter.mit.edu ___ Freesurfer mailing list 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list
[Freesurfer] mris_preproc error
Hi All, I am getting a consistent error when I try to run mris_preproc - I'm baffled as I've used all of my scripts and fsgd files before. There are 2 groups with 3 covariates but I keep getting this error: mris_preproc --fsgd fsgd/HRR60.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out mris_preproc/lh.HRR60.thickness.10.mgh ERROR: no subjects specified But my fsgd file lists all subject numbers: GroupDescriptorFile 1 Title ACCE HRR60 Class Control Class Cancer Variables Age_demeaned Ed_demeaned HRR60 Input 505_1 Cancer -5.63 1.5 43 Input 506_1 Cancer 7.37 3.5 53 Input 509_1 Cancer 4.37 -0.5 44 Input 517_1 Cancer -20.63 -1.5 38 Input 518_1 Cancer -4.63 -2.5 35 Input 520_1 Cancer 0.37 1.5 37 Input 521_1 Control 3.37 1.5 49 Input 524_1 Cancer 3.37 -0.5 32 Input 525_1 Control -12.63 -2.5 51 #Input 528_1 Cancer 10.37 3.5 Input 529_1 Control -28.63 4.5 32 Input 530_1 Cancer 1.37 1.5 24 Input 531_1 Cancer 6.37 7.5 55 Input 532_1 Cancer -1.63 1.5 14 Input 533_1 Cancer -10.63 3.5 36 Input 534_1 Control -3.63 1.5 25 Input 536_1 Control -11.63 0 47 Input 547_1 Control 10.37 1.5 25 Input 548_1 Control -18.63 -0.5 46 Input 549_1 Cancer -21.63 -0.5 38 Input 554_1 Control -21.63 -0.5 38 Input 558_1 Cancer 9.37 -1.5 24 Input 563_1 Control 0.37 0.5 30 Input 564_1 Control 7.37 1.5 14 Any help is greatly appreciated! Gill _ Gillian Cooke, Ph.D. Postdoctoral Research Associate Lifelong Brain Cognition Lab Decision Neuroscience Lab Beckman Institute University of Illinois, Urbana ___ Freesurfer mailing list 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.
Re: [Freesurfer] Infinite loop in mri_convert
Hi Nooshin if you can upload that dataset we will take a look cheers Bruce On Wed, 5 Nov 2014, Nooshin Zadeh wrote: Dear FreeSurfer experts, I get a new message when I use mri_convert command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I get the new message. In addition, it does not create mgz file, and goes to infinite loop. mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /M1/t1_se_ax_5/IM-0004-0001.dcm... Getting Series No Scanning Directory INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5 INFO: Scanning for Series Number 5INFO: found 37 files in series INFO: loading series header info. I appreciate if you can advise me. Regards, Nooshin PhD Candidate Departments of Electrical Computer Engineering University of Miami Email: n.za...@miami.edu ___ Freesurfer mailing list 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.
Re: [Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview
Hi PPJ I'm not sure it is. Tksurfer has an offscreen rendering option : setenv renderoffscreen 1 used to work, and maybe still does, but I don't think we ever implemented it in tkmedit, and I'm not sure about freeview. Ruopeng can answer that part On Wed, 5 Nov 2014, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm sorry if this has been answered before, I have browsed the mailing and found nothing answering this. I need to generate three views of the T1 data superimposed with Aseg data automatically for Quality Control without using FreeView or Tkmedit (the server generating this has no X11) Is it possible to do it with the command line tools? Thanks - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ Freesurfer mailing list 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.
Re: [Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview
Have you tried installing 'xauth' on the server and connecting via 'ssh -X'? That should show all graphical output on the local machine. On 11/05/2014 05:03 PM, Bruce Fischl wrote: Hi PPJ I'm not sure it is. Tksurfer has an offscreen rendering option : setenv renderoffscreen 1 used to work, and maybe still does, but I don't think we ever implemented it in tkmedit, and I'm not sure about freeview. Ruopeng can answer that part On Wed, 5 Nov 2014, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm sorry if this has been answered before, I have browsed the mailing and found nothing answering this. I need to generate three views of the T1 data superimposed with Aseg data automatically for Quality Control without using FreeView or Tkmedit (the server generating this has no X11) Is it possible to do it with the command line tools? Thanks - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ Freesurfer mailing list 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. ___ Freesurfer mailing list 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.
Re: [Freesurfer] mris_preproc error
Can you run it with --debug as the first argument and send the terminal output? doug On 11/05/2014 04:21 PM, Cooke, Gillian wrote: Hi All, I am getting a consistent error when I try to run mris_preproc - I'm baffled as I've used all of my scripts and fsgd files before. There are 2 groups with 3 covariates but I keep getting this error: mris_preproc --fsgd fsgd/HRR60.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out mris_preproc/lh.HRR60.thickness.10.mgh ERROR: no subjects specified But my fsgd file lists all subject numbers: GroupDescriptorFile 1 Title ACCE HRR60 Class Control Class Cancer VariablesAge_demeanedEd_demeanedHRR60 Input505_1Cancer-5.631.543 Input506_1Cancer7.373.553 Input509_1Cancer4.37-0.544 Input517_1Cancer-20.63-1.538 Input518_1Cancer-4.63-2.535 Input520_1Cancer0.371.537 Input521_1Control3.371.549 Input524_1Cancer3.37-0.532 Input525_1Control-12.63-2.551 #Input528_1Cancer10.373.5 Input529_1Control-28.634.532 Input530_1Cancer1.371.524 Input531_1Cancer6.377.555 Input532_1Cancer-1.631.514 Input533_1Cancer-10.633.536 Input534_1Control-3.631.525 Input536_1Control-11.63047 Input547_1Control10.371.525 Input548_1Control-18.63-0.546 Input549_1Cancer-21.63-0.538 Input554_1Control-21.63-0.538 Input558_1Cancer9.37-1.524 Input563_1Control0.370.530 Input564_1Control7.371.514 Any help is greatly appreciated! Gill _ Gillian Cooke, Ph.D. Postdoctoral Research Associate Lifelong Brain Cognition Lab Decision Neuroscience Lab Beckman Institute University of Illinois, Urbana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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.
Re: [Freesurfer] mris_preproc error
Unfortunately I'm getting this error in the terminal: bash: --debug: command not found From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, November 05, 2014 4:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error Can you run it with --debug as the first argument and send the terminal output? doug On 11/05/2014 04:21 PM, Cooke, Gillian wrote: Hi All, I am getting a consistent error when I try to run mris_preproc - I'm baffled as I've used all of my scripts and fsgd files before. There are 2 groups with 3 covariates but I keep getting this error: mris_preproc --fsgd fsgd/HRR60.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out mris_preproc/lh.HRR60.thickness.10.mgh ERROR: no subjects specified But my fsgd file lists all subject numbers: GroupDescriptorFile 1 Title ACCE HRR60 Class Control Class Cancer VariablesAge_demeanedEd_demeanedHRR60 Input505_1Cancer-5.631.543 Input506_1Cancer7.373.553 Input509_1Cancer4.37-0.544 Input517_1Cancer-20.63-1.538 Input518_1Cancer-4.63-2.535 Input520_1Cancer0.371.537 Input521_1Control3.371.549 Input524_1Cancer3.37-0.532 Input525_1Control-12.63-2.551 #Input528_1Cancer10.373.5 Input529_1Control-28.634.532 Input530_1Cancer1.371.524 Input531_1Cancer6.377.555 Input532_1Cancer-1.631.514 Input533_1Cancer-10.633.536 Input534_1Control-3.631.525 Input536_1Control-11.63047 Input547_1Control10.371.525 Input548_1Control-18.63-0.546 Input549_1Cancer-21.63-0.538 Input554_1Control-21.63-0.538 Input558_1Cancer9.37-1.524 Input563_1Control0.370.530 Input564_1Control7.371.514 Any help is greatly appreciated! Gill _ Gillian Cooke, Ph.D. Postdoctoral Research Associate Lifelong Brain Cognition Lab Decision Neuroscience Lab Beckman Institute University of Illinois, Urbana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_preproc error
run it like this mris_preproc --debug --fsgd fsgd/HRR60.fsgd ... doug On 11/05/2014 05:32 PM, Cooke, Gillian wrote: Unfortunately I'm getting this error in the terminal: bash: --debug: command not found From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, November 05, 2014 4:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error Can you run it with --debug as the first argument and send the terminal output? doug On 11/05/2014 04:21 PM, Cooke, Gillian wrote: Hi All, I am getting a consistent error when I try to run mris_preproc - I'm baffled as I've used all of my scripts and fsgd files before. There are 2 groups with 3 covariates but I keep getting this error: mris_preproc --fsgd fsgd/HRR60.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out mris_preproc/lh.HRR60.thickness.10.mgh ERROR: no subjects specified But my fsgd file lists all subject numbers: GroupDescriptorFile 1 Title ACCE HRR60 Class Control Class Cancer VariablesAge_demeanedEd_demeanedHRR60 Input505_1Cancer-5.631.543 Input506_1Cancer7.373.553 Input509_1Cancer4.37-0.544 Input517_1Cancer-20.63-1.538 Input518_1Cancer-4.63-2.535 Input520_1Cancer0.371.537 Input521_1Control3.371.549 Input524_1Cancer3.37-0.532 Input525_1Control-12.63-2.551 #Input528_1Cancer10.373.5 Input529_1Control-28.634.532 Input530_1Cancer1.371.524 Input531_1Cancer6.377.555 Input532_1Cancer-1.631.514 Input533_1Cancer-10.633.536 Input534_1Control-3.631.525 Input536_1Control-11.63047 Input547_1Control10.371.525 Input548_1Control-18.63-0.546 Input549_1Cancer-21.63-0.538 Input554_1Control-21.63-0.538 Input558_1Cancer9.37-1.524 Input563_1Control0.370.530 Input564_1Control7.371.514 Any help is greatly appreciated! Gill _ Gillian Cooke, Ph.D. Postdoctoral Research Associate Lifelong Brain Cognition Lab Decision Neuroscience Lab Beckman Institute University of Illinois, Urbana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_preproc error
Thanks Doug - this is what it produces:
out mris_preproc/lh.HRR60.thickness.10.mgh
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 10 != 0 )
set flag = $argv[1] ; shift ;
set flag = --fsgd
shift
switch ( $flag )
switch ( --fsgd )
if ( $#argv == 0 ) goto arg1err ;
if ( 9 == 0 ) goto arg1err
set fsgdf = $argv[1] ; shift ;
set fsgdf = fsgd/HRR60.fsgd
shift
if ( ! -e $fsgdf ) then
if ( ! -e fsgd/HRR60.fsgd ) then
set sl = `cat $fsgdf | awk '{if($1 == Input) print $2}'` ;
set sl = `cat $fsgdf | awk '{if($1 == Input) print $2}'`
cat fsgd/HRR60.fsgd
awk {if($1 == Input) print $2}
set subjlist = ( $subjlist $sl ) ;
set subjlist = ( )
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 8 != 0 )
set flag = $argv[1] ; shift ;
set flag = --cache-in
shift
switch ( $flag )
switch ( --cache-in )
if ( $#argv 1 ) goto arg1err ;
if ( 7 1 ) goto arg1err
set meas = $argv[1] ; shift ;
set meas = thickness.fwhm10.fsaverage
shift
set srcsurf = 1 ;
set srcsurf = 1
set CacheIn = 1 ;
set CacheIn = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 6 != 0 )
set flag = $argv[1] ; shift ;
set flag = --target
shift
switch ( $flag )
switch ( --target )
if ( $#argv == 0 ) goto arg1err ;
if ( 5 == 0 ) goto arg1err
set target = $argv[1] ; shift ;
set target = fsaverage
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 4 != 0 )
set flag = $argv[1] ; shift ;
set flag = --hemi
shift
switch ( $flag )
switch ( --hemi )
if ( $#argv == 0 ) goto arg1err ;
if ( 3 == 0 ) goto arg1err
set srchemi = $argv[1] ; shift ;
set srchemi = lh
shift
set trghemi = $srchemi ;
set trghemi = lh
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = --out
shift
switch ( $flag )
switch ( --out )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set outpath = $argv[1] ; shift ;
set outpath = mris_preproc/lh.HRR60.thickness.10.mgh
shift
set outstem = `fname2stem $outpath`
set outstem = `fname2stem $outpath`
fname2stem mris_preproc/lh.HRR60.thickness.10.mgh
if ( $status ) then
if ( 0 ) then
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto handle_fsfast ;
goto handle_fsfast
if ( $#SessFile ) then
if ( 0 ) then
goto handle_fsfast_return ;
goto handle_fsfast_return
goto check_params ;
goto check_params
if ( $#subjlistfile $#ivplist ) then
if ( 0 0 ) then
if ( $#subjlistfile $#fsgdf ) then
if ( 0 1 ) then
if ( $#ivplist $#fsgdf ) then
if ( 0 1 ) then
if ( $#subjlist == 0 ) then
if ( 0 == 0 ) then
echo ERROR: no subjects specified
echo ERROR: no subjects specified
ERROR: no subjects specified
exit 1 ;
exit 1
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 05, 2014 4:41 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
run it like this
mris_preproc --debug --fsgd fsgd/HRR60.fsgd ...
doug
On 11/05/2014 05:32 PM, Cooke, Gillian wrote:
Unfortunately I'm getting this error in the terminal:
bash: --debug: command not found
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 05, 2014 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
Can you run it with --debug as the first argument and send the terminal
output?
doug
On 11/05/2014 04:21 PM, Cooke, Gillian wrote:
Hi All,
I am getting a consistent error when I try to run mris_preproc - I'm
baffled as I've used all of my scripts and fsgd files before.
There are 2 groups with 3 covariates but I keep getting this error:
mris_preproc --fsgd fsgd/HRR60.fsgd --cache-in
thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out
mris_preproc/lh.HRR60.thickness.10.mgh
ERROR: no subjects specified
But my fsgd file lists all subject numbers:
GroupDescriptorFile 1
Title ACCE HRR60
Class Control
Class Cancer
VariablesAge_demeanedEd_demeanedHRR60
Input505_1Cancer-5.631.543
Input506_1Cancer7.373.553
Input509_1Cancer4.37-0.544
Input517_1Cancer-20.63-1.538
Input518_1Cancer-4.63-2.535
Input520_1Cancer0.371.537
Input521_1Control3.371.549
Input524_1Cancer3.37-0.532
Input525_1Control-12.63-2.551
#Input528_1Cancer10.373.5
Input529_1Control-28.634.532
Input530_1Cancer1.371.524
Input531_1Cancer6.377.555
Input532_1Cancer-1.631.514
Input533_1Cancer-10.633.536
Input534_1Control-3.631.525
Input536_1Control-11.63047
Input547_1Control10.371.525
Input548_1Control-18.63-0.546
Input549_1Cancer-21.63-0.538
Input554_1Control-21.63-0.538
Input558_1Cancer9.37-1.524
Input563_1Control0.370.530
Input564_1Control7.371.514
Any help is greatly appreciated!
Re: [Freesurfer] mris_preproc error
Hmm, still not sure what's up. Can you attach your fsgd file to an email?
doug
On 11/05/2014 05:48 PM, Cooke, Gillian wrote:
Thanks Doug - this is what it produces:
out mris_preproc/lh.HRR60.thickness.10.mgh
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 10 != 0 )
set flag = $argv[1] ; shift ;
set flag = --fsgd
shift
switch ( $flag )
switch ( --fsgd )
if ( $#argv == 0 ) goto arg1err ;
if ( 9 == 0 ) goto arg1err
set fsgdf = $argv[1] ; shift ;
set fsgdf = fsgd/HRR60.fsgd
shift
if ( ! -e $fsgdf ) then
if ( ! -e fsgd/HRR60.fsgd ) then
set sl = `cat $fsgdf | awk '{if($1 == Input) print $2}'` ;
set sl = `cat $fsgdf | awk '{if($1 == Input) print $2}'`
cat fsgd/HRR60.fsgd
awk {if($1 == Input) print $2}
set subjlist = ( $subjlist $sl ) ;
set subjlist = ( )
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 8 != 0 )
set flag = $argv[1] ; shift ;
set flag = --cache-in
shift
switch ( $flag )
switch ( --cache-in )
if ( $#argv 1 ) goto arg1err ;
if ( 7 1 ) goto arg1err
set meas = $argv[1] ; shift ;
set meas = thickness.fwhm10.fsaverage
shift
set srcsurf = 1 ;
set srcsurf = 1
set CacheIn = 1 ;
set CacheIn = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 6 != 0 )
set flag = $argv[1] ; shift ;
set flag = --target
shift
switch ( $flag )
switch ( --target )
if ( $#argv == 0 ) goto arg1err ;
if ( 5 == 0 ) goto arg1err
set target = $argv[1] ; shift ;
set target = fsaverage
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 4 != 0 )
set flag = $argv[1] ; shift ;
set flag = --hemi
shift
switch ( $flag )
switch ( --hemi )
if ( $#argv == 0 ) goto arg1err ;
if ( 3 == 0 ) goto arg1err
set srchemi = $argv[1] ; shift ;
set srchemi = lh
shift
set trghemi = $srchemi ;
set trghemi = lh
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = --out
shift
switch ( $flag )
switch ( --out )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set outpath = $argv[1] ; shift ;
set outpath = mris_preproc/lh.HRR60.thickness.10.mgh
shift
set outstem = `fname2stem $outpath`
set outstem = `fname2stem $outpath`
fname2stem mris_preproc/lh.HRR60.thickness.10.mgh
if ( $status ) then
if ( 0 ) then
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto handle_fsfast ;
goto handle_fsfast
if ( $#SessFile ) then
if ( 0 ) then
goto handle_fsfast_return ;
goto handle_fsfast_return
goto check_params ;
goto check_params
if ( $#subjlistfile $#ivplist ) then
if ( 0 0 ) then
if ( $#subjlistfile $#fsgdf ) then
if ( 0 1 ) then
if ( $#ivplist $#fsgdf ) then
if ( 0 1 ) then
if ( $#subjlist == 0 ) then
if ( 0 == 0 ) then
echo ERROR: no subjects specified
echo ERROR: no subjects specified
ERROR: no subjects specified
exit 1 ;
exit 1
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 05, 2014 4:41 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
run it like this
mris_preproc --debug --fsgd fsgd/HRR60.fsgd ...
doug
On 11/05/2014 05:32 PM, Cooke, Gillian wrote:
Unfortunately I'm getting this error in the terminal:
bash: --debug: command not found
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 05, 2014 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
Can you run it with --debug as the first argument and send the terminal
output?
doug
On 11/05/2014 04:21 PM, Cooke, Gillian wrote:
Hi All,
I am getting a consistent error when I try to run mris_preproc - I'm
baffled as I've used all of my scripts and fsgd files before.
There are 2 groups with 3 covariates but I keep getting this error:
mris_preproc --fsgd fsgd/HRR60.fsgd --cache-in
thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out
mris_preproc/lh.HRR60.thickness.10.mgh
ERROR: no subjects specified
But my fsgd file lists all subject numbers:
GroupDescriptorFile 1
Title ACCE HRR60
Class Control
Class Cancer
VariablesAge_demeanedEd_demeanedHRR60
Input505_1Cancer-5.631.543
Input506_1Cancer7.373.553
Input509_1Cancer4.37-0.544
Input517_1Cancer-20.63-1.538
Input518_1Cancer-4.63-2.535
Input520_1Cancer0.371.537
Input521_1Control3.371.549
Input524_1Cancer3.37-0.532
Input525_1Control-12.63-2.551
#Input528_1Cancer10.373.5
Input529_1Control-28.634.532
Input530_1Cancer1.371.524
Input531_1Cancer6.377.555
Input532_1Cancer-1.631.514
Input533_1Cancer-10.633.536
Input534_1Control-3.631.525
Re: [Freesurfer] mris_preproc error
Hi Doug,
The FSGD file is attached.
Best wishes,
Gill
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 05, 2014 5:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
Hmm, still not sure what's up. Can you attach your fsgd file to an email?
doug
On 11/05/2014 05:48 PM, Cooke, Gillian wrote:
Thanks Doug - this is what it produces:
out mris_preproc/lh.HRR60.thickness.10.mgh
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 10 != 0 )
set flag = $argv[1] ; shift ;
set flag = --fsgd
shift
switch ( $flag )
switch ( --fsgd )
if ( $#argv == 0 ) goto arg1err ;
if ( 9 == 0 ) goto arg1err
set fsgdf = $argv[1] ; shift ;
set fsgdf = fsgd/HRR60.fsgd
shift
if ( ! -e $fsgdf ) then
if ( ! -e fsgd/HRR60.fsgd ) then
set sl = `cat $fsgdf | awk '{if($1 == Input) print $2}'` ;
set sl = `cat $fsgdf | awk '{if($1 == Input) print $2}'`
cat fsgd/HRR60.fsgd
awk {if($1 == Input) print $2}
set subjlist = ( $subjlist $sl ) ;
set subjlist = ( )
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 8 != 0 )
set flag = $argv[1] ; shift ;
set flag = --cache-in
shift
switch ( $flag )
switch ( --cache-in )
if ( $#argv 1 ) goto arg1err ;
if ( 7 1 ) goto arg1err
set meas = $argv[1] ; shift ;
set meas = thickness.fwhm10.fsaverage
shift
set srcsurf = 1 ;
set srcsurf = 1
set CacheIn = 1 ;
set CacheIn = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 6 != 0 )
set flag = $argv[1] ; shift ;
set flag = --target
shift
switch ( $flag )
switch ( --target )
if ( $#argv == 0 ) goto arg1err ;
if ( 5 == 0 ) goto arg1err
set target = $argv[1] ; shift ;
set target = fsaverage
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 4 != 0 )
set flag = $argv[1] ; shift ;
set flag = --hemi
shift
switch ( $flag )
switch ( --hemi )
if ( $#argv == 0 ) goto arg1err ;
if ( 3 == 0 ) goto arg1err
set srchemi = $argv[1] ; shift ;
set srchemi = lh
shift
set trghemi = $srchemi ;
set trghemi = lh
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = --out
shift
switch ( $flag )
switch ( --out )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set outpath = $argv[1] ; shift ;
set outpath = mris_preproc/lh.HRR60.thickness.10.mgh
shift
set outstem = `fname2stem $outpath`
set outstem = `fname2stem $outpath`
fname2stem mris_preproc/lh.HRR60.thickness.10.mgh
if ( $status ) then
if ( 0 ) then
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto handle_fsfast ;
goto handle_fsfast
if ( $#SessFile ) then
if ( 0 ) then
goto handle_fsfast_return ;
goto handle_fsfast_return
goto check_params ;
goto check_params
if ( $#subjlistfile $#ivplist ) then
if ( 0 0 ) then
if ( $#subjlistfile $#fsgdf ) then
if ( 0 1 ) then
if ( $#ivplist $#fsgdf ) then
if ( 0 1 ) then
if ( $#subjlist == 0 ) then
if ( 0 == 0 ) then
echo ERROR: no subjects specified
echo ERROR: no subjects specified
ERROR: no subjects specified
exit 1 ;
exit 1
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 05, 2014 4:41 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
run it like this
mris_preproc --debug --fsgd fsgd/HRR60.fsgd ...
doug
On 11/05/2014 05:32 PM, Cooke, Gillian wrote:
Unfortunately I'm getting this error in the terminal:
bash: --debug: command not found
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 05, 2014 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
Can you run it with --debug as the first argument and send the terminal
output?
doug
On 11/05/2014 04:21 PM, Cooke, Gillian wrote:
Hi All,
I am getting a consistent error when I try to run mris_preproc - I'm
baffled as I've used all of my scripts and fsgd files before.
There are 2 groups with 3 covariates but I keep getting this error:
mris_preproc --fsgd fsgd/HRR60.fsgd --cache-in
thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out
mris_preproc/lh.HRR60.thickness.10.mgh
ERROR: no subjects specified
But my fsgd file lists all subject numbers:
GroupDescriptorFile 1
Title ACCE HRR60
Class Control
Class Cancer
VariablesAge_demeanedEd_demeanedHRR60
Input505_1Cancer-5.631.543
Input506_1Cancer7.373.553
Input509_1Cancer4.37-0.544
Re: [Freesurfer] mris_preproc error
The FSGD file is not plain text. Did you make it file on a Windows
computer? Try cut and pasting it into emacs or vi or wordpad
doug
On 11/5/14 8:26 PM, Cooke, Gillian wrote:
Hi Doug,
The FSGD file is attached.
Best wishes,
Gill
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 05, 2014 5:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
Hmm, still not sure what's up. Can you attach your fsgd file to an email?
doug
On 11/05/2014 05:48 PM, Cooke, Gillian wrote:
Thanks Doug - this is what it produces:
out mris_preproc/lh.HRR60.thickness.10.mgh
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 10 != 0 )
set flag = $argv[1] ; shift ;
set flag = --fsgd
shift
switch ( $flag )
switch ( --fsgd )
if ( $#argv == 0 ) goto arg1err ;
if ( 9 == 0 ) goto arg1err
set fsgdf = $argv[1] ; shift ;
set fsgdf = fsgd/HRR60.fsgd
shift
if ( ! -e $fsgdf ) then
if ( ! -e fsgd/HRR60.fsgd ) then
set sl = `cat $fsgdf | awk '{if($1 == Input) print $2}'` ;
set sl = `cat $fsgdf | awk '{if($1 == Input) print $2}'`
cat fsgd/HRR60.fsgd
awk {if($1 == Input) print $2}
set subjlist = ( $subjlist $sl ) ;
set subjlist = ( )
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 8 != 0 )
set flag = $argv[1] ; shift ;
set flag = --cache-in
shift
switch ( $flag )
switch ( --cache-in )
if ( $#argv 1 ) goto arg1err ;
if ( 7 1 ) goto arg1err
set meas = $argv[1] ; shift ;
set meas = thickness.fwhm10.fsaverage
shift
set srcsurf = 1 ;
set srcsurf = 1
set CacheIn = 1 ;
set CacheIn = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 6 != 0 )
set flag = $argv[1] ; shift ;
set flag = --target
shift
switch ( $flag )
switch ( --target )
if ( $#argv == 0 ) goto arg1err ;
if ( 5 == 0 ) goto arg1err
set target = $argv[1] ; shift ;
set target = fsaverage
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 4 != 0 )
set flag = $argv[1] ; shift ;
set flag = --hemi
shift
switch ( $flag )
switch ( --hemi )
if ( $#argv == 0 ) goto arg1err ;
if ( 3 == 0 ) goto arg1err
set srchemi = $argv[1] ; shift ;
set srchemi = lh
shift
set trghemi = $srchemi ;
set trghemi = lh
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = --out
shift
switch ( $flag )
switch ( --out )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set outpath = $argv[1] ; shift ;
set outpath = mris_preproc/lh.HRR60.thickness.10.mgh
shift
set outstem = `fname2stem $outpath`
set outstem = `fname2stem $outpath`
fname2stem mris_preproc/lh.HRR60.thickness.10.mgh
if ( $status ) then
if ( 0 ) then
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto handle_fsfast ;
goto handle_fsfast
if ( $#SessFile ) then
if ( 0 ) then
goto handle_fsfast_return ;
goto handle_fsfast_return
goto check_params ;
goto check_params
if ( $#subjlistfile $#ivplist ) then
if ( 0 0 ) then
if ( $#subjlistfile $#fsgdf ) then
if ( 0 1 ) then
if ( $#ivplist $#fsgdf ) then
if ( 0 1 ) then
if ( $#subjlist == 0 ) then
if ( 0 == 0 ) then
echo ERROR: no subjects specified
echo ERROR: no subjects specified
ERROR: no subjects specified
exit 1 ;
exit 1
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 05, 2014 4:41 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
run it like this
mris_preproc --debug --fsgd fsgd/HRR60.fsgd ...
doug
On 11/05/2014 05:32 PM, Cooke, Gillian wrote:
Unfortunately I'm getting this error in the terminal:
bash: --debug: command not found
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 05, 2014 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
Can you run it with --debug as the first argument and send the terminal
output?
doug
On 11/05/2014 04:21 PM, Cooke, Gillian wrote:
Hi All,
I am getting a consistent error when I try to run mris_preproc - I'm
baffled as I've used all of my scripts and fsgd files before.
There are 2 groups with 3 covariates but I keep getting this error:
mris_preproc --fsgd fsgd/HRR60.fsgd --cache-in
thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out
mris_preproc/lh.HRR60.thickness.10.mgh
ERROR: no subjects specified
But my fsgd file lists all subject numbers:
GroupDescriptorFile 1
Title ACCE HRR60
Class Control
Class Cancer
VariablesAge_demeanedEd_demeanedHRR60
Input505_1Cancer-5.631.543
Input506_1Cancer7.373.553
Input509_1Cancer4.37-0.544
Re: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)
Hello Zeke, I have tried giving permissions to multiple folders (freesurfer, bin, Documents, bert etc.) using this command with no luck. Here is where it keeps dying. Is it possibly an issue with something else other than permissions? #@# Talairach Wed Nov 5 23:58:06 EST 2014 /Users/adick/Documents/013_new/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin dizzy.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 recon-all -s 013_new exited with ERRORS at Wed Nov 5 23:58:13 EST 2014 For more details, see the log file /Users/adick/Documents/013_new/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On 11/5/14, 2:51 PM, Z K wrote: Hello Anthony, The problem isnt with the location of the bert folder but rather with the permissions of the bert folder itself (and the permissions within). To run the bert case please 'cd' into the directory containing the bert folder and type the following: sudo chmod -R a+wr bert -Zeke On 11/05/2014 02:42 PM, Anthony Dick wrote: Hello Martin, I did this (ran it from both the Desktop and Documents). Also tried re-installing Freesurfer. The subjects folder also has permissions: drwx--+ 1632 adick staff54K Nov 5 13:01 Desktop drwx--+ 42 adick staff 1.4K Nov 5 12:48 Documents I also set permissions for freesurfer/bin using the chmod command: chmod -R a+x freesufer/bin/* Not really sure what the issue is, but it seems to be related to the upgrade to Yosemite. Anthony On 11/5/14, 1:39 PM, Martin Reuter wrote: Hi Anthony, wasnt the answer (by Mathew Riddle 10/23) to this to move Bert to a place where you have write permissions (as User). Best, Martin On 11/05/2014 12:56 PM, Anthony Dick wrote: Hello, I am encountering the exact same problem on Yosemite (10.10). The log file is attached. Any ideas? I am pretty stumped. Anthony *From:* freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Matthew Riddle mrid...@nyspi.columbia.edu *Sent:* Thursday, October 23, 2014 7:48 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite) Dear Freesurfer Team, I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I’m still experiencing an issue with freesurfer that I’m hoping you might have some idea about. Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal: sudo –E recon-all –s bert –all The processes crashes in a minute or two at the same place each time, and this is the last bit of output. MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz # #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014 I tried this on an almost identical machine running Mavericks, and got the exact same problem. From my bugr output: FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.0.0 x86_64 The recon-all.log file doesn’t provide any additional information, it just mirrors the output from the terminal. Thanks, -Matt ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web :http://reuter.mit.edu
[Freesurfer] notal-check/pial edits
Dear All, this is very basic. I have Analyze volumes, and I was suggested to use -notal-check to bypass the 3rd recon step. I wanted to make sure skipping the T registration step would not have the potential to mess up the spherical registration in autorecon3 in any way on a case by case basis. I do not want to spend time in tkregister2 unless is necessary for the spherical registration step. Also, I anticipate losts of pial edits (let's exclude the wm edits/cp), and I wanted to make sure different command scenarios are correct: 1. recon-all -autorecon1 -subjid edit pia, save brainmask.mgz recon-all -autorecon2 -autorecon3 -subjid 2. recon-all -autorecon1 -autorecon2 -subjid edit pia, save brainmask.mgz recon-all -autorecon2-pial -autorecon3 -subjid (preferred) 3. recon-all -subjid edit pia, save brainmask.mgz recon-all -autorecon-pial -subjid Please comment, thank you, Octavian ___ Freesurfer mailing list 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.
[Freesurfer] White matter volume
Dear Bruce, My questions is just to learn and to improve my understanding. The commands recon-all and dt-recon are routinely generating the statistics at the end of there running and we can check the results in aseg.stats (the output of recon-all) and fa.stats (the output of dt-recon for FA). In those files we have the white matter volume for many different parts of the brain like the right and left cerebral white matter. If we check the volumes in those files we can see that we have differences between the numbers and I can explain that by the following: in aseg.stats the white matter volume is derived from the T1 segmentation in the structural space and in fa.stats the white matter volume is derived from the FA map in diffusion space and the difference between the volumes is the difference between the accuracy of the images in different spaces. Now: 1. If we want to study the relationship between the FA and the right hemispheric white matter volume for example, we should not care about the volumes in fa.stasts because it is not accurate?! in this case what is the optimal and correct method in freeSurfer to do such like this comparison, is it by moving the FA map to the structural space by registering the FA map to T1 or by using the volumes in aseg.stats and the metrics values from fa.stats? or we can use the fa values and the volumes from fa.stats? 2.What is the exact usage for the volumes mentioned in FA.stats 3. What is the meaning and the exact usage of min-max intensity range (intensity of what) in aseg.stats and fa.stats So Sorry for this long email but as always I am looking forward to learn from you Thanks Mohamad ___ Freesurfer mailing list 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.
[Freesurfer] Different significant regions with different cluster wise thresholds
Dear Freesurfer Mailing list, While running a glm anlaysis with monte carlo correction (using cluster wise thresholds of .05 .01), I encountered the following issue: When examining the clusters formed for each of the different cluster wise thresholds, the .05 threshold resulted in a superior temporal cluster, while the .01 threshold resulted in a two lateral occipital clusters that did not overlap with the cluster from the .05 threshold. Do you know why there would be no overlap between significant regions at different cluster wise thresholds? I was aware that a cluster which is significant at .05 may split or be smaller at .01, but I do not know why entirely different regions would be significant. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list 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.
