[Freesurfer] asegstats2table error message
Hi, I'm getting the following error when trying to use the asegstats2table command, I can't see anything similar from previous emails, any ideas what the issue is? Thanks v much in advance. asegstats2table --subjects baseline 12m 24m 36m --meas volume --tablefile aseg_stats.txt File "/Applications/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' SyntaxError: invalid syntax ___ 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] Basic error
Hi freesurfer team, I think this is a very basic error with the mri_convert command but I can't seem to make it work, I'm getting this: mri_convert $PWD 001.nii mri_convert /Applications/freesurfer/subjects/DEM009/dicom/20140731/1835 001.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/DEM009/dicom/20140731/1835... corRead(): can't open file /Applications/freesurfer/subjects/DEM009/dicom/20140731/1835/COR-.info Any ideas what I'm missing? Thanks, Hugh ___ 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] (no subject)
Hi everyone, I'm getting the follow error and it's jus started happening after updating Xquartz.. any ideas what I can do? Also, i dont have a .debug_tkmedit file, when tkmedit was running normally the first line would say could not create debug file. Many thanks, Hugh ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... ___ 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] (no subject)
i've tried reinstalling xquartz (this is on a mac by the way) and now I'm getting this error when trying to run tkmedit, any ideas would be hugely appreciated! Thanks, Hugh Couldn't create output file .xdebug_tkmeditGLUT: Fatal Error in tkmedit.bin: could not open display: /tmp/launch-ivIjwf/org.macosforge.xquartz:0 On 14 July 2014 09:41, Hugh Pemberton hughpembert...@gmail.com wrote: Hi everyone, I'm getting the follow error and it's jus started happening after updating Xquartz.. any ideas what I can do? Also, i dont have a .debug_tkmedit file, when tkmedit was running normally the first line would say could not create debug file. Many thanks, Hugh ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... ___ 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] (no subject)
Another problem now is that my terminal is not recognising the freesurfer folder.. it's just saying that the directory doesn't exist even though i can see and interact with all the files through the finder.. any ideas what might have happened/how I can check for the problem would be much appreciated. Many thanks, Hugh On 14 July 2014 15:25, Hugh Pemberton hughpembert...@gmail.com wrote: i've tried reinstalling xquartz (this is on a mac by the way) and now I'm getting this error when trying to run tkmedit, any ideas would be hugely appreciated! Thanks, Hugh Couldn't create output file .xdebug_tkmeditGLUT: Fatal Error in tkmedit.bin: could not open display: /tmp/launch-ivIjwf/org.macosforge.xquartz:0 On 14 July 2014 09:41, Hugh Pemberton hughpembert...@gmail.com wrote: Hi everyone, I'm getting the follow error and it's jus started happening after updating Xquartz.. any ideas what I can do? Also, i dont have a .debug_tkmedit file, when tkmedit was running normally the first line would say could not create debug file. Many thanks, Hugh ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... ___ 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] Vol stats of precentral gyrus
Hi everyone, I got in touch last week about asking if someone could comment on which portion of the precentral gyrus is used to produce subcortical volume stats? Is it just medial or lateral the whole gyrus? Just wondering if anyone has any thought on this? Many thanks and all the best, Hugh On 6 June 2014 12:00, Hugh Pemberton hughpembert...@gmail.com wrote: Hi everyone, I was wondering if someone could comment on which portion of the precentral gyrus is used to produce subcortical volume stats? Is it just medial or lateral the whole gyrus? Many thanks and all the best, Hugh On 5 June 2014 12:25, Hugh Pemberton hughpembert...@gmail.com wrote: Hi everyone, I was wondering if someone could comment on which portion of the precentral gyrus is used to produce subcortical volume stats? Is it just medial or lateral the whole gyrus? Many thanks and all the best, Hugh ___ 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] Vol stats of precentral gyrus
Hi everyone, I was wondering if someone could comment on which portion of the precentral gyrus is used to produce subcortical volume stats? Is it just medial or lateral the whole gyrus? Many thanks and all the best, Hugh On 5 June 2014 12:25, Hugh Pemberton hughpembert...@gmail.com wrote: Hi everyone, I was wondering if someone could comment on which portion of the precentral gyrus is used to produce subcortical volume stats? Is it just medial or lateral the whole gyrus? Many thanks and all the best, Hugh ___ 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] Vol stats of precentral gyrus
Hi everyone, I was wondering if someone could comment on which portion of the precentral gyrus is used to produce subcortical volume stats? Is it just medial or lateral the whole gyrus? Many thanks and all the best, Hugh ___ 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] (no subject)
Hi guys, just wondering what you'd say is the best measure for whole brain volume? Cortex volume.. Cortical white matter volume.. Total gray volume.. Intracranial volume.. etc. Cheers! Hugh ___ 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] (no subject)
Hi freesurfer crew, I found some details through this website http://www.stat.uchicago.edu/faculty/InMemoriam/worsley/research/surfstat/index.htm about cortical thickness maps with freesurfer. I have done some reading but can't really make much sense of how I might do this for a single subject through freesurfer. I have already done autorecon 2 and 3 and so have the cortical thickness stats but would like to put it into a map such as this one: [image: [Click to enlarge image]]http://www.stat.uchicago.edu/faculty/InMemoriam/worsley/research/surfstat/figs/FS.jpg Could you possibly advise on how I might go about this? Would be much appreciated. Many thanks and all the best, Hugh ___ 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] (no subject)
hi guys i'm getting a 'Couldn't create output file .xdebug_tkmedit' before loading volumes, any suggestions on what I can do would be most welcome. Also got: ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... : When taking a volume snapshot and then freesurfer shut down but there's no file for me to send you, I've just installed on a mac lion v5.3.0 Cheers! Hugh ___ 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] (no subject)
Hi, did anyone have a chance to see my last e mail? See below, cheers! Hugh On 16 November 2012 10:48, Hugh Pemberton hughpembert...@gmail.com wrote: Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/subjects/B__/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B__ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Many thanks in advance, Best, Hugh ___ 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] (no subject)
that'd great, cheers! Hugh On 5 December 2012 10:29, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Hugh this is fixed in 5.2. If you need a fix right away Nick or Zeke can get you an updated mris_topo_fixer binary cheers Bruce On Wed, 5 Dec 2012, Hugh Pemberton wrote: Hi, did anyone have a chance to see my last e mail? See below, cheers!Hugh On 16 November 2012 10:48, Hugh Pemberton hughpembert...@gmail.com wrote: Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/**subjects/B__/**scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B__ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Many thanks in advance, Best, Hugh 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/**compliancelinehttp://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] (no subject)
Excellent, will look into it. Cheers Nick. On 29 November 2012 04:58, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Hugh, That fix is described in the Known Issues section of 5.1 on the Release Notes page: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes look for the section where you need to edit your recon-all script to comment-out the line where the control point is used by ca_norm. Nick On Tue, 2012-11-27 at 22:53 -0500, Bruce Fischl wrote: Try it with nicks control point-fixed recon-all and see if it works better On Nov 27, 2012, at 10:44 PM, Hugh Pemberton hughpembert...@gmail.com wrote: 5.1.0 On 28 November 2012 13:59, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: What version are you running? On Nov 27, 2012, at 8:51 PM, Hugh Pemberton hughpembert...@gmail.com wrote: Generally about 4 or 5 slices away, no other images unfortunately! Any ideas or is the atrophy just too great? Also meant to ask about another control point based issue I've had - occasionally, if I've added a few to the temporal lobes because only a small amount has been left out and then run autorecon2 and autorecon3 the result is just a load more of the temporal lobe being left out, I've attached another couple of screen shots, in this example there's about 20 slices of left out matter. Cheers, Hugh On 28 November 2012 12:34, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Hugh how far is the closest visible white matter? Do you have any other image types (e.g. a FLAIR)? Bruce On Wed, 28 Nov 2012, Hugh Pemberton wrote: Hi freesurfers, Just want to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples.. Cheers, Hugh On 21 November 2012 11:29, Hugh Pemberton hughpembert...@gmail.com wrote: Hi Bruce, Just to let you know the new mris_topo_fixer worked and there was no error with the recon. I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples.. Cheers, Hugh On 16 November 2012 14:44, Hugh Pemberton hughpembert...@gmail.com wrote: Hi Bruce, I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a few screen shots as examples.. Cheers, Hugh On 16 November 2012 11:14, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: this is a bug in the topology fixer. Maybe Zeke or Nick can post a new version of it? Was it mris_topo_fixer that was runing or mris_fix_topology? On Fri, 16 Nov 2012, Hugh Pemberton wrote
Re: [Freesurfer] (no subject)
5.1.0 On 28 November 2012 13:59, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: What version are you running? On Nov 27, 2012, at 8:51 PM, Hugh Pemberton hughpembert...@gmail.com wrote: Generally about 4 or 5 slices away, no other images unfortunately! Any ideas or is the atrophy just too great? Also meant to ask about another control point based issue I've had - occasionally, if I've added a few to the temporal lobes because only a small amount has been left out and then run autorecon2 and autorecon3 the result is just a load more of the temporal lobe being left out, I've attached another couple of screen shots, in this example there's about 20 slices of left out matter. Cheers, Hugh On 28 November 2012 12:34, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Hugh how far is the closest visible white matter? Do you have any other image types (e.g. a FLAIR)? Bruce On Wed, 28 Nov 2012, Hugh Pemberton wrote: Hi freesurfers, Just want to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples.. Cheers, Hugh On 21 November 2012 11:29, Hugh Pemberton hughpembert...@gmail.com wrote: Hi Bruce, Just to let you know the new mris_topo_fixer worked and there was no error with the recon. I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples.. Cheers, Hugh On 16 November 2012 14:44, Hugh Pemberton hughpembert...@gmail.com wrote: Hi Bruce, I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a few screen shots as examples.. Cheers, Hugh On 16 November 2012 11:14, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: this is a bug in the topology fixer. Maybe Zeke or Nick can post a new version of it? Was it mris_topo_fixer that was runing or mris_fix_topology? On Fri, 16 Nov 2012, Hugh Pemberton wrote: Hi Bruce, Thanks for getting back to me. In terminal window it says freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0 but recon-all -version give me $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ Hugh On 16 November 2012 11:05, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Hugh This is fixed in the newest version. What version are you running? Bruce On Nov 15, 2012, at 6:48 PM, Hugh Pemberton hughpembert...@gmail.com wrote: Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/**subjects/B__/**scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B__ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Many thanks in advance, Best, Hugh __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurferhttps://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/**compliancelinehttp://www.partners.org/complianceline
[Freesurfer] (no subject)
Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/subjects/B__/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B__ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Many thanks in advance, Best, Hugh ___ 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] (no subject)
Hi Bruce, Thanks for getting back to me. In terminal window it says freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 but recon-all -version give me $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ Hugh On 16 November 2012 11:05, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Hugh This is fixed in the newest version. What version are you running? Bruce On Nov 15, 2012, at 6:48 PM, Hugh Pemberton hughpembert...@gmail.com wrote: Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/subjects/B__/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B__ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Many thanks in advance, Best, Hugh ___ 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] (no subject)
Looks like it tried both - mris_fix_topology failed! (euler number != 2) Trying mris_topo_fixer... cp ../surf/lh.orig.nofix ../surf/lh.orig euler # = v-e+f = 2g-2: 144765 - 434289 + 289525 = 1 -- 1 holes F =2V-4: 289525 != 289530-4 (1) 2E=3F:868578 != 868575 (3) total defect index = 4 cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm /home/hughp/freesurfer/subjects/B__/scripts mris_topo_fixer -mgz -warnings -seed 1234 B_ lh On 16 November 2012 11:14, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: this is a bug in the topology fixer. Maybe Zeke or Nick can post a new version of it? Was it mris_topo_fixer that was runing or mris_fix_topology? On Fri, 16 Nov 2012, Hugh Pemberton wrote: Hi Bruce, Thanks for getting back to me. In terminal window it says freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0 but recon-all -version give me $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ Hugh On 16 November 2012 11:05, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Hugh This is fixed in the newest version. What version are you running? Bruce On Nov 15, 2012, at 6:48 PM, Hugh Pemberton hughpembert...@gmail.com wrote: Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/**subjects/B__/**scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B__ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Many thanks in advance, Best, Hugh __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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.
[Freesurfer] hippocampal segmentation
Dear freesurfer crew, I'm having a few issues with segmentation around the hippocampus, I have included a few screenshots of main and aux vol where the hippocampus has been excluded even with the addition of control points. Have you got any tips for rectifying this? It's happened a fair few times with my subjects. Thanks very much in advance and all the best, Hugh ___ 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] (no subject)
Yeah had 4/5 other processes going together, shall I just sort memory and re-do? Thanks for such a speedy response! Hugh On 29 Aug 2012, at 12:35, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Looks like the careg died, probably because you ran out of memory. Was anything else running on the machine? On Aug 28, 2012, at 10:17 PM, Hugh Pemberton hughpembert...@gmail.com wrote: Hi Freesurfers, Have had this error come up after recon-all for a number of subjects and was wondering if you know what the issue is..? I have attached the recon-all.log too FYI. INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ MRISread(/home/hughp/freesurfer/subjects/FAC/surf/lh.qsphere.nofix): could not open file reading input surface /home/hughp/freesurfer/subjects/FAC/surf/lh.qsphere.nofix... No such file or directory mris_fix_topology: could not read input surface /home/hughp/freesurfer/subjects/FAC/surf/lh.qsphere.nofix No such file or directory As the error suggests cannot read lh.qsphere, there is indeed nothing at all in the surf folder. Thanks for all your help, Hugh recon-all.error 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] sulcal depth/cortical folding
HI Doug, I tried the mris_anatomical_stats and may well be doing it wrong but got this as the result: hughp@naoshi-WS:~/freesurfer/subjects$ mris_anatomical_stats -a ABM/surf/lh.sulc -b ABM lh computing statistics for each annotation in ABM/surf/lh.sulc. reading volume /home/hughp/freesurfer/subjects/ABM/mri/wm.mgz... reading input surface /home/hughp/freesurfer/subjects/ABM/surf/lh.white... reading input pial surface /home/hughp/freesurfer/subjects/ABM/surf/lh.pial... reading input white surface /home/hughp/freesurfer/subjects/ABM/surf/lh.white... CTABfindAnnotation: ct was NULL No such file or directory Segmentation fault (core dumped) Not sure how to rectify this, any ideas? Many thanks again, Hugh On 15 August 2012 01:42, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Hugh, you can run mris_anatomical_stats passing it the sulc file as input. This will give you averages within aparc. I'm not sure what you mean by measuring cortical folding. What measure would you accept? There's the sulcal depth and then there's curvature (?h.curv). There are two types of normalization. One is intensity normalization which is a preprocessing step before the segmentation. Normalization is also refers to intersubject registration. Probably you mean the latter. doug On 08/13/2012 09:56 PM, Hugh Pemberton wrote: Hi Doug, Thanks so much for getting back to my original question (have included below) and apologies if my question seems trivial but I'm a bit of a novice with freesurfer.. I've found the ?h.sulc file but how do I go about extracting the sulcal depth measurements? Is there a command like aparcsstats2table? Also, is there a way of measuring cortical folding with freesurfer? And I've read about the noramlization step but am still not completely clear on it, is this part of the segmentation of white/gray surface and pial surface? Thanks so much for your help, Best, Hugh Message: 5 Date: Sun, 12 Aug 2012 22:25:02 -0400 From: Douglas Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject) To: freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.** harvard.edu freesurfer@nmr.mgh.harvard.edu Message-ID: 5028657e.8070...@nmr.mgh.**harvard.edu5028657e.8070...@nmr.mgh.harvard.edumailto: 5028657E.8070908@nmr.**mgh.harvard.edu5028657e.8070...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=iso-8859-1 The values are in the ?h.sulc file doug On 8/12/12 10:12 PM, Hugh Pemberton wrote: Hi, How can I get sulcal depth measurements from Freesurfer? Cheers, Hugh -- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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/**compliancelinehttp://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.
[Freesurfer] (no subject)
Hi, How can I get sulcal depth measurements from Freesurfer? Cheers, Hugh ___ 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] (no subject)
Hi, I have resolved the issue below, apologies, was a stupid question! Thanks, Hugh On 1 August 2012 15:59, Hugh Pemberton hughpembert...@gmail.com wrote: Hi, So when using command tkmedit *subjID* brainmask.mgz -aux -wm.mgz -surfs I receive the message: Error: Parsing -aux option Expected an argument This option needs an argument: the image type, directory, or file name of the data to load as the aux volume. My apologies if there is an obvious answer but I can't see what is wrong (there are wm.mgz files in all subject directories), plus there doesn't seem to be anything missing as a result of this error message. Cheers for your help, Best, Hugh ___ 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] (no subject)
Hi, So when using command tkmedit *subjID* brainmask.mgz -aux -wm.mgz -surfs I receive the message: Error: Parsing -aux option Expected an argument This option needs an argument: the image type, directory, or file name of the data to load as the aux volume. My apologies if there is an obvious answer but I can't see what is wrong (there are wm.mgz files in all subject directories), plus there doesn't seem to be anything missing as a result of this error message. Cheers for your help, Best, Hugh ___ 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.
