Re: [Freesurfer] problems with aparcstats2table
Hi Doug, my command line is aparcstats2table --subjects subject1 subject2 subject3 --hemi rh --meas thickness --tablefile aparc_stats.txt I tried it on single subjects randomly chosen from the complete list and it worksanyway it's still not working on the complete list while it works fine for the left hemisphere (same list of subjects). Sorry for bothering and thanks again for your help, Pietro 2013/8/29 Douglas N Greve gr...@nmr.mgh.harvard.edu What is your command line? Try it on a single subject to see if it fails doug On 08/29/2013 02:00 PM, Pietro De Rossi wrote: Hi Doug, It doesn't seem it is failing on a particular subject...or I am not able to get it from the error. Futhermore, nothing changes if I use the --skip flag. What does it mean when it says: List index out of range? Inviato da iPhone Il giorno 29/ago/2013, alle ore 19:38, Douglas N Greve gr...@nmr.mgh.harvard.edu ha scritto: Is it failing on one particular subject? On 08/29/2013 09:38 AM, pietro de rossi wrote: Dear FreeSurfers, I am extracting thickness values through the aparcstats2table command line. Everything works just fine for --hemi lh using the --skip flag. However, when it comes to the right hemisphere I get SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File /usr/local/freesurfer/bin/**aparcstats2table, line 321, in module parc_measure_map = parsed.parse(options.meas) File /usr/local/freesurfer/bin/**fsutils.py, line 194, in parse parcid = strlist[0] IndexError: list index out of range I find it weird given that I am extracting thickness values for the same subjects. Can anybody help me find out what the problem is? Thank you in advance, Pietro -- Pietro De Rossi, MD --**--- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA __**_ 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 -- 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: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ 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/**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. -- 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: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di
Re: [Freesurfer] problems with aparcstats2table
it seems that it is failing on a particular subjectwhen I exclude this subject from the list then the command works and when I try to give the command on that particular subject I get the error: SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File /usr/local/freesurfer/bin/aparcstats2table, line 321, in module parc_measure_map = parsed.parse(options.meas) File /usr/local/freesurfer/bin/fsutils.py, line 194, in parse parcid = strlist[0] IndexError: list index out of range I visually inspected the subject...there are some processing defects (i.e. the superior temporal girus is not well segmented despite editing). Could that be the problem? Thanks 2013/9/2 pietro de rossi deross...@gmail.com Hi Doug, my command line is aparcstats2table --subjects subject1 subject2 subject3 --hemi rh --meas thickness --tablefile aparc_stats.txt I tried it on single subjects randomly chosen from the complete list and it worksanyway it's still not working on the complete list while it works fine for the left hemisphere (same list of subjects). Sorry for bothering and thanks again for your help, Pietro 2013/8/29 Douglas N Greve gr...@nmr.mgh.harvard.edu What is your command line? Try it on a single subject to see if it fails doug On 08/29/2013 02:00 PM, Pietro De Rossi wrote: Hi Doug, It doesn't seem it is failing on a particular subject...or I am not able to get it from the error. Futhermore, nothing changes if I use the --skip flag. What does it mean when it says: List index out of range? Inviato da iPhone Il giorno 29/ago/2013, alle ore 19:38, Douglas N Greve gr...@nmr.mgh.harvard.edu ha scritto: Is it failing on one particular subject? On 08/29/2013 09:38 AM, pietro de rossi wrote: Dear FreeSurfers, I am extracting thickness values through the aparcstats2table command line. Everything works just fine for --hemi lh using the --skip flag. However, when it comes to the right hemisphere I get SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File /usr/local/freesurfer/bin/**aparcstats2table, line 321, in module parc_measure_map = parsed.parse(options.meas) File /usr/local/freesurfer/bin/**fsutils.py, line 194, in parse parcid = strlist[0] IndexError: list index out of range I find it weird given that I am extracting thickness values for the same subjects. Can anybody help me find out what the problem is? Thank you in advance, Pietro -- Pietro De Rossi, MD --**--- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA __**_ 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 -- 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: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ 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/**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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs:
Re: [Freesurfer] mri_surf2surf to fsaverageX introduces offset
Dear Doug, thank you so much, the fix works great. The problem now is that when I mris_convert the newly generated surface to .gii the volume geometry is lost again and the offset reintroduced. Is there a way to fix this? I have tried to give mri_surf2surf a register.dat that would correct for the c_ras offset, but that did not work. Thanks, Franz Am 30.08.2013 um 17:41 schrieb Douglas N Greve: Sorry, I'm answering your emails in reverse order. Your command should do what youwant once you use the new version below ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf.snowleopard note the --tval-xyz requires an argument (give it the orig.mgz) doug On 08/30/2013 03:51 AM, Franz Liem wrote: Hi Doug, thanks a lot. I am using Darwin-snowleopard and centos6_x86_64. What I am trying to do is to use the white surface as seed for probtrackx. Therefore, I would like to reduce the number of vertices and at the same time bring the surfaces into a common space (so that vertex x is meaning the same thing in all subjects, while respecting the individual coordinates). I think my command did this but did not take the c_ras offset into account. Is there a better way to do this. Thank you very much, Franz Am 29.08.2013 um 20:54 schrieb Douglas N Greve: Hi Franz, I just programmed a fix into mri_surf2surf. What platform do you use? As for the shift, you would not expect them to line up. In fact, that command line does not make a lot of sense. What it is doing is mapping the xyz coordinates in the native space to a new tesselation. The xyz coorindates don't change at all. It is surprising that they are as close as they are. What are you trying to do? doug On 08/29/2013 07:41 AM, Franz Liem wrote: Dear Freesurfers, sorry for the bump, but my message seems to have gone unnoticed. Thanks so much for any ideas. Franz Am 22.08.2013 um 13:37 schrieb Franz Liem: Dear Freesurfers, I tried to map a single subject surface to fsaverageX (for the sake of demonstration lets take fsaverage6). I did the following: mri_surf2surf --hemi lh --srcsubject $s --sval-xyz white --trgsubject fsaverage6 --tval-xyz --tval ./lh.white.ico6 This produces a surface that seems systematically shifted (see figure). Also the newly generated surface does not contain valid geomery information (see mris_info print of lh.white and lh.white.ico6). Is there a way to fix this? Another question: is there a reason why mris_decimate is not included in the freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 build Any help is very much appreciated. Best, Franz mris_info $s/surf/lh.white SURFACE INFO type: MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 118611 num faces : 237218 num strips : 0 surface area: 77595.6 AvgVtxArea 0.654202 AvgVtxDist 0.885026 StdVtxDist 0.251941 ctr : (-33.3535, -11.9536, 42.7693) vertex locs : surfaceRAS talairch.xfm: 1.045 -0.093 -0.014 1.081; 0.099 1.095 0.070 -4.263; 0.010 -0.083 1.290 -41.092; 0.000 0.000 0.000 1.000; surfaceRAS to talaraiched surfaceRAS: 1.045 -0.093 -0.014 1.177; 0.099 1.095 0.070 13.377; 0.010 -0.083 1.290 -49.756; 0.000 0.000 0.000 1.000; talairached surfaceRAS to surfaceRAS: 0.949 0.081 0.006 -1.900; -0.085 0.902 -0.050 -14.449; -0.013 0.058 0.772 37.650; 0.000 0.000 0.000 1.000; volume geometry: extent : (256, 256, 256) voxel : ( 1., 1., 1.) x_(ras) : (-1., -0., 0.) y_(ras) : (-0., 0., -1.) z_(ras) : ( 0., 1., -0.) c_(ras) : ( 0.0989, 0.9660, 0.9027) ... mris_info lh.white.ico6 SURFACE INFO type: MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 40962 num faces : 81920 num strips : 0 surface area: 75477.4 AvgVtxArea 1.842620 AvgVtxDist 1.573724 StdVtxDist 0.523314 ctr : (-33.3983, -12.0872, 42.7743) vertex locs : surfaceRAS volume geometry info is either not contained or not valid. ... surfPics.png___ 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
[Freesurfer] apply fnirt transformation on a surface
Dear freesurfer people, Any idea whether I can apply transformation that was calculated by fsl fnirt on the white/pial surfaces calculated using the freesurfer stream? Thanks! Shani ___ 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] Tracula error - unknown queue long.q, short.q
Dear Anastasia and FreeSurfers, I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc: INFO: SUBJECTS_DIR is /data-02/joana/Last INFO: Diffusion root is /data-02/joana/tracula/ Actual FREESURFER_HOME /usr/local/freesurfer-5.3 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri subjectdir is /data-02/joana/tracula/XXX/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue short.q. Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue long.q. Exiting. Queuing post processing stage Unable to run job: denied: 60 is not a valid object name (cannot start with a digit) Job was rejected because job requests unknown queue long.q. Exiting. Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress. Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the queued tasks. You will get an email at the end of the post-processing stage. So far no slices have been processed. Does anyone know how to solve it? Thanks! ___ 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] problems with aparcstats2table
Hi Pietro, that would not be the problem, at least not directly. The problem is with the stats file itself. Compare the file to others to see if it looks different. Is the disk full? doug On 9/2/13 4:38 AM, pietro de rossi wrote: it seems that it is failing on a particular subjectwhen I exclude this subject from the list then the command works and when I try to give the command on that particular subject I get the error: SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File /usr/local/freesurfer/bin/aparcstats2table, line 321, in module parc_measure_map = parsed.parse(options.meas) File /usr/local/freesurfer/bin/fsutils.py, line 194, in parse parcid = strlist[0] IndexError: list index out of range I visually inspected the subject...there are some processing defects (i.e. the superior temporal girus is not well segmented despite editing). Could that be the problem? Thanks 2013/9/2 pietro de rossi deross...@gmail.com mailto:deross...@gmail.com Hi Doug, my command line is aparcstats2table --subjects subject1 subject2 subject3 --hemi rh --meas thickness --tablefile aparc_stats.txt I tried it on single subjects randomly chosen from the complete list and it worksanyway it's still not working on the complete list while it works fine for the left hemisphere (same list of subjects). Sorry for bothering and thanks again for your help, Pietro 2013/8/29 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu What is your command line? Try it on a single subject to see if it fails doug On 08/29/2013 02:00 PM, Pietro De Rossi wrote: Hi Doug, It doesn't seem it is failing on a particular subject...or I am not able to get it from the error. Futhermore, nothing changes if I use the --skip flag. What does it mean when it says: List index out of range? Inviato da iPhone Il giorno 29/ago/2013, alle ore 19:38, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu ha scritto: Is it failing on one particular subject? On 08/29/2013 09:38 AM, pietro de rossi wrote: Dear FreeSurfers, I am extracting thickness values through the aparcstats2table command line. Everything works just fine for --hemi lh using the --skip flag. However, when it comes to the right hemisphere I get SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File /usr/local/freesurfer/bin/aparcstats2table, line 321, in module parc_measure_map = parsed.parse(options.meas) File /usr/local/freesurfer/bin/fsutils.py, line 194, in parse parcid = strlist[0] IndexError: list index out of range I find it weird given that I am extracting thickness values for the same subjects. Can anybody help me find out what the problem is? Thank you in advance, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D.
Re: [Freesurfer] mri_surf2surf to fsaverageX introduces offset
What if you specify the output of surf2surf to be a gii file? On 9/2/13 6:47 AM, Franz Liem wrote: Dear Doug, thank you so much, the fix works great. The problem now is that when I mris_convert the newly generated surface to .gii the volume geometry is lost again and the offset reintroduced. Is there a way to fix this? I have tried to give mri_surf2surf a register.dat that would correct for the c_ras offset, but that did not work. Thanks, Franz Am 30.08.2013 um 17:41 schrieb Douglas N Greve: Sorry, I'm answering your emails in reverse order. Your command should do what youwant once you use the new version below ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf.snowleopard note the --tval-xyz requires an argument (give it the orig.mgz) doug On 08/30/2013 03:51 AM, Franz Liem wrote: Hi Doug, thanks a lot. I am using Darwin-snowleopard and centos6_x86_64. What I am trying to do is to use the white surface as seed for probtrackx. Therefore, I would like to reduce the number of vertices and at the same time bring the surfaces into a common space (so that vertex x is meaning the same thing in all subjects, while respecting the individual coordinates). I think my command did this but did not take the c_ras offset into account. Is there a better way to do this. Thank you very much, Franz Am 29.08.2013 um 20:54 schrieb Douglas N Greve: Hi Franz, I just programmed a fix into mri_surf2surf. What platform do you use? As for the shift, you would not expect them to line up. In fact, that command line does not make a lot of sense. What it is doing is mapping the xyz coordinates in the native space to a new tesselation. The xyz coorindates don't change at all. It is surprising that they are as close as they are. What are you trying to do? doug On 08/29/2013 07:41 AM, Franz Liem wrote: Dear Freesurfers, sorry for the bump, but my message seems to have gone unnoticed. Thanks so much for any ideas. Franz Am 22.08.2013 um 13:37 schrieb Franz Liem: Dear Freesurfers, I tried to map a single subject surface to fsaverageX (for the sake of demonstration lets take fsaverage6). I did the following: mri_surf2surf --hemi lh --srcsubject $s --sval-xyz white --trgsubject fsaverage6 --tval-xyz --tval ./lh.white.ico6 This produces a surface that seems systematically shifted (see figure). Also the newly generated surface does not contain valid geomery information (see mris_info print of lh.white and lh.white.ico6). Is there a way to fix this? Another question: is there a reason why mris_decimate is not included in the freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 build Any help is very much appreciated. Best, Franz mris_info $s/surf/lh.white SURFACE INFO type: MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 118611 num faces : 237218 num strips : 0 surface area: 77595.6 AvgVtxArea 0.654202 AvgVtxDist 0.885026 StdVtxDist 0.251941 ctr : (-33.3535, -11.9536, 42.7693) vertex locs : surfaceRAS talairch.xfm: 1.045 -0.093 -0.014 1.081; 0.099 1.095 0.070 -4.263; 0.010 -0.083 1.290 -41.092; 0.000 0.000 0.000 1.000; surfaceRAS to talaraiched surfaceRAS: 1.045 -0.093 -0.014 1.177; 0.099 1.095 0.070 13.377; 0.010 -0.083 1.290 -49.756; 0.000 0.000 0.000 1.000; talairached surfaceRAS to surfaceRAS: 0.949 0.081 0.006 -1.900; -0.085 0.902 -0.050 -14.449; -0.013 0.058 0.772 37.650; 0.000 0.000 0.000 1.000; volume geometry: extent : (256, 256, 256) voxel : ( 1., 1., 1.) x_(ras) : (-1., -0., 0.) y_(ras) : (-0., 0., -1.) z_(ras) : ( 0., 1., -0.) c_(ras) : ( 0.0989, 0.9660, 0.9027) ... mris_info lh.white.ico6 SURFACE INFO type: MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 40962 num faces : 81920 num strips : 0 surface area: 75477.4 AvgVtxArea 1.842620 AvgVtxDist 1.573724 StdVtxDist 0.523314 ctr : (-33.3983, -12.0872, 42.7743) vertex locs : surfaceRAS volume geometry info is either not contained or not valid. ... surfPics.png___ 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
Re: [Freesurfer] apply fnirt transformation on a surface
Hi Shani, I don't think you can apply a FNIRT transform to a surface. doug On 9/2/13 8:20 AM, Shani Ben Amitay wrote: Dear freesurfer people, Any idea whether I can apply transformation that was calculated by fsl fnirt on the white/pial surfaces calculated using the freesurfer stream? Thanks! Shani ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] apply fnirt transformation on a surface
you might check on the FSL list. I think I've seen some traffic indicating that there are some tools for doing this. I'l cc Saad as he might know cheers Bruce On Mon, 2 Sep 2013, Douglas Greve wrote: Hi Shani, I don't think you can apply a FNIRT transform to a surface. doug On 9/2/13 8:20 AM, Shani Ben Amitay wrote: Dear freesurfer people, Any idea whether I can apply transformation that was calculated by fsl fnirt on the white/pial surfaces calculated using the freesurfer stream? Thanks! Shani ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] tkmedit font size on scalebar
Dear FreeSurfer experts, how can I increase the font size on the tkmedit scale bar? Cheers Joerg ___ 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] apply fnirt transformation on a surface
A veritable game of telephone! Thanks Jesper. Matt? On Mon, 2 Sep 2013, Jesper Andersson wrote: Hi guys, I didn't think we had any tools for doing that, and said so much on the FSL mailbase. But apparently the WashU people has something that does just that for you. I think the best person to contact about the details is Matt Glasser. J On 2 Sep 2013, at 15:58, Saad Jbabdi s...@fmrib.ox.ac.uk wrote: Hi In Probtrackx, this is done internally. If you just want to transform the vertex coordinates, then I think you'll need to play with the FNIRT source code - I've CC'd Jesper who knows better. Cheers, Saad On 2 Sep 2013, at 15:56, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: you might check on the FSL list. I think I've seen some traffic indicating that there are some tools for doing this. I'l cc Saad as he might know cheers Bruce On Mon, 2 Sep 2013, Douglas Greve wrote: Hi Shani, I don't think you can apply a FNIRT transform to a surface. doug On 9/2/13 8:20 AM, Shani Ben Amitay wrote: Dear freesurfer people, Any idea whether I can apply transformation that was calculated by fsl fnirt on the white/pial surfaces calculated using the freesurfer stream? Thanks! Shani ___ 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. -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi ___ 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] tkmedit font size on scalebar
Hi Joerg sorry, there doesn't seem to be any way to do this other than recompiling the code. I could build you a version with a specific font if that would help, assuming glut supports it cheers Bruce On Mon, 2 Sep 2013, Jörg Pfannmöller wrote: Dear FreeSurfer experts, how can I increase the font size on the tkmedit scale bar? Cheers Joerg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] FW: apply fnirt transformation on a surface
On 9/2/13 12:02 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: Hi Bruce, Connectome Workbench commandline utilities can do this with FSL warp fields: wb_command -surface-apply-warpfield One needs to use the inverse warp as the warpfield argument and the forward warp as the -fnirt forward-warp. Peace, Matt. On 9/2/13 11:19 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: A veritable game of telephone! Thanks Jesper. Matt? On Mon, 2 Sep 2013, Jesper Andersson wrote: Hi guys, I didn't think we had any tools for doing that, and said so much on the FSL mailbase. But apparently the WashU people has something that does just that for you. I think the best person to contact about the details is Matt Glasser. J On 2 Sep 2013, at 15:58, Saad Jbabdi s...@fmrib.ox.ac.uk wrote: Hi In Probtrackx, this is done internally. If you just want to transform the vertex coordinates, then I think you'll need to play with the FNIRT source code - I've CC'd Jesper who knows better. Cheers, Saad On 2 Sep 2013, at 15:56, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: you might check on the FSL list. I think I've seen some traffic indicating that there are some tools for doing this. I'l cc Saad as he might know cheers Bruce On Mon, 2 Sep 2013, Douglas Greve wrote: Hi Shani, I don't think you can apply a FNIRT transform to a surface. doug On 9/2/13 8:20 AM, Shani Ben Amitay wrote: Dear freesurfer people, Any idea whether I can apply transformation that was calculated by fsl fnirt on the white/pial surfaces calculated using the freesurfer stream? Thanks! Shani ___ 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. -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_surf2surf to fsaverageX introduces offset
Hi Doug, this gives exactly the same surface as surf2surf followed by mris_convert (i.e. with offset). Thanks, Franz Am 02.09.2013 um 16:50 schrieb Douglas Greve: What if you specify the output of surf2surf to be a gii file? On 9/2/13 6:47 AM, Franz Liem wrote: Dear Doug, thank you so much, the fix works great. The problem now is that when I mris_convert the newly generated surface to .gii the volume geometry is lost again and the offset reintroduced. Is there a way to fix this? I have tried to give mri_surf2surf a register.dat that would correct for the c_ras offset, but that did not work. Thanks, Franz Am 30.08.2013 um 17:41 schrieb Douglas N Greve: Sorry, I'm answering your emails in reverse order. Your command should do what youwant once you use the new version below ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf.snowleopard note the --tval-xyz requires an argument (give it the orig.mgz) doug On 08/30/2013 03:51 AM, Franz Liem wrote: Hi Doug, thanks a lot. I am using Darwin-snowleopard and centos6_x86_64. What I am trying to do is to use the white surface as seed for probtrackx. Therefore, I would like to reduce the number of vertices and at the same time bring the surfaces into a common space (so that vertex x is meaning the same thing in all subjects, while respecting the individual coordinates). I think my command did this but did not take the c_ras offset into account. Is there a better way to do this. Thank you very much, Franz Am 29.08.2013 um 20:54 schrieb Douglas N Greve: Hi Franz, I just programmed a fix into mri_surf2surf. What platform do you use? As for the shift, you would not expect them to line up. In fact, that command line does not make a lot of sense. What it is doing is mapping the xyz coordinates in the native space to a new tesselation. The xyz coorindates don't change at all. It is surprising that they are as close as they are. What are you trying to do? doug On 08/29/2013 07:41 AM, Franz Liem wrote: Dear Freesurfers, sorry for the bump, but my message seems to have gone unnoticed. Thanks so much for any ideas. Franz Am 22.08.2013 um 13:37 schrieb Franz Liem: Dear Freesurfers, I tried to map a single subject surface to fsaverageX (for the sake of demonstration lets take fsaverage6). I did the following: mri_surf2surf --hemi lh --srcsubject $s --sval-xyz white --trgsubject fsaverage6 --tval-xyz --tval ./lh.white.ico6 This produces a surface that seems systematically shifted (see figure). Also the newly generated surface does not contain valid geomery information (see mris_info print of lh.white and lh.white.ico6). Is there a way to fix this? Another question: is there a reason why mris_decimate is not included in the freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 build Any help is very much appreciated. Best, Franz mris_info $s/surf/lh.white SURFACE INFO type: MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 118611 num faces : 237218 num strips : 0 surface area: 77595.6 AvgVtxArea 0.654202 AvgVtxDist 0.885026 StdVtxDist 0.251941 ctr : (-33.3535, -11.9536, 42.7693) vertex locs : surfaceRAS talairch.xfm: 1.045 -0.093 -0.014 1.081; 0.099 1.095 0.070 -4.263; 0.010 -0.083 1.290 -41.092; 0.000 0.000 0.000 1.000; surfaceRAS to talaraiched surfaceRAS: 1.045 -0.093 -0.014 1.177; 0.099 1.095 0.070 13.377; 0.010 -0.083 1.290 -49.756; 0.000 0.000 0.000 1.000; talairached surfaceRAS to surfaceRAS: 0.949 0.081 0.006 -1.900; -0.085 0.902 -0.050 -14.449; -0.013 0.058 0.772 37.650; 0.000 0.000 0.000 1.000; volume geometry: extent : (256, 256, 256) voxel : ( 1., 1., 1.) x_(ras) : (-1., -0., 0.) y_(ras) : (-0., 0., -1.) z_(ras) : ( 0., 1., -0.) c_(ras) : ( 0.0989, 0.9660, 0.9027) ... mris_info lh.white.ico6 SURFACE INFO type: MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 40962 num faces : 81920 num strips : 0 surface area: 75477.4 AvgVtxArea 1.842620 AvgVtxDist 1.573724 StdVtxDist 0.523314 ctr : (-33.3983, -12.0872, 42.7743) vertex locs : surfaceRAS volume geometry info is either not contained or not valid. ... surfPics.png___ 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
Re: [Freesurfer] apply fnirt transformation on a surface
thanks Matt Bruce On Mon, 2 Sep 2013, Glasser, Matthew wrote: Hi Bruce, Connectome Workbench commandline utilities can do this with FSL warp fields: wb_command -surface-apply-warpfield One needs to use the inverse warp as the warpfield argument and the forward warp as the -fnirt forward-warp. Peace, Matt. On 9/2/13 11:19 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: A veritable game of telephone! Thanks Jesper. Matt? On Mon, 2 Sep 2013, Jesper Andersson wrote: Hi guys, I didn't think we had any tools for doing that, and said so much on the FSL mailbase. But apparently the WashU people has something that does just that for you. I think the best person to contact about the details is Matt Glasser. J On 2 Sep 2013, at 15:58, Saad Jbabdi s...@fmrib.ox.ac.uk wrote: Hi In Probtrackx, this is done internally. If you just want to transform the vertex coordinates, then I think you'll need to play with the FNIRT source code - I've CC'd Jesper who knows better. Cheers, Saad On 2 Sep 2013, at 15:56, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: you might check on the FSL list. I think I've seen some traffic indicating that there are some tools for doing this. I'l cc Saad as he might know cheers Bruce On Mon, 2 Sep 2013, Douglas Greve wrote: Hi Shani, I don't think you can apply a FNIRT transform to a surface. doug On 9/2/13 8:20 AM, Shani Ben Amitay wrote: Dear freesurfer people, Any idea whether I can apply transformation that was calculated by fsl fnirt on the white/pial surfaces calculated using the freesurfer stream? Thanks! Shani ___ 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. -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tracula error - unknown queue long.q, short.q
Hi Joana - What system are you running this on? a.y On Mon, 2 Sep 2013, Joana Braga Pereira wrote: Dear Anastasia and FreeSurfers, I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc: INFO: SUBJECTS_DIR is /data-02/joana/Last INFO: Diffusion root is /data-02/joana/tracula/ Actual FREESURFER_HOME /usr/local/freesurfer-5.3 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri subjectdir is /data-02/joana/tracula/XXX/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue short.q. Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue long.q. Exiting. Queuing post processing stage Unable to run job: denied: 60 is not a valid object name (cannot start with a digit) Job was rejected because job requests unknown queue long.q. Exiting. Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress. Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the queued tasks. You will get an email at the end of the post-processing stage. So far no slices have been processed. Does anyone know how to solve it? Thanks! ___ 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] Tracula error - unknown queue long.q, short.q
This is an FSL problem. You can try the FSL list, and check out some links: https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira [jbragapere...@gmail.com] Sent: Monday, September 02, 2013 9:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula error - unknown queue long.q, short.q Dear Anastasia and FreeSurfers, I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc: INFO: SUBJECTS_DIR is /data-02/joana/Last INFO: Diffusion root is /data-02/joana/tracula/ Actual FREESURFER_HOME /usr/local/freesurfer-5.3 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri subjectdir is /data-02/joana/tracula/XXX/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue short.q. Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue long.q. Exiting. Queuing post processing stage Unable to run job: denied: 60 is not a valid object name (cannot start with a digit) Job was rejected because job requests unknown queue long.q. Exiting. Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress. Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the queued tasks. You will get an email at the end of the post-processing stage. So far no slices have been processed. Does anyone know how to solve it? Thanks! ___ 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] mri_surf2surf to fsaverageX introduces offset
This info is probably not stored in the gii header. I'll have to take a look which could take a while. Depending on what you are doing, it might not be important. doug On 9/2/13 2:58 PM, Franz Liem wrote: Hi Doug, this gives exactly the same surface as surf2surf followed by mris_convert (i.e. with offset). Thanks, Franz Am 02.09.2013 um 16:50 schrieb Douglas Greve: What if you specify the output of surf2surf to be a gii file? On 9/2/13 6:47 AM, Franz Liem wrote: Dear Doug, thank you so much, the fix works great. The problem now is that when I mris_convert the newly generated surface to .gii the volume geometry is lost again and the offset reintroduced. Is there a way to fix this? I have tried to give mri_surf2surf a register.dat that would correct for the c_ras offset, but that did not work. Thanks, Franz Am 30.08.2013 um 17:41 schrieb Douglas N Greve: Sorry, I'm answering your emails in reverse order. Your command should do what youwant once you use the new version below ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf.snowleopard note the --tval-xyz requires an argument (give it the orig.mgz) doug On 08/30/2013 03:51 AM, Franz Liem wrote: Hi Doug, thanks a lot. I am using Darwin-snowleopard and centos6_x86_64. What I am trying to do is to use the white surface as seed for probtrackx. Therefore, I would like to reduce the number of vertices and at the same time bring the surfaces into a common space (so that vertex x is meaning the same thing in all subjects, while respecting the individual coordinates). I think my command did this but did not take the c_ras offset into account. Is there a better way to do this. Thank you very much, Franz Am 29.08.2013 um 20:54 schrieb Douglas N Greve: Hi Franz, I just programmed a fix into mri_surf2surf. What platform do you use? As for the shift, you would not expect them to line up. In fact, that command line does not make a lot of sense. What it is doing is mapping the xyz coordinates in the native space to a new tesselation. The xyz coorindates don't change at all. It is surprising that they are as close as they are. What are you trying to do? doug On 08/29/2013 07:41 AM, Franz Liem wrote: Dear Freesurfers, sorry for the bump, but my message seems to have gone unnoticed. Thanks so much for any ideas. Franz Am 22.08.2013 um 13:37 schrieb Franz Liem: Dear Freesurfers, I tried to map a single subject surface to fsaverageX (for the sake of demonstration lets take fsaverage6). I did the following: mri_surf2surf --hemi lh --srcsubject $s --sval-xyz white --trgsubject fsaverage6 --tval-xyz --tval ./lh.white.ico6 This produces a surface that seems systematically shifted (see figure). Also the newly generated surface does not contain valid geomery information (see mris_info print of lh.white and lh.white.ico6). Is there a way to fix this? Another question: is there a reason why mris_decimate is not included in the freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 build Any help is very much appreciated. Best, Franz mris_info $s/surf/lh.white SURFACE INFO type: MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 118611 num faces : 237218 num strips : 0 surface area: 77595.6 AvgVtxArea 0.654202 AvgVtxDist 0.885026 StdVtxDist 0.251941 ctr : (-33.3535, -11.9536, 42.7693) vertex locs : surfaceRAS talairch.xfm: 1.045 -0.093 -0.014 1.081; 0.099 1.095 0.070 -4.263; 0.010 -0.083 1.290 -41.092; 0.000 0.000 0.000 1.000; surfaceRAS to talaraiched surfaceRAS: 1.045 -0.093 -0.014 1.177; 0.099 1.095 0.070 13.377; 0.010 -0.083 1.290 -49.756; 0.000 0.000 0.000 1.000; talairached surfaceRAS to surfaceRAS: 0.949 0.081 0.006 -1.900; -0.085 0.902 -0.050 -14.449; -0.013 0.058 0.772 37.650; 0.000 0.000 0.000 1.000; volume geometry: extent : (256, 256, 256) voxel : ( 1., 1., 1.) x_(ras) : (-1., -0., 0.) y_(ras) : (-0., 0., -1.) z_(ras) : ( 0., 1., -0.) c_(ras) : ( 0.0989, 0.9660, 0.9027) ... mris_info lh.white.ico6 SURFACE INFO type: MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 40962 num faces : 81920 num strips : 0 surface area: 75477.4 AvgVtxArea 1.842620 AvgVtxDist 1.573724 StdVtxDist 0.523314 ctr : (-33.3983, -12.0872, 42.7743) vertex locs : surfaceRAS volume geometry info is either not contained or not valid. ... surfPics.png___ 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
Re: [Freesurfer] Tracula error - unknown queue long.q, short.q
Thanks for the pointers, Chris. I'd call it an opportunity for FSL customization rather than an FSL problem per se :o) On Mon, 2 Sep 2013, Watson, Christopher wrote: This is an FSL problem. You can try the FSL list, and check out some links: https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira [jbragapere...@gmail.com] Sent: Monday, September 02, 2013 9:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula error - unknown queue long.q, short.q Dear Anastasia and FreeSurfers, I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc: INFO: SUBJECTS_DIR is /data-02/joana/Last INFO: Diffusion root is /data-02/joana/tracula/ Actual FREESURFER_HOME /usr/local/freesurfer-5.3 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri subjectdir is /data-02/joana/tracula/XXX/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue short.q. Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue long.q. Exiting. Queuing post processing stage Unable to run job: denied: 60 is not a valid object name (cannot start with a digit) Job was rejected because job requests unknown queue long.q. Exiting. Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress. Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the queued tasks. You will get an email at the end of the post-processing stage. So far no slices have been processed. Does anyone know how to solve it? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] Tracula error - unknown queue long.q, short.q
Indeed. It's actually really easy to set up, too. From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Monday, September 02, 2013 3:46 PM To: Watson, Christopher Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error - unknown queue long.q, short.q Thanks for the pointers, Chris. I'd call it an opportunity for FSL customization rather than an FSL problem per se :o) On Mon, 2 Sep 2013, Watson, Christopher wrote: This is an FSL problem. You can try the FSL list, and check out some links: https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira [jbragapere...@gmail.com] Sent: Monday, September 02, 2013 9:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula error - unknown queue long.q, short.q Dear Anastasia and FreeSurfers, I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc: INFO: SUBJECTS_DIR is /data-02/joana/Last INFO: Diffusion root is /data-02/joana/tracula/ Actual FREESURFER_HOME /usr/local/freesurfer-5.3 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri subjectdir is /data-02/joana/tracula/XXX/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue short.q. Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue long.q. Exiting. Queuing post processing stage Unable to run job: denied: 60 is not a valid object name (cannot start with a digit) Job was rejected because job requests unknown queue long.q. Exiting. Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress. Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the queued tasks. You will get an email at the end of the post-processing stage. So far no slices have been processed. Does anyone know how to solve it? Thanks! ___ 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] questions regarding longitudinal processing
Hi All, This may seem to be an easy question, I would just like to confirm... I have two groups that underwent different types of training and were measured at two time points (before and after training). My understanding is that I should use the longitudinal scheme in freesurfer to run recon-all? I have processed all data using normal recon-all command, and was wondering if I should rerun them all with the longitudinal command: recon-all -subjid tpNid -all Thanks in advance, Catherine ___ 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.
