[Freesurfer] wm edit freeview
Dear all, Is there any documentation on doing em edit using freeview. Thanks, SK ___ 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] recon-all problem
Hi everyone I run freesurfer recon-all command with the flag -all and I have this error ERROR:mpr2mni305 failed, see transforms/talairach_avi.log Some one have any idea? Thanks this is the whole process: Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig/001.mgz /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tm mri_convert /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/rawavg.mgz /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) Original Data has (1.33, 1, 1) mm size and (128, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig.mgz... mri_add_xform_to_header -c /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/transforms/talairach.xfm /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig.mgz /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_ ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux wn033.grid.scg.nuigalway.ie 2.6.18-274.7.1.el5 #1 SMP Thu Oct 20 15:20:36 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 6559183 exited with ERRORS at Wed Dec 28 16:21:01 GMT 2011 For more details, see the log file /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa___ 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] Setting Up Source File Automatically
Hi - I am trying to setup the FreeSurfer program so that when I open the terminal it sources the file automatically. As per the instructions, I have changed my .tcshrc file in my Home Directory so that both the setenv and source commands are in there. I have also permanently changed my shell type to tcsh. However, when I open my terminal, it doesn't start automatically. I must type 'tcsh' and then it runs. What am I missing? Thanks. Brian James Technical Applications Analyst North Bay Regional Health Centrehttp://www.nbrhc.on.ca/ The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately. L'information contenue dans ce message ?lectronique est destin?e uniquement au destinataire ou aux destinataires vis?s. La transmission de ce message ? une personne autre que son destinataire ou ses destinataires vis?s ne supprime en rien l'obligation d'en respecter la confidentialit?. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient ?tre soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la sant?. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires vis?s sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer imm?diatement et en avertir l'exp?diteur. ___ 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] error with cvs registration
Dear Lilla, I solved the problem with my registration so now is working well but I will be very grateful if you can help me with the following questions: For the DTI group analysis study I am interested to see any changes in the FA values within two groups: controls versus patients (children with epilepsy). As you suggested I introduced a white matter mask that will ensure that I am only considering diffusion values in the white matter and then also I did corrected for multiple comparison running mri_glmfit-sim with the option grf (as Doug recommend me). My questions are: 1)How can I conclude if there is an increase and/or decrease in the FA values in one group (for example patients) versus another group (example controls). In other words what I can conclude regarding the FA values based on the GLM results: blue versus red clusters from the http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion (I don't see anymore the image with red and blue clusters posted on this website!) 2) If my fa-mask was defined using the wmparc2diff.mgz so is a segmentation volume, in order to resample this volume (wmparc or aseg) in CVS space, do I need to use the nearest neighbor (nearest) interpolation option instead of --interp trilin? What will be the difference and is the difference visible in the intensity or in another parameter such as a smoother registration? Thank you very much and Happy New Year! Antonella___ 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] recon-all problem
what does the file transforms/talairach_avi.log say? and are those pathnames real? or something the email added? n. On Wed, 2011-12-28 at 17:08 +, LAOUCHEDI MAKHLOUF wrote: Hi everyone I run freesurfer recon-all command with the flag -all and I have this error ERROR:mpr2mni305 failed, see transforms/talairach_avi.log Some one have any idea? Thanks this is the whole process: Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig/001.mgz /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tm mri_convert /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/rawavg.mgz /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) Original Data has (1.33, 1, 1) mm size and (128, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig.mgz... mri_add_xform_to_header -c /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/transforms/talairach.xfm /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig.mgz /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_ ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux wn033.grid.scg.nuigalway.ie 2.6.18-274.7.1.el5 #1 SMP Thu Oct 20 15:20:36 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 6559183 exited with ERRORS at Wed Dec 28 16:21:01 GMT 2011 For more details, see the log file /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa ___ 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] Setting Up Source File Automatically
when you changed your shell, did you run: chsh -s `which tcsh` ? usually it will prompt for your password. then you will need to logout/login. when you type 'ps', you should see 'tcsh' as one of the processes. also, you can try copying the .tcshrc to .cshrc, but probably that shouldn't matter. n. On Wed, 2011-12-28 at 17:38 +, James, Brian wrote: Hi – I am trying to setup the FreeSurfer program so that when I open the terminal it sources the file automatically. As per the instructions, I have changed my .tcshrc file in my Home Directory so that both the setenv and source commands are in there. I have also permanently changed my shell type to tcsh. However, when I open my terminal, it doesn’t start automatically. I must type ‘tcsh’ and then it runs. What am I missing? Thanks. Brian James Technical Applications Analyst North Bay Regional Health Centre The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately. L'information contenue dans ce message électronique est destinée uniquement au destinataire ou aux destinataires visés. La transmission de ce message à une personne autre que son destinataire ou ses destinataires visés ne supprime en rien l'obligation d'en respecter la confidentialité. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient être soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la santé. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires visés sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer immédiatement et en avertir l'expéditeur. ___ 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] Setting Up Source File Automatically
The log off/on fixed it. Thanks. Brian. -Original Message- From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] Sent: December-28-11 3:28 PM To: James, Brian Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Setting Up Source File Automatically when you changed your shell, did you run: chsh -s `which tcsh` ? usually it will prompt for your password. then you will need to logout/login. when you type 'ps', you should see 'tcsh' as one of the processes. also, you can try copying the .tcshrc to .cshrc, but probably that shouldn't matter. n. On Wed, 2011-12-28 at 17:38 +, James, Brian wrote: Hi – I am trying to setup the FreeSurfer program so that when I open the terminal it sources the file automatically. As per the instructions, I have changed my .tcshrc file in my Home Directory so that both the setenv and source commands are in there. I have also permanently changed my shell type to tcsh. However, when I open my terminal, it doesn’t start automatically. I must type ‘tcsh’ and then it runs. What am I missing? Thanks. Brian James Technical Applications Analyst North Bay Regional Health Centre The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately. L'information contenue dans ce message électronique est destinée uniquement au destinataire ou aux destinataires visés. La transmission de ce message à une personne autre que son destinataire ou ses destinataires visés ne supprime en rien l'obligation d'en respecter la confidentialité. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient être soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la santé. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires visés sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer immédiatement et en avertir l'expéditeur. ___ 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. The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately. L'information contenue dans ce message électronique est destinée uniquement au destinataire ou aux destinataires visés. La transmission de ce message à une personne autre que son destinataire ou ses destinataires visés ne supprime en rien l'obligation d'en respecter la confidentialité. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient être soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la santé. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires visés sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer immédiatement et en avertir l'expéditeur. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] How to export non spatial normalization fMRI images?
Hi, I have run preproc-sess to analyze fMRI images. I'd like to analyze fMRI images in the individual space, but I found that the final output (i.e., fmcpr.up.sm4.fsaverage.lh.nii.gz) were already spatial normalized. So, How to just smooth fMRI images in surface space and export them as the co-registered fMRI images in volume space? I think it could start at fmcpr.up.nii.gz? Thank you in advance! Best, Xiangyu Long ___ 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] fixing hemisphere leakage
Hi David what version are you running? Bruce On Wed, 28 Dec 2011, David Groppe wrote: Hi FreeSurfers, I'm trying to fix FreeSurfer's pial and white matter surface boundary estimates on a brain missing a large part of the right hemisphere. I've manually filled in the greatly expanded ventricles in the damaged hemisphere as white matter (see attached) and tried rerunning recon-all with -autorecon2-wm and -autorecon3 flags. This fails to help. Is there sometime else I can do? thanks in advance, -David ___ 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] fixing hemisphere leakage
Thanks for the speedy response Bruce. I'm running: $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ -David On Wed, Dec 28, 2011 at 7:44 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi David what version are you running? Bruce On Wed, 28 Dec 2011, David Groppe wrote: Hi FreeSurfers, I'm trying to fix FreeSurfer's pial and white matter surface boundary estimates on a brain missing a large part of the right hemisphere. I've manually filled in the greatly expanded ventricles in the damaged hemisphere as white matter (see attached) and tried rerunning recon-all with -autorecon2-wm and -autorecon3 flags. This fails to help. Is there sometime else I can do? thanks in advance, -David 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. -- David Groppe, Ph.D. Postdoctoral Researcher North Shore LIJ Health System New Hyde Park, New York http://www.cogsci.ucsd.edu/~dgroppe/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fixing hemisphere leakage
Try fixing the aseg and running from there forward On Dec 28, 2011, at 9:05 PM, David Groppe david.m.gro...@gmail.com wrote: Thanks for the speedy response Bruce. I'm running: $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ -David On Wed, Dec 28, 2011 at 7:44 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi David what version are you running? Bruce On Wed, 28 Dec 2011, David Groppe wrote: Hi FreeSurfers, I'm trying to fix FreeSurfer's pial and white matter surface boundary estimates on a brain missing a large part of the right hemisphere. I've manually filled in the greatly expanded ventricles in the damaged hemisphere as white matter (see attached) and tried rerunning recon-all with -autorecon2-wm and -autorecon3 flags. This fails to help. Is there sometime else I can do? thanks in advance, -David 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. -- David Groppe, Ph.D. Postdoctoral Researcher North Shore LIJ Health System New Hyde Park, New York http://www.cogsci.ucsd.edu/~dgroppe/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
