[Freesurfer] Cannot access Apply button in Configure Overlay Display dialog
Dear developers/users, This is completely ridiculous known issue on a low resolution monitor :( Presumably, it was solved here: http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer, but the file is inaccessible via ftp. Any other workaround? All I need is to change Min statistic threshold and hit apply button. Probably, something via command line? Unfortunately, there are no hot-keys and it is impossible to reach with a tab because the non-visible dialog elements presumable do not exist (tab goes to the top of the dialog after the last visible dialog element). I am using Ubuntu virtual box FS 5.1. Thanks a lot, Vadim ___ 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] Flipped and non-flipped data
To add on to Bruce's explanation, the freesurfer parcellation atlas (which for example specifies the probability of precentral gyrus at a particular location) is not symmetric, thus it will treat the left and right hemispheres of your subject differently if you flipped it. --Thomas On Sun, Jun 17, 2012 at 10:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Remmelt folding patterns are not symmetric across the hemispheres, so the cortical parcellation will change if you flip things left/right, which is appropriate. I would be surprised if you see much change in the thickness though. cheers Bruce On Fri, 15 Jun 2012, Schur, Remmelt R. wrote: Dear Freesurfers, Grey matter volumes of the same structure seem to be measured differently depending on if FreeSurfer establishes it as in the left or in the right hemisphere. For example, if I take a look at the caudal anterior cingulate in the right hemisphere and I flip the image (creating a mirror image of the same hemisphere, which will then be treated by FreeSurfer as a left hemisphere), the same structure has a totally different grey matter volume (see attachment, on the right the original and on the left the flipped version). Does anybody know what's the logic behind this and what's the best way to avoid FreeSurfer creating asymmetry between left and right hemisphere (maybe averaging flipped and non-flipped data?) Thanks! Kind regards, Remmelt Schür IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. ___ 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] .license file
I am assuming you are on a OSX box which has that stupid protection. Just open a Terminal and run cat $FREESURFER_HOME/.license then type in the 3 lines and Enter and then do a Control-D to exit -- Paul Raines (http://help.nmr.mgh.harvard.edu) On Sun, 17 Jun 2012 1:45am, Monica Giraldo wrote: Hello, I created a file with this data, but when I'm going to save it as .license doesnt let me because a message appears and says that files starting with . are of the system and that i have to choose another name. What can I do? Thanks. Mónica Giraldo Chica PhD. Candidate Biomedicine Sherman Health Science Research Centre www.monicagiraldochica.com ___ 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] .license file
If FreeSurfer on Mac has been installed on /Applications you may need to type sudo cat $FREESURFER_HOME/.license and enter your account password when asked - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Mon, Jun 18, 2012 at 10:57 AM, Paul Raines rai...@nmr.mgh.harvard.eduwrote: I am assuming you are on a OSX box which has that stupid protection. Just open a Terminal and run cat $FREESURFER_HOME/.license then type in the 3 lines and Enter and then do a Control-D to exit -- Paul Raines (http://help.nmr.mgh.harvard.**eduhttp://help.nmr.mgh.harvard.edu ) On Sun, 17 Jun 2012 1:45am, Monica Giraldo wrote: Hello, I created a file with this data, but when I'm going to save it as .license doesnt let me because a message appears and says that files starting with . are of the system and that i have to choose another name. What can I do? Thanks. Mónica Giraldo Chica PhD. Candidate Biomedicine Sherman Health Science Research Centre www.monicagiraldochica.com __**_ 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 ___ 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.
[Freesurfer] memory allocation error with mris_register for one subject
hello! i am able to run mris_register on all of the OASIS brain images that i have tested except for one: OAS1_0061_MR1: mris_register -curv OASIS-0061_MR1/surf/rh.sphere templates/freesurfer/rh.OASIS_template.tif OASIS-0061_MR1/surf/rh.sphere_to_OASIS_template.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from OASIS-0061_MR1/surf/rh.sphere... TAGskip: tag=1717658469, failed to calloc 1868656640 bytes! Cannot allocate memory the .sphere files are the same size, but i get a memory error. any idea why this might be? cheers, @rno ___ 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] memory allocation error with mris_register for one subject
Hi Arno can you load that sphere file in tksurfer? And run mris_info or mris_euler_number on it? I'm wondering if it is corrupted. Bruce On Mon, 18 Jun 2012, Arno Klein wrote: hello! i am able to run mris_register on all of the OASIS brain images that i have tested except for one: OAS1_0061_MR1: mris_register -curv OASIS-0061_MR1/surf/rh.sphere templates/freesurfer/rh.OASIS_template.tif OASIS-0061_MR1/surf/rh.sphere_to_OASIS_template.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from OASIS-0061_MR1/surf/rh.sphere... TAGskip: tag=1717658469, failed to calloc 1868656640 bytes! Cannot allocate memory the .sphere files are the same size, but i get a memory error. any idea why this might be? cheers, @rno ___ 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] memory allocation error with mris_register for one subject
aha -- it seems that just the .sphere files, not the .pial or .white files, are corrupted. is there an easy way to generate just the .sphere files again? cheers, @rno On Mon, Jun 18, 2012 at 11:32 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Arno can you load that sphere file in tksurfer? And run mris_info or mris_euler_number on it? I'm wondering if it is corrupted. Bruce On Mon, 18 Jun 2012, Arno Klein wrote: hello! i am able to run mris_register on all of the OASIS brain images that i have tested except for one: OAS1_0061_MR1: mris_register -curv OASIS-0061_MR1/surf/rh.sphere templates/freesurfer/rh.OASIS_**template.tif OASIS-0061_MR1/surf/rh.**sphere_to_OASIS_template.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from OASIS-0061_MR1/surf/rh.sphere.**.. TAGskip: tag=1717658469, failed to calloc 1868656640 bytes! Cannot allocate memory the .sphere files are the same size, but i get a memory error. any idea why this might be? cheers, @rno 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] Cannot access Apply button in Configure Overlay Display dialog
Hi Vadim, When you enter the new min statistic threshold, you can hit the spacebar to apply. -Louis On Mon, 18 Jun 2012, Vadim Axel wrote: Dear developers/users, This is completely ridiculous known issue on a low resolution monitor :( Presumably, it was solved here: http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer, but the file is inaccessible via ftp. Any other workaround? All I need is to change Min statistic threshold and hit apply button. Probably, something via command line? Unfortunately, there are no hot-keys and it is impossible to reach with a tab because the non-visible dialog elements presumable do not exist (tab goes to the top of the dialog after the last visible dialog element). I am using Ubuntu virtual box FS 5.1. Thanks a lot, Vadim ___ 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] memory allocation error with mris_register for one subject
sure. The mris_sphere command line should be in the recon-all.log file in the subject's scripts dir. Either run that directly, or look at the recon-all help to figure out how to do it through recon-all cheers Bruce On Mon, 18 Jun 2012, Arno Klein wrote: aha -- it seems that just the .sphere files, not the .pial or .white files, are corrupted. is there an easy way to generate just the .sphere files again? cheers, @rno On Mon, Jun 18, 2012 at 11:32 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Arno can you load that sphere file in tksurfer? And run mris_info or mris_euler_number on it? I'm wondering if it is corrupted. Bruce On Mon, 18 Jun 2012, Arno Klein wrote: hello! i am able to run mris_register on all of the OASIS brain images that i have tested except for one: OAS1_0061_MR1: mris_register -curv OASIS-0061_MR1/surf/rh.sphere templates/freesurfer/rh.OASIS_template.tif OASIS-0061_MR1/surf/rh.sphere_to_OASIS_template.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from OASIS-0061_MR1/surf/rh.sphere... TAGskip: tag=1717658469, failed to calloc 1868656640 bytes! Cannot allocate memory the .sphere files are the same size, but i get a memory error. any idea why this might be? cheers, @rno 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.
[Freesurfer] Correction for Multiple Comparisons - Sign Question
Freesurfers- When choosing the simulation type does the ending have to match the sim sign? for instance i see examples with --sim mc-z 1 3 mc-z.pos.3 --sim sign pos or --sim mc-z 1 3 mc-z.neg.3 --sim sign neg I guess what i am asking is what does the first sign (in the mc-z.(SIGN).3 mean? michael -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkrue...@gmail.com (262)-483-7449 ___ 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] mri_cnr
hi fellas, i am trying to run mri_cnr command in freesurfer to compute and see CNR for gray/white/csf the command gives following info as help: -bash-3.2$ mri_cnr usage: mri_cnr [options] surf directory vol 1 vol 2 ... -s slope fname dist in dist out step in step out i understand that 'surf directory'= subjects 'surf' folder ; but i am not able to figure out what it means by vol1, vol2 and slope fname..it doesnt show any error but just doesnt do anything even if i mention the surf directory to this command. i checked on freesurfer mail archive, but no info since 2009 about any update on this command. may someone please give an info if anyone ever used this command thanks kk ___ 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_cnr
Hi KK this is something i wrote for myself, but you are welcome to try it out. YOu don't need to give it the slope stuff, that is optional. The vol command line parms are the volumes that you want to assess CNR in. For example: mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/norm.mgz processing MRI volume /homes/4/fischl/local_subjects/bruce/mri/norm.mgz... white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2 gray/white CNR = 2.241, gray/csf CNR = 1.026 lh CNR = 1.633 white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4 gray/white CNR = 2.205, gray/csf CNR = 0.937 rh CNR = 1.571 total CNR = 1.602 On Mon, 18 Jun 2012, Kushal Kapse wrote: hi fellas, i am trying to run mri_cnr command in freesurfer to compute and see CNR for gray/white/csf the command gives following info as help: -bash-3.2$ mri_cnr usage: mri_cnr [options] surf directory vol 1 vol 2 ... -s slope fname dist in dist out step in step out i understand that 'surf directory'= subjects 'surf' folder ; but i am not able to figure out what it means by vol1, vol2 and slope fname..it doesnt show any error but just doesnt do anything even if i mention the surf directory to this command. i checked on freesurfer mail archive, but no info since 2009 about any update on this command. may someone please give an info if anyone ever used this command thanks kk ___ 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] mri_cnr
thanks Dr. B.that helped a lot - Original Message - From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Kushal Kapse kka...@mail.med.upenn.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Monday, June 18, 2012 2:27:29 PM Subject: Re: [Freesurfer] mri_cnr Hi KK this is something i wrote for myself, but you are welcome to try it out. YOu don't need to give it the slope stuff, that is optional. The vol command line parms are the volumes that you want to assess CNR in. For example: mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/norm.mgz processing MRI volume /homes/4/fischl/local_subjects/bruce/mri/norm.mgz... white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2 gray/white CNR = 2.241, gray/csf CNR = 1.026 lh CNR = 1.633 white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4 gray/white CNR = 2.205, gray/csf CNR = 0.937 rh CNR = 1.571 total CNR = 1.602 On Mon, 18 Jun 2012, Kushal Kapse wrote: hi fellas, i am trying to run mri_cnr command in freesurfer to compute and see CNR for gray/white/csf the command gives following info as help: -bash-3.2$ mri_cnr usage: mri_cnr [options] surf directory vol 1 vol 2 ... -s slope fname dist in dist out step in step out i understand that 'surf directory'= subjects 'surf' folder ; but i am not able to figure out what it means by vol1, vol2 and slope fname..it doesnt show any error but just doesnt do anything even if i mention the surf directory to this command. i checked on freesurfer mail archive, but no info since 2009 about any update on this command. may someone please give an info if anyone ever used this command thanks kk ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Ridiculous story about Freesurfer
Did anyone else happen to see this ridiculous story on Gizmodo today? http://gizmodo.com/5919149/your-brain-scan-looks-different-on-mac-and-pc It cites the recent article The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements as its only source, and then goes on to completely misinterpret it. This sentence (if I had to pick one) is particularly troubling to me: The finding is completely crazy, and casts doubt over the way many scans—such as CT and MRI—are analyzed in routine practice. Crazy, right? Enjoy... Andrew ___ 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] Choosing a Scanning Sequence
Hello, We are working with previously acquired data, so unfortunately we are unable to use the MPRAGE sequence for the current data set. We would like to use T1 images to compute volumetric results. We are using a Philips 3T Achieva, and the sequences received by most participants are a T1-FFE (FLASH in Siemens terms or SPGR in GE terms) and a T1 TFE sequence (I believe this is TurboFLASH in Siemens terms, although I am not fully familiar with it). Are either of these scans appropriate for performing volumetric analysis of grey/white matter using FreeSurfer? Is either scan preferable to the other? Patrick Sullivan Research Assistant, Chapman Lab War Related Illness and Injury Study Center Veteran's Affairs Medical Center Washington, D.C. 20422 (202) 745-8000 (ext 7566) ___ 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] Correction for Multiple Comparisons - Sign Question
That is just the name. It must be different for each call so that the files are not overwritten. It does not have to match the sign, but it will be less confusing if it does. doug On 06/18/2012 12:38 PM, mdkrue...@uwalumni.com wrote: Freesurfers- When choosing the simulation type does the ending have to match the sim sign? for instance i see examples with --sim mc-z 1 3 mc-z.pos.3 --sim sign pos or --sim mc-z 1 3 mc-z.neg.3 --sim sign neg I guess what i am asking is what does the first sign (in the mc-z.(SIGN).3 mean? michael -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkrue...@gmail.com mailto:mdkrue...@gmail.com (262)-483-7449 tel:%28262%29-483-7449 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] map ROI-based measures back to surface
Hi, FreeSurfer experts I used mri_make_surface_parcellation and parcellated the brain into 200 ROIs. Then some measures were derived based on the ROIs and now I have 200*1 matrix with each ROI having a value. What I want to do is to map the ROI-based measures back to the surface files and show the intensity differences between these 200 ROIs on surfaces. Could someone tell me what is the best way to realize that? Forgive me if this question has bee asked before, but I really do not know how to input best keywords for the question to search in the archive. Many thanks in advance! Leon ___ 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] qdec group analysis
Hello Freesurfers, I have created an ROI label for 80 subjects in qdec. My question is the following: Is there a command that will create a .stats file for all my subjects rather than using the below command on each person individually? mris_anatomical_stats -l rh.ento.label \ -t rh.thickness -b -f 4000/stats/rh.ento.stats 4000 rh best regards, Cat___ 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] qdec group analysis
Hi Cat, you can use something like: mri_segstats --i y.mgh --slabel fsaverage lh your.label --id 1 --avgwf avgwf.dat where y.mgh is the file created by qdec that has stack of subjects' data avgwf.dat will have a value for each subject that is the mean over your ROI doug On 06/18/2012 06:56 PM, Cat Chong wrote: Hello Freesurfers, I have created an ROI label for 80 subjects in qdec. My question is the following: Is there a command that will create a .stats file for all my subjects rather than using the below command on each person individually? mris_anatomical_stats -l rh.ento.label \ -t rh.thickness -b -f 4000/stats/rh.ento.stats 4000 rh best regards, Cat ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] map ROI-based measures back to surface
There's not an easy way to do this. You can load the parcellation into matlab and create a matrix of size nverticesx1, then map the value you want into each vertex, then mri.vol = yourmatrix; MRIwrite(mri,'lh.matrix.mgh') then load that lh.matrix.mgh as an overlay in tksurfer doug On 06/18/2012 06:50 PM, Leon wrote: Hi, FreeSurfer experts I used mri_make_surface_parcellation and parcellated the brain into 200 ROIs. Then some measures were derived based on the ROIs and now I have 200*1 matrix with each ROI having a value. What I want to do is to map the ROI-based measures back to the surface files and show the intensity differences between these 200 ROIs on surfaces. Could someone tell me what is the best way to realize that? Forgive me if this question has bee asked before, but I really do not know how to input best keywords for the question to search in the archive. Many thanks in advance! Leon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] position open
Hi! We have an algorithm developer position open. Below is the job description. Although it stats in a very general term, the person will spend most of time working on freesurfer related algorithms and services. Experience in PhD or Post doc did count as long as it is related to algorithm development. Please send resume to me directly. Thanks Gennan Chen (gennan.c...@synarc.com) Engineering Manager, Engineering Department, CCBR-Synarc (www.synarc.com) Algorithm Development Engineer Analyzes, prototype, designs, programs, debugs, and modifies medical imaging processing algorithms used in clinical trials settings. Responsibilities: * Prototype, Design, develop, unit test and release medical imaging processing algorithms to support Synarc's business. * Work with end users to understand requirements. * Write and contribute to design specifications, installation guides and other technical documentation in accordance with Synarc best practices. * Work with other technical staff to support system installations, upgrades, and configurations of software. * Assist in training of users and creation of user manuals. * Ensure that systems are released in accordance with regulatory and Synarc standards. * Work with end users, other developers, software QA, product managers and software project managers to deliver applications, bug fixes and enhancements. * Use professional experience to provide creative, effective solutions to complex problems. Qualifications: Education: PhD in biomedical engineering, physics or computer science Experience: 4+ years of design and implement complex medical imaging algorithms in related fields such as registration and segmentation. Expert in Matlab and extending Matlab in C/C++ Experience in Freesurfer and related processing stream. Experience with DICOM standard Experience with cloud, cluster and other high performance computation environment. Experience with Java enterprise application development stack Experience with SQL and relational database Skills: Good problem solving, technical troubleshooting, organizational, interpersonal and team skills. Good written and verbal communication skills. This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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.
