[Freesurfer] R: Re: R: Re: incomplete tracts
No I did not try it. Now I'm trying to perform it. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 9-apr-2013 17.50 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: incomplete tracts Hi Stefano - Did you try CVS for the inter-subject registration? It doesn't look like it from the configuration file. a.y On Tue, 9 Apr 2013, std...@virgilio.it wrote: Hi Anastasia, yes, I tried.I'm attacking the last configuration file that I used. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 9-apr-2013 1.42 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] incomplete tracts What registration methods are you using for the intra-subject and inter-subject registration? Have you tried the different options? On Fri, 5 Apr 2013, std...@virgilio.it wrote: Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely fminor. Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 5-apr-2013 18.57 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts What you say again you mean with 5.2? On Fri, 5 Apr 2013, std...@virgilio.it wrote: Hi Anastasia, yes, for some subject the low-b volume is in the end. Some subjects have again incomplete tracts. I'm attacking an example of configuration file that I'm using. I hope that you can check it please. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 5-apr-2013 18.45 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] incomplete tracts Hi Stefano - In your case we determined that the ones that had the low-b volume in the end didn't run correctly, right? In that case, I didn't need to see anything, you were going to try running 5.2. a.y On Fri, 5 Apr 2013, std...@virgilio.it wrote: Hi Anastasia, could I send you the data of a subject that I don't run correctly? I still have some subjects with tracts incomplete and I do not know if it depends from my analysis or whether the images are not good. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 5-apr-2013 17.37 A: Gerit Pfuhlgerit.pf...@gmail.com Cc: freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] incomplete tracts Hi Gerit - If it's not an issue with the gradient table but instead a tractography initialization issue, I strongly recommend running 5.2 with bbregister for the registration (which is the default in 5.2 anyway). You can also upload an example data set with issues (include: dmri, dmri.bedpostX, dlabel, dpath, scripts) here for me to take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Hope this helps, a.y On Fri, 5 Apr 2013, Gerit Pfuhl wrote: Dear Anastasia, thanks for the help. There is also a line option in freeview. However we still have brains with missing tracks, I rerun them with increasing the ncpts and registering to bbr (since that is default in Tracula 5.2.). We are reasonable confident that our bvel and bvac are correct, since we have roughly 20 cases out of 90 processed brains where there are no missing tracts. Further sometimes only one tract is missing, sometimes it is more severe. We could not find any correlation with recon-all problems or DTI raw data issues (all but one were without moving artefacts). Since we are running bedpostx outside of trac-all (i.e. trac-prep then bedpostx then trac-path) might it be an issue that is solved with installing the 5.2. version? Would that run in freesurfer 5.1.0? I guess we need to change the dcmrirc files only a bit. Kind regards Gerit Pfuhl On 3 April 2013 16:59, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Benjamin - I'd look in a coronal view to see if the lines in the corpus callosum follow the curvature of the corpus callosum, and in a sagittal view to see if the lines in the cingulum follow the curvature of the cingulum. Does this make sense? a.y On Wed, 3 Apr 2013, Roschinski, Benjamin wrote: Dear Anastasia, we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because our gradient table is wrong but I am not really sure how to analyse these informations. You wrote to Stefano the lines have to point in the right direction and that the eigenvectors are not pointing
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical black spaces within pial surfaces, compared to FS 5.1? I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/19/13 7:07 AM, Yang, Daniel yung-jui.y...@yale.edu wrote: Posting one of the brains. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn It seems to me that neither version is perfect; however, 5.2.0 is capturing more black spaces in the region I'm looking at. It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20). Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the region I examined with my samples, it's not a systematic predictable bias. Any solution? -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/18/13 6:27 PM, Matt Glasser m...@ma-tea.com wrote: Do the surfaces look correct in these regions? You might post some screenshots of subjects who have a big difference between 5.1 and 5.2 with the 5.1 and 5.2 white and pial surfaces on volume slices that highlight the difference. Without this kind of info, its hard to know which was more correct, 5.1 or 5.2. Peace, Matt. On 3/18/13 5:13 PM, Ritobrato Datta rida...@mail.med.upenn.edu wrote: I concur. I have seen similar results in primary visual cortex from ~40 subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to 1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3. Ritobrato Datta, Ph.D. Post Doctoral Researcher Department of Neurology University of Pennsylvania School of Medicine 3rd Floor, Room 312 3710 Hamilton Walk (Goddard Laboratories) Philadelphia, PA 19104-6241 email - rida...@mail.med.upenn.edu - Original Message - From: Daniel Yang yung-jui.y...@yale.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT) Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0 Dear FreeSurfer Experts, I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161 subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in particular. Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in 5.2.0. They are significantly different, t(160) = 56.71. The correlation between the two versions is r = .33 Is this something possible?? I can't see what went wrong in my procedures. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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] Very different results between 5.1.0 and 5.2.0
We are investigating it. I did fix one thing that you can try if you want - give us your hardware/software info and we will send you a new version of mris_make_surfaces Bruce P.s. you can also upload and we will take a look On Apr 10, 2013, at 6:11 AM, Yang, Daniel yung-jui.y...@yale.edu wrote: Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical black spaces within pial surfaces, compared to FS 5.1? I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/19/13 7:07 AM, Yang, Daniel yung-jui.y...@yale.edu wrote: Posting one of the brains. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn It seems to me that neither version is perfect; however, 5.2.0 is capturing more black spaces in the region I'm looking at. It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20). Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the region I examined with my samples, it's not a systematic predictable bias. Any solution? -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/18/13 6:27 PM, Matt Glasser m...@ma-tea.com wrote: Do the surfaces look correct in these regions? You might post some screenshots of subjects who have a big difference between 5.1 and 5.2 with the 5.1 and 5.2 white and pial surfaces on volume slices that highlight the difference. Without this kind of info, its hard to know which was more correct, 5.1 or 5.2. Peace, Matt. On 3/18/13 5:13 PM, Ritobrato Datta rida...@mail.med.upenn.edu wrote: I concur. I have seen similar results in primary visual cortex from ~40 subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to 1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3. Ritobrato Datta, Ph.D. Post Doctoral Researcher Department of Neurology University of Pennsylvania School of Medicine 3rd Floor, Room 312 3710 Hamilton Walk (Goddard Laboratories) Philadelphia, PA 19104-6241 email - rida...@mail.med.upenn.edu - Original Message - From: Daniel Yang yung-jui.y...@yale.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT) Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0 Dear FreeSurfer Experts, I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161 subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in particular. Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in 5.2.0. They are significantly different, t(160) = 56.71. The correlation between the two versions is r = .33 Is this something possible?? I can't see what went wrong in my procedures. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
I have processed more that 600 brains with both versions in the last weeks and the only difference I'm seeing between version 5.2.0 and 5.1, besides the obvious new features, is processing time. Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance. Besides that there's no visible difference in terms of cortical thickness, volumes, etc. If you have access to computer resources to spare you can run recon-all of both versions in some well known database of images and do a more formal test. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel yung-jui.y...@yale.eduwrote: Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical black spaces within pial surfaces, compared to FS 5.1? I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/19/13 7:07 AM, Yang, Daniel yung-jui.y...@yale.edu wrote: Posting one of the brains. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn It seems to me that neither version is perfect; however, 5.2.0 is capturing more black spaces in the region I'm looking at. It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20). Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the region I examined with my samples, it's not a systematic predictable bias. Any solution? -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/18/13 6:27 PM, Matt Glasser m...@ma-tea.com wrote: Do the surfaces look correct in these regions? You might post some screenshots of subjects who have a big difference between 5.1 and 5.2 with the 5.1 and 5.2 white and pial surfaces on volume slices that highlight the difference. Without this kind of info, its hard to know which was more correct, 5.1 or 5.2. Peace, Matt. On 3/18/13 5:13 PM, Ritobrato Datta rida...@mail.med.upenn.edu wrote: I concur. I have seen similar results in primary visual cortex from ~40 subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to 1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3. Ritobrato Datta, Ph.D. Post Doctoral Researcher Department of Neurology University of Pennsylvania School of Medicine 3rd Floor, Room 312 3710 Hamilton Walk (Goddard Laboratories) Philadelphia, PA 19104-6241 email - rida...@mail.med.upenn.edu - Original Message - From: Daniel Yang yung-jui.y...@yale.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT) Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0 Dear FreeSurfer Experts, I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161 subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in particular. Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in 5.2.0. They are significantly different, t(160) = 56.71. The correlation between the two versions is r = .33 Is this something possible?? I can't see what went wrong in my procedures. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
Hi PPJ That's exactly what we are doing. Good to hear its stable for you Bruce On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalhães Oliveira Juniorp...@netfilter.com.br wrote: I have processed more that 600 brains with both versions in the last weeks and the only difference I'm seeing between version 5.2.0 and 5.1, besides the obvious new features, is processing time. Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance. Besides that there's no visible difference in terms of cortical thickness, volumes, etc. If you have access to computer resources to spare you can run recon-all of both versions in some well known database of images and do a more formal test. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel yung-jui.y...@yale.edu wrote: Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical black spaces within pial surfaces, compared to FS 5.1? I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/19/13 7:07 AM, Yang, Daniel yung-jui.y...@yale.edu wrote: Posting one of the brains. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn It seems to me that neither version is perfect; however, 5.2.0 is capturing more black spaces in the region I'm looking at. It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20). Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the region I examined with my samples, it's not a systematic predictable bias. Any solution? -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/18/13 6:27 PM, Matt Glasser m...@ma-tea.com wrote: Do the surfaces look correct in these regions? You might post some screenshots of subjects who have a big difference between 5.1 and 5.2 with the 5.1 and 5.2 white and pial surfaces on volume slices that highlight the difference. Without this kind of info, its hard to know which was more correct, 5.1 or 5.2. Peace, Matt. On 3/18/13 5:13 PM, Ritobrato Datta rida...@mail.med.upenn.edu wrote: I concur. I have seen similar results in primary visual cortex from ~40 subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to 1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3. Ritobrato Datta, Ph.D. Post Doctoral Researcher Department of Neurology University of Pennsylvania School of Medicine 3rd Floor, Room 312 3710 Hamilton Walk (Goddard Laboratories) Philadelphia, PA 19104-6241 email - rida...@mail.med.upenn.edu - Original Message - From: Daniel Yang yung-jui.y...@yale.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT) Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0 Dear FreeSurfer Experts, I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161 subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in particular. Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in 5.2.0. They are significantly different, t(160) = 56.71. The correlation between the two versions is r = .33 Is this something possible?? I can't see what went wrong in my procedures. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tracula FS 5.2
Hi Daria - How much memory does your system have? Were you ever able to run trac-all from the 5.1 version on the same system? a.y On Wed, 10 Apr 2013, Antonenko, Daria wrote: Hi FS experts, I tried to run Tracula with the new FS 5.2 release and came across memory allocation problems in the preprocessing step and would appreciate some advice on solving them: MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice Cannot allocate memory Linux daria-Think 3.5.0-17-generic #28-Ubuntu SMP Tue Oct 9 19:32:08 UTC 2012 i686 i686 i686 GNU/Linux trac-preproc exited with ERRORS at Tue Apr 9 22:21:43 CEST 2013 I attached the log-file. Let me know if you need further information about my system. Thank you in advance, Daria ___ 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] Very different results between 5.1.0 and 5.2.0
Hi PPJ, Thanks! It looks interesting. I also found FS 5.2 is faster. Is there any chance you could also provide the cortical thickness of the 2009 atlas (e.g., rh)? I will take a look into the aseg.volume in my data too. Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 From: Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.brmailto:p...@netfilter.com.br Date: Wednesday, April 10, 2013 10:49 AM To: Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu Cc: Daniel Yang yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu, freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 You'll find attached some preliminary data of the comparison we did among versions. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.brhttp://www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 10:42 AM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi PPJ That's exactly what we are doing. Good to hear its stable for you Bruce On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalhães Oliveira Juniorp...@netfilter.com.brmailto:p...@netfilter.com.br wrote: I have processed more that 600 brains with both versions in the last weeks and the only difference I'm seeing between version 5.2.0 and 5.1, besides the obvious new features, is processing time. Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance. Besides that there's no visible difference in terms of cortical thickness, volumes, etc. If you have access to computer resources to spare you can run recon-all of both versions in some well known database of images and do a more formal test. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.brhttp://www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical black spaces within pial surfaces, compared to FS 5.1? I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454tel:%28203%29%20737-5454 On 3/19/13 7:07 AM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Posting one of the brains. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn It seems to me that neither version is perfect; however, 5.2.0 is capturing more black spaces in the region I'm looking at. It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20). Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the region I examined with my samples, it's not a systematic predictable bias. Any solution? -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454tel:%28203%29%20737-5454 On 3/18/13 6:27 PM, Matt Glasser m...@ma-tea.commailto:m...@ma-tea.com wrote: Do the surfaces look correct in these regions? You might post some screenshots of subjects who have a big difference between 5.1 and 5.2 with the 5.1 and 5.2 white and pial surfaces on volume slices that highlight the difference. Without this kind of info, its hard to know which was more correct, 5.1 or 5.2. Peace, Matt. On 3/18/13 5:13 PM, Ritobrato Datta rida...@mail.med.upenn.edumailto:rida...@mail.med.upenn.edu wrote: I concur. I have seen similar results in primary visual cortex from ~40 subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to 1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3. Ritobrato Datta, Ph.D. Post Doctoral Researcher Department of Neurology University of Pennsylvania School of Medicine 3rd Floor, Room 312 3710 Hamilton Walk (Goddard Laboratories) Philadelphia, PA 19104-6241 email - rida...@mail.med.upenn.edumailto:rida...@mail.med.upenn.edu - Original Message - From: Daniel Yang yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT) Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0 Dear FreeSurfer Experts, I ran
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
Ok, I'll try to put together a stat from aparc too. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 12:04 PM, Yang, Daniel yung-jui.y...@yale.eduwrote: Hi PPJ, Thanks! It looks interesting. I also found FS 5.2 is faster. Is there any chance you could also provide the cortical thickness of the 2009 atlas (e.g., rh)? I will take a look into the aseg.volume in my data too. Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 From: Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Date: Wednesday, April 10, 2013 10:49 AM To: Bruce Fischl fis...@nmr.mgh.harvard.edu Cc: Daniel Yang yung-jui.y...@yale.edu, freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 You'll find attached some preliminary data of the comparison we did among versions. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 10:42 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi PPJ That's exactly what we are doing. Good to hear its stable for you Bruce On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br wrote: I have processed more that 600 brains with both versions in the last weeks and the only difference I'm seeing between version 5.2.0 and 5.1, besides the obvious new features, is processing time. Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance. Besides that there's no visible difference in terms of cortical thickness, volumes, etc. If you have access to computer resources to spare you can run recon-all of both versions in some well known database of images and do a more formal test. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel yung-jui.y...@yale.eduwrote: Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical black spaces within pial surfaces, compared to FS 5.1? I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/19/13 7:07 AM, Yang, Daniel yung-jui.y...@yale.edu wrote: Posting one of the brains. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn It seems to me that neither version is perfect; however, 5.2.0 is capturing more black spaces in the region I'm looking at. It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20). Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the region I examined with my samples, it's not a systematic predictable bias. Any solution? -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/18/13 6:27 PM, Matt Glasser m...@ma-tea.com wrote: Do the surfaces look correct in these regions? You might post some screenshots of subjects who have a big difference between 5.1 and 5.2 with the 5.1 and 5.2 white and pial surfaces on volume slices that highlight the difference. Without this kind of info, its hard to know which was more correct, 5.1 or 5.2. Peace, Matt. On 3/18/13 5:13 PM, Ritobrato Datta rida...@mail.med.upenn.edu wrote: I concur. I have seen similar results in primary visual cortex from ~40 subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to 1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3. Ritobrato Datta, Ph.D. Post Doctoral Researcher Department of Neurology University of Pennsylvania School of Medicine 3rd Floor, Room 312 3710 Hamilton Walk (Goddard Laboratories) Philadelphia, PA 19104-6241 email - rida...@mail.med.upenn.edu - Original Message - From: Daniel Yang yung-jui.y...@yale.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT) Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0 Dear FreeSurfer Experts, I ran FreeSurfer 5.1.0 and FreeSurfer
[Freesurfer] freesurfer 5.1 vs 5.2
Hi: How can install version 5.2 in a computer without uninstalling version 5.1 ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] freesurfer 5.1 vs 5.2
Hi Gonzalo, You can untar the 5.2 files in a separate directory, and then just source the SetUpFreeSurfer.csh from the directory of the version of FreeSurfer you want to use. You can run 'which recon-all' to check which version you have sourced. -Louis On Wed, 10 Apr 2013, Gonzalo Rojas Costa wrote: Hi: How can install version 5.2 in a computer without uninstalling version 5.1 ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] Finding adjacent vertices/labels
Hello Freesurfers, I was wondering if there is information embedded in the annotation/label files that could be used to determine whether two labels represent anatomically adjacent regions? For example, I have parcellated a bunch of participants using connectomemapper into 1000 ROIs. I was just now reading Power et al. (2011), who looked at functional connectivity, but specifically excluded connections between spheroid ROIs that were less than 20mm apart. Analogously, I might wish to exclude connections between adjacent labels, but it seemed that manually creating an adjacency matrix for 1000 regions would be impractical, and a good candidate for an automated approach. I'm just not clear what information such an approach might have to work with. Can the adjacency between two vertices be determined based on their values? If so, one approach might be: for each pair of labels (A,B): get set of vertices within A get set of vertices within B for each vertex pair (Ai, Bj) if Ai and Bj are adjacent, stop, and mark A and B as adjacent Cheers, Chris ___ 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] merging dti data
we captured some dti data. there were 2 runs. we acquired in the axial plane, 2mm slice thickness the first run captured the lower half of the brain, slice locations: I56-S20, and the second run captured the upper half of the brain S16-S92. i have made briks from each of these runs. I can convert the briks to nifti files I want to merge the nifti files together to analyze the data in tracula In the past i have merged data from two dti runs, but each run have covered the entire brain, with the following commands mri_convert MJ0001dti1+orig.BRIK MJ0001dti1.nii.gz mri_convert MJ0001dti2+orig.BRIK MJ0001dti2.nii.gz mri_concat --i MJ0001dti1.nii.gz MJ0001dti2.nii.gz --o MJ0001dti12.nii.gz would it work to concat the two half brain niftis into one file and analyze that with tracula? (I will concat the bvec and bvals files too) would this cause problems doing it this way? Thanks Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 ___ 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] Very different results between 5.1.0 and 5.2.0
Daniel, We're repeating our paired-analysis of thickness measures between 5.1 and 5.2. In the meantime, to check for correctness, open the brain.finalsurfs.mgz file with the surfaces overlayed, and check the intensity value of the voxels which appear to be non-cortical 'black spaces', relative to neighboring gm voxels. ignore the aseg.mgz gm voxels, as those are not accurate (ie, dont load aseg.mgz when inspecting surfaces, or at least turn if off when inspecting gm regionsits still handy to see where hippocampus sits). Nick On Wed, 2013-04-10 at 11:11 +, Yang, Daniel wrote: Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical black spaces within pial surfaces, compared to FS 5.1? I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel ___ 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] FS-FAST motion correction / register
One of my subjects exhibited motion during the middle time point of one the functional scans. FS-FAST then reads all other time points as having a significant amount of motion because the subject was out of place during the point that is marked as the origin. Is there some way that I can set a different time point? I am worried that there will be some over-correction for motion that isn't really there because my middle time point it out of an anomaly. -Ronny attachment: fsfast.mc.run010.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.
Re: [Freesurfer] FS-FAST motion correction / register
Hi Ronny, the time point used to as the template is hard-coded to be the middle time point. If this is just the case for one subject, a silly but simple solution is to remove the last two time points from the time series. This will cause the middle time point to shift to an earlier time point. Would this work? doug On 04/10/2013 01:48 PM, preci...@nmr.mgh.harvard.edu wrote: One of my subjects exhibited motion during the middle time point of one the functional scans. FS-FAST then reads all other time points as having a significant amount of motion because the subject was out of place during the point that is marked as the origin. Is there some way that I can set a different time point? I am worried that there will be some over-correction for motion that isn't really there because my middle time point it out of an anomaly. -Ronny ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FS-FAST motion correction / register
If anything I was thinking of removing the first two time points, as those are going to get nixed anyway. I was hoping it wouldn't come to that but i f that's the only way... -Ronny Hi Ronny, the time point used to as the template is hard-coded to be the middle time point. If this is just the case for one subject, a silly but simple solution is to remove the last two time points from the time series. This will cause the middle time point to shift to an earlier time point. Would this work? doug On 04/10/2013 01:48 PM, preci...@nmr.mgh.harvard.edu wrote: One of my subjects exhibited motion during the middle time point of one the functional scans. FS-FAST then reads all other time points as having a significant amount of motion because the subject was out of place during the point that is marked as the origin. Is there some way that I can set a different time point? I am worried that there will be some over-correction for motion that isn't really there because my middle time point it out of an anomaly. -Ronny ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] Comparing HRF undershoots between conditions
Hi, I want to generate a map to show the significant difference between HRF undershoot (negative peak of activity) between two conditions independent from the positive peak. Is there anyway, to generate this map? P.S.: Please note that I need a map and not a time course graph. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Comparing HRF undershoots between conditions
Hi Shahin, there are several ways that you could do it. The one that immediately comes to mind is to use an FIR and then test for a difference at a particular post stimulus time point. doug On 04/10/2013 03:54 PM, SHAHIN NASR wrote: Hi, I want to generate a map to show the significant difference between HRF undershoot (negative peak of activity) between two conditions independent from the positive peak. Is there anyway, to generate this map? P.S.: Please note that I need a map and not a time course graph. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fwd: Comparing HRF undershoots between conditions
That's the problem Doug. I have already generated the FIR model but how can I show the sig MAP for one particulat time point. What are the other ways? On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Shahin, there are several ways that you could do it. The one that immediately comes to mind is to use an FIR and then test for a difference at a particular post stimulus time point. doug On 04/10/2013 03:54 PM, SHAHIN NASR wrote: Hi, I want to generate a map to show the significant difference between HRF undershoot (negative peak of activity) between two conditions independent from the positive peak. Is there anyway, to generate this map? P.S.: Please note that I need a map and not a time course graph. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Rejoindre mon réseau sur LinkedIn
LinkedIn Sima Chalavi souhaite se connecter à vous sur LinkedIn : -- Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Sima Chalavi http://www.linkedin.com/e/-qq80um-hfd0ug20-5o/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59qYFaT9QmQ47Ub3yw/blk/I427517471_65/3wOtCVFbmdxnSVFbm8JrnpKqlZJrmZzbmNJpjRQnOpBtn9QfmhBt71BoSd1p65Lr6lOfPkSnP4Td3sNdjsOd4ALen1Fsmx4en4Ldz0TcPAPdjoPcz4LrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=falsetok=1BZKYjafcQj5I1 Voir le profil de Sima Chalavi http://www.linkedin.com/e/-qq80um-hfd0ug20-5o/rso/245935493/G7CW/name/66471168_I427517471_65/?hs=falsetok=3vNr3vrw4Qj5I1 -- Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hfd0ug20-5o/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=falsetok=2jMrhiThsQj5I1 (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. ___ 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] Comparing HRF undershoots between conditions
If you run tkmedit-sess, then open the overlay configuration window, then advance the time point to the delay you want. Otherwise, you can create a contrast where you just look at the delay you want. To do this, run mkcontrast-sess with -setwdelays and specify 0 for all delays and 1 for the delay you want to see. doug On 04/10/2013 04:15 PM, SHAHIN NASR wrote: That's the problem Doug. I have already generated the FIR model but how can I show the sig MAP for one particulat time point. What are the other ways? On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Shahin, there are several ways that you could do it. The one that immediately comes to mind is to use an FIR and then test for a difference at a particular post stimulus time point. doug On 04/10/2013 03:54 PM, SHAHIN NASR wrote: Hi, I want to generate a map to show the significant difference between HRF undershoot (negative peak of activity) between two conditions independent from the positive peak. Is there anyway, to generate this map? P.S.: Please note that I need a map and not a time course graph. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions
yes, that is what you want. The only other way that comes to mind is to model each event type as two event types one delayed relative to the other. Then model the responseto each as a gamma. If the delay is right, then the first gamma should model the main positive response and the second gamma will model the negative response. both will be independent from the other. doug On 04/10/2013 05:00 PM, sha...@nmr.mgh.harvard.edu wrote: I think I figured it out but I want to double check. I am generating group-average map for my subjects using isxconcat-sess command which generates ces maps for each time frame. I think these maps are what I wanted. Right? If you still have other solutions that you think may generate more reliable results, I am eager to know. For instance, is there anyway to fit a model as we do for spmhrf or fslhrf, but just for the negative peak? Regards That's the problem Doug. I have already generated the FIR model but how can I show the sig MAP for one particulat time point. What are the other ways? On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Shahin, there are several ways that you could do it. The one that immediately comes to mind is to use an FIR and then test for a difference at a particular post stimulus time point. doug On 04/10/2013 03:54 PM, SHAHIN NASR wrote: Hi, I want to generate a map to show the significant difference between HRF undershoot (negative peak of activity) between two conditions independent from the positive peak. Is there anyway, to generate this map? P.S.: Please note that I need a map and not a time course graph. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Finding adjacent vertices/labels
Hi Chris the easiest way would be to load the surfaces and parcellation in in matlab and look for adjacency that way Bruce On Wed, 10 Apr 2013, Chris McNorgan wrote: Hello Freesurfers, I was wondering if there is information embedded in the annotation/label files that could be used to determine whether two labels represent anatomically adjacent regions? For example, I have parcellated a bunch of participants using connectomemapper into 1000 ROIs. I was just now reading Power et al. (2011), who looked at functional connectivity, but specifically excluded connections between spheroid ROIs that were less than 20mm apart. Analogously, I might wish to exclude connections between adjacent labels, but it seemed that manually creating an adjacency matrix for 1000 regions would be impractical, and a good candidate for an automated approach. I'm just not clear what information such an approach might have to work with. Can the adjacency between two vertices be determined based on their values? If so, one approach might be: for each pair of labels (A,B): get set of vertices within A get set of vertices within B for each vertex pair (Ai, Bj) if Ai and Bj are adjacent, stop, and mark A and B as adjacent Cheers, Chris ___ 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] merging dti data
Hi Jon, I don't know how to make this work, but I'm sure that those commands will not do it. Sorry:( doug On 4/10/13 1:13 PM, Jon Wieser wrote: we captured some dti data. there were 2 runs. we acquired in the axial plane, 2mm slice thickness the first run captured the lower half of the brain, slice locations: I56-S20, and the second run captured the upper half of the brain S16-S92. i have made briks from each of these runs. I can convert the briks to nifti files I want to merge the nifti files together to analyze the data in tracula In the past i have merged data from two dti runs, but each run have covered the entire brain, with the following commands mri_convert MJ0001dti1+orig.BRIK MJ0001dti1.nii.gz mri_convert MJ0001dti2+orig.BRIK MJ0001dti2.nii.gz mri_concat --i MJ0001dti1.nii.gz MJ0001dti2.nii.gz --o MJ0001dti12.nii.gz would it work to concat the two half brain niftis into one file and analyze that with tracula? (I will concat the bvec and bvals files too) would this cause problems doing it this way? Thanks Jon ___ 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.
