[Freesurfer] glm question
Dear FreeSurfer experts, I'm doing some group analyses and I'm a little stocked with this: I have Six Groups (2 Factors, one with three levels and the other one with two levels), and one covariate. I don't know the rule for setting the contrasts for an ANOVA and for the interaction between the two factors regressing out the covariate. I've checked at the FS wiki and found the following contrast for six groups (two factors) and zero covariates. Contrast 6 gender-x-handedness.mtx (interaction between gender and handedness) [0.333 -0.333 -0.333 0.333 0.000 0.000 0.000 0.000 0.000] [0.000 0.000 0.000 0.000 0.000 0.333 -0.333 -0.333 0.333] I don’t understand the rule that has been followed. Can any one help me with this? Bests, Gabriel ___ 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] CUDA comparable to non-CUDA?
Hi FreeSurfer Experts, Just a quick question: Generally speaking, assuming everything else remains the same, are subjects run through a CUDA-enabled recon-all comparable to subjects run through recon-all without CUDA? Thanks, Marcus Marcus N Schmidt Department of Child Adolescent Psychiatry Erasmus MC Rotterdam, The Netherlands ___ 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] CUDA comparable to non-CUDA?
We assume that. On Tue, Mar 8, 2011 at 09:58, Marcus N Schmidt m.schm...@erasmusmc.nlwrote: Hi FreeSurfer Experts, Just a quick question: Generally speaking, assuming everything else remains the same, are subjects run through a CUDA-enabled recon-all comparable to subjects run through recon-all without CUDA? Thanks, Marcus * Marcus N Schmidt* Department of Child Adolescent Psychiatry Erasmus MC Rotterdam, The Netherlands ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Intensity Problem
Thanks Bruce, The parcellation looks good in general, except that this part of the temporal lobe is consistently missed due to that anomaly. Best, Matt On Fri, Mar 4, 2011 at 7:52 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi matt Does the parcellation look correct? If so you might be ok if you stay away from the affected regions. It's hard to tell from one slice. Cheers Bruce On Mar 3, 2011, at 9:47 PM, Matt Russell russ0...@umn.edu wrote: Dear FreeSurfer Experts, I'm currently working with a data set that seems to have a systematic problem with intensity. I attached an image of a brain with this problem for your reference. As you can see, the unprocessed MRI file has an intensity problem in the temporal lobe, almost like a flashlight is lighting it up. When FreeSurfer processes this part of the brain it fails to detect it. My question is a) is this data still usable? We aren't actually looking for any effects in this area of the brain, but are worried that it is a bigger symptom of problematic data and b) if this data is still usable, is there anything we can do to work around it? Thanks, Matthew Russell IntensityIssueMattRussell.jpg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Custom and Short Term Programs APU Short Term Program Coordinator International Student and Scholar Services 190 Hubert Humphrey Center 301 19th Ave. S. Minneapolis, MN 55455 russ0...@umn.edu ___ 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] Pial view
Hi Everyone, I am hoping to visualize the insula using the pial view in TkSurfer. Is there a way to make the surfaces translucent, or to crop away specific areas? I would like to use the pial view instead of inflated views to do this. Thanks, Allie Rosen, MSc Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto ___ 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] Pial view
I think you can do this in freeview cheers Bruce On Tue, 8 Mar 2011, Allie Rosen wrote: Hi Everyone, I am hoping to visualize the insula using the pial view in TkSurfer. Is there a way to make the surfaces translucent, or to crop away specific areas? I would like to use the pial view instead of inflated views to do this. Thanks, Allie Rosen, MSc Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto ___ 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 problems
Wang, have a look at: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis and also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons which itself has some links explaining the necessity for correcting for multiple comparisons. the newer qdec has the 'simulation' method for correction built-in to it, which is superior to FDR for this kind of analysis. this simulation method calls the freesurfer utility mri_glmfit-sim, described here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ClusterwiseCorrectionforMultipleComparisons in the cluster output data, 'Max' is maximum (log)p-value for that cluster, VtxMax is the vertex where that max was found, NVtxs is the number of vertices in that cluster. n. On Tue, 2011-03-08 at 10:05 +0800, 汪贵宏 wrote: Hi,all: I have several problems about the qdec in freesurfer 5.0. Firstly,can somebody explain the function of the buttons in the qdec's third step (display),such as Set using FDR in the False Discovery Rate ,Monte Carlo Null-Z simulation.If I just let these buttons as the default ,is it right ? Secondly, what does the MAX and VtxMAX and NVtxsmean just as follows,which is output from the teminal. Generating cluster stats using min threshold of 2... Found 5 clusters Contrast: 'rh-Diff-Yes-No-Intercept-thickness', 10fwhm, DOF: 21 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation - --- -- - - -- 1 -3.41598928 51.5031.9 -34.9 46.8 146 postcentral 2 -2.6111 120796 42.3030.5 -6.5 -32.9 79 entorhinal 3 -2.5302 122287 22.2835.4 -68.1 43.1 41 inferiorparietal 42.3762 145773 21.2440.3 22.6 20.6 46 parsopercularis 52.1491 24852 19.94 4.8 -40.1 71.5 55 paracentral Thanks, Wang ___ 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] Cortical thickness in the template space
Hello, We try to look at the two group difference of cortical thickness, but I need the lh(or rh).thickness file, which reported in template space (FS average space), but after run recon-all -all, what I have is only lh.thickness, or rh.thickness, which is in subject's space. Would someone point me where or how I can get them? Thanks. Aize ___ 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] Cortical thickness in the template space
Aize, run: recon-all -s subjid -qcache -measure thickness and this will create files in the /surf dir which sample the thickness data at different smoothing levels onto the fsaverage subject space. n. On Wed, 2011-03-09 at 05:46 +0800, caoaize wrote: Hello, We try to look at the two group difference of cortical thickness, but I need the lh(or rh).thickness file, which reported in template space (FS average space), but after run recon-all -all, what I have is only lh.thickness, or rh.thickness, which is in subject's space. Would someone point me where or how I can get them? Thanks. Aize ___ 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] Newbie - problems compiling project tree
Hi All, I am having some problems compiling freesurfer . I checked out the recent development version from the CVS, ran setup_configure successfully, but upon ./configure, I end up with the following annoying message: checking for nccreate in -lnetcdf... no configure: error: FATAL: netcdf lib not found. Set LDFLAGS or --with-mni-dir. I attempted to install the netcdf-bin and libnetcdf6 packages using Synaptic, but this did not seem to help. How do I continue from here? -- Shay ___ 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] Newbie - problems compiling project tree
libnetcdf-dev or netcdf-dev will do the trick On Tue, Mar 8, 2011 at 19:42, Shay Ohayon shay.oha...@gmail.com wrote: Hi All, I am having some problems compiling freesurfer . I checked out the recent development version from the CVS, ran setup_configure successfully, but upon ./configure, I end up with the following annoying message: checking for nccreate in -lnetcdf... no configure: error: FATAL: netcdf lib not found. Set LDFLAGS or --with-mni-dir. I attempted to install the netcdf-bin and libnetcdf6 packages using Synaptic, but this did not seem to help. How do I continue from here? -- Shay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Newbie - problems compiling project tree
Hi All, OK. Installed those packages, but now I end up with this error: checking for miopen in -lminc... no configure: error: FATAL: minc lib not found. Set LDFLAGS or --with-mni-dir. I installed libminc2-1, libminc-dev and minc-tools, but I still get this error. How do I proceed ? Thanks! -- Shay 2011/3/8 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br: libnetcdf-dev or netcdf-dev will do the trick On Tue, Mar 8, 2011 at 19:42, Shay Ohayon shay.oha...@gmail.com wrote: Hi All, I am having some problems compiling freesurfer . I checked out the recent development version from the CVS, ran setup_configure successfully, but upon ./configure, I end up with the following annoying message: checking for nccreate in -lnetcdf... no configure: error: FATAL: netcdf lib not found. Set LDFLAGS or --with-mni-dir. I attempted to install the netcdf-bin and libnetcdf6 packages using Synaptic, but this did not seem to help. How do I continue from here? -- Shay ___ 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] Aparc Cutting?
I've never used that, but you can use mris_annotation2label to break the annotation in to individual labels,then use mris_label2annot to put the ones you want back together. doug On 3/8/11 10:13 PM, Allie Rosen wrote: Hi Everyone, I'm wondering if it is possible to use the cut function in TkSurfer to delete specific atlas annotations. For example, can I create a label of my specific area of interest, inverse the label to highlight the rest of the brain, and then either cut out these regions or make them transparent? Can anyone help me out? Thank you, Allie Rosen, MSc Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto ___ 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] Miao Wen wants to stay in touch on LinkedIn
LinkedIn Miao Wen souhaite se connecter à vous sur LinkedIn : -- Freesurfer, I'd like to add you to my professional network on LinkedIn. - Miao Wen Accepter l'invitation de Miao Wen http://www.linkedin.com/e/-qq80um-gl1us5y3-j/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59qYFaT9QmQ47Ub3yw/blk/I18596485_65/pmpxnSRJrSdvj4R5fnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_djpvdjwQdzARe359bQdyt6gRj4dfbPgRc34NczASd38LrCBxbOYWrSlI/EML_comm_afe/ Voir l'invitation de Miao Wen http://www.linkedin.com/e/-qq80um-gl1us5y3-j/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59qYFaT9QmQ47Ub3yw/blk/I18596485_65/0RdBYRe3gSejkUckALqnpPbOYWrSlI/svi/ -- SAVEZ-VOUS que votre profil LinkedIn vous permet de contrôler votre image professionnelle sur le Web ? Si vous le rendez public, votre profil LinkedIn apparaîtra quand un internaute effectuera une recherche en ligne sur votre nom. Soignez votre image sur le Web ! http://www.linkedin.com/e/-qq80um-gl1us5y3-j/ewp/inv-22/ -- (c) 2011, LinkedIn Corporation___ 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.
