Re: [Freesurfer] Segmentation problems
Hi Tetiana, do you mean the bit of skull left over that is misclassified? I wouldn't worry about it unless it causes the ?h.white/?h.pial surfaces to be inaccurate. In general we use the surface-based measures to estimate gray/white morphometry and the aseg for everything else. It is a minor skull strip failure and you could either fix it by manually erasing it from the brainmask.mgz or trying to mess with the watershed/gcut. cheers Bruce On Mon, 31 Jan 2011, Tetiana Dadakova wrote: Dear FreeSurfer users, I run a recon-all -all for one of my subjects. When I check the segmentation, it looks incorrect (see attached picture). What can be the problem? At which step can I change something? Should I do manual correction? Thank you, Tetiana. ___ 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] white matter volume and qdec
Dear Freesufer experts,I would like to do the group comparison of white matter volume in various white matter regions base on white matter parcellation. I have no idea about how to do that. Is it the same as cortical thickness comparison in qdec ? could any one give some guide about how to do that ? thank in advancebestJLH--- 本郵件來自HiNet WebMail ---___ 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] white matter volume and qdec
You can use the data in the wmparc.stats file. You can load that as a spreadsheet into any stats program (eg, SPSS). doug t...@ms36.hinet.net wrote: Dear Freesufer experts, I would like to do the group comparison of white matter volume in various white matter regions base on white matter parcellation. I have no idea about how to do that. Is it the same as cortical thickness comparison in qdec ? could any one give some guide about how to do that ? thank in advance best JLH --- 本郵件來自HiNet WebMail --- ___ 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] Regression: Activation as a function of condition
Hi Doug and Freesurfers, Now that I have re-processed some of my data in Stable 5, I would like to re-open a previous problem I was trying to tackle: We are using the Sternberg Item Recognition Paradigm in our study, which involves the memorization and recognition of groups of 1, 3, 5, and 7 letters. Each run has two sets of each condition (load). We want to determine if any regions of the brain activate in a linear pattern with increased task load (# of letters). I have already done regression analyses using genotype, but that was between subjects, while this analysis would be within subjects. Does anyone know how I could structure an analysis that would allow me to look at this? Is this something I have to do at the mkanalysis-sess level? I had tried doing this in Stable 4 using the method described here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-December/016557.html However, I was unable to generate the desired results, so I decided to switch over to Stable 5 as suggested. Thanks, Adam Original Message Subject: Re: [Freesurfer] Regression: Activation as a function of condition From:Douglas N Greve gr...@nmr.mgh.harvard.edu Date:Tue, January 11, 2011 11:52 am To: Adam Nitenson niten...@nmr.mgh.harvard.edu -- You don't need to re-unpack. you don't run recon-all on the functional, only the anatomicals. Adam Nitenson wrote: So this means I will have to start at the unpacksdcmdir command and then recon-all to rerun the functionals? You don't need to re-run the anatomicals, but you will need to rerun the functionals. doug Adam Nitenson wrote: Hmm...it appears that we might need to make the transition over to Stable 5 then. Would I have to reprocess all Stable 4 subjects again in Stable 5 (including the whole recon-all from bourget) process, or is there some sort of jumping off point from which I can start using the new stable? Thanks, Adam you can't do it in stable4, but you can in stable 5. doug Adam Nitenson wrote: Hello Freesurfers, We are using the Sternberg Item Recognition Paradigm in our study, which involves the memorization and recognition of groups of 1, 3, 5, and 7 letters. Each run has two sets of each condition (load). We want to determine if any regions of the brain activate in a linear pattern with increased task load. I have already done regression analyses using genotype, but that was between subjects, while this analysis would be within subjects. Does anyone know how I could structure an analysis (STABLE 4) that would allow me to look at this? Is this something I have to do at the mkanalysis-sess level? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ 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 Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital -- 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 Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital -- 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 Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ 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] Regression: Activation as a function of condition
what do you mean that you were not able to get the desired result? doug Adam Nitenson wrote: Hi Doug and Freesurfers, Now that I have re-processed some of my data in Stable 5, I would like to re-open a previous problem I was trying to tackle: We are using the Sternberg Item Recognition Paradigm in our study, which involves the memorization and recognition of groups of 1, 3, 5, and 7 letters. Each run has two sets of each condition (load). We want to determine if any regions of the brain activate in a linear pattern with increased task load (# of letters). I have already done regression analyses using genotype, but that was between subjects, while this analysis would be within subjects. Does anyone know how I could structure an analysis that would allow me to look at this? Is this something I have to do at the mkanalysis-sess level? I had tried doing this in Stable 4 using the method described here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-December/016557.html However, I was unable to generate the desired results, so I decided to switch over to Stable 5 as suggested. Thanks, Adam Original Message Subject: Re: [Freesurfer] Regression: Activation as a function of condition From:Douglas N Greve gr...@nmr.mgh.harvard.edu Date:Tue, January 11, 2011 11:52 am To: Adam Nitenson niten...@nmr.mgh.harvard.edu -- You don't need to re-unpack. you don't run recon-all on the functional, only the anatomicals. Adam Nitenson wrote: So this means I will have to start at the unpacksdcmdir command and then recon-all to rerun the functionals? You don't need to re-run the anatomicals, but you will need to rerun the functionals. doug Adam Nitenson wrote: Hmm...it appears that we might need to make the transition over to Stable 5 then. Would I have to reprocess all Stable 4 subjects again in Stable 5 (including the whole recon-all from bourget) process, or is there some sort of jumping off point from which I can start using the new stable? Thanks, Adam you can't do it in stable4, but you can in stable 5. doug Adam Nitenson wrote: Hello Freesurfers, We are using the Sternberg Item Recognition Paradigm in our study, which involves the memorization and recognition of groups of 1, 3, 5, and 7 letters. Each run has two sets of each condition (load). We want to determine if any regions of the brain activate in a linear pattern with increased task load. I have already done regression analyses using genotype, but that was between subjects, while this analysis would be within subjects. Does anyone know how I could structure an analysis (STABLE 4) that would allow me to look at this? Is this something I have to do at the mkanalysis-sess level? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ 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 Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital -- 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 Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital -- 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 Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ 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
[Freesurfer] Phantom data
Hi Bruce, Nick, Doug and others: I have Phantom data from around 900 scans collected across 5 sites in the US. Does FS have a way of processing Phantom data. Thanks much, Alan Alan Francis Beth Israel Deaconess Medical Center ___ 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] Phantom data
Hi Alan what kind of phantom? And what would you want to do with it? Bruce On Mon, 31 Jan 2011, Alan Francis wrote: Hi Bruce, Nick, Doug and others: I have Phantom data from around 900 scans collected across 5 sites in the US. Does FS have a way of processing Phantom data. Thanks much, Alan Alan Francis Beth Israel Deaconess Medical Center ___ 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] Phantom data
Hi Bruce: This is an ADNI (Alzheimer's Disease Neuroimaging Initiative) Phantom principally used for structural T1s. The scans have been acquired over 5 sites all over the US on different 3T scanners (Siemens. Philips, GE etc). Basically we are trying to morphometrically evaluate Phantom data to look for inconsistencies between scanners. thanks, Alan On Mon, Jan 31, 2011 at 1:07 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Alan what kind of phantom? And what would you want to do with it? Bruce On Mon, 31 Jan 2011, Alan Francis wrote: Hi Bruce, Nick, Doug and others: I have Phantom data from around 900 scans collected across 5 sites in the US. Does FS have a way of processing Phantom data. Thanks much, Alan Alan Francis Beth Israel Deaconess Medical Center 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] Phantom data
Do you mean a phantom with the uniform grid of beads? I don't think that we had anything that would process that. We mainly just visualized it before and after gradient unwarping. doug Alan Francis wrote: Hi Bruce: This is an ADNI (Alzheimer's Disease Neuroimaging Initiative) Phantom principally used for structural T1s. The scans have been acquired over 5 sites all over the US on different 3T scanners (Siemens. Philips, GE etc). Basically we are trying to morphometrically evaluate Phantom data to look for inconsistencies between scanners. thanks, Alan On Mon, Jan 31, 2011 at 1:07 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Alan what kind of phantom? And what would you want to do with it? Bruce On Mon, 31 Jan 2011, Alan Francis wrote: Hi Bruce, Nick, Doug and others: I have Phantom data from around 900 scans collected across 5 sites in the US. Does FS have a way of processing Phantom data. Thanks much, Alan Alan Francis Beth Israel Deaconess Medical Center 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 -- 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
Re: [Freesurfer] Regression: Activation as a function of condition
The Something-vs-fix of the original paradigm will not relate to the 2-v-fix of the slope test, though they should look something like the 1-v-fix of the slope test. Have you looked at that? The 2-v-fix will look more like a difference in the loads from the original (eg, 7-1). doug Adam Nitenson wrote: The supposed load regression map that I generated did not make sense given the maps of the individual loads vs fix. I attached the original paradigm (run1.par), the slope paradigm which I tried to adapt from the other thread (SIRP_Run1_LoadSlopeTest.par) and an image showing the 1vfix, 3vfix, 5vfix, and 7vfix images from the original paradigm, as well as a large 2vFix image from the new paradigm, which I thought would have shown the within subjects regression (condition 2 being the weighted loads). Desired results was a poor description...it is more that the results do not seems to represent the load regression based on the individual load maps. -Adam what do you mean that you were not able to get the desired result? doug Adam Nitenson wrote: Hi Doug and Freesurfers, Now that I have re-processed some of my data in Stable 5, I would like to re-open a previous problem I was trying to tackle: We are using the Sternberg Item Recognition Paradigm in our study, which involves the memorization and recognition of groups of 1, 3, 5, and 7 letters. Each run has two sets of each condition (load). We want to determine if any regions of the brain activate in a linear pattern with increased task load (# of letters). I have already done regression analyses using genotype, but that was between subjects, while this analysis would be within subjects. Does anyone know how I could structure an analysis that would allow me to look at this? Is this something I have to do at the mkanalysis-sess level? I had tried doing this in Stable 4 using the method described here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-December/016557.html However, I was unable to generate the desired results, so I decided to switch over to Stable 5 as suggested. Thanks, Adam Original Message Subject: Re: [Freesurfer] Regression: Activation as a function of condition From:Douglas N Greve gr...@nmr.mgh.harvard.edu Date:Tue, January 11, 2011 11:52 am To: Adam Nitenson niten...@nmr.mgh.harvard.edu -- You don't need to re-unpack. you don't run recon-all on the functional, only the anatomicals. Adam Nitenson wrote: So this means I will have to start at the unpacksdcmdir command and then recon-all to rerun the functionals? You don't need to re-run the anatomicals, but you will need to rerun the functionals. doug Adam Nitenson wrote: Hmm...it appears that we might need to make the transition over to Stable 5 then. Would I have to reprocess all Stable 4 subjects again in Stable 5 (including the whole recon-all from bourget) process, or is there some sort of jumping off point from which I can start using the new stable? Thanks, Adam you can't do it in stable4, but you can in stable 5. doug Adam Nitenson wrote: Hello Freesurfers, We are using the Sternberg Item Recognition Paradigm in our study, which involves the memorization and recognition of groups of 1, 3, 5, and 7 letters. Each run has two sets of each condition (load). We want to determine if any regions of the brain activate in a linear pattern with increased task load. I have already done regression analyses using genotype, but that was between subjects, while this analysis would be within subjects. Does anyone know how I could structure an analysis (STABLE 4) that would allow me to look at this? Is this something I have to do at the mkanalysis-sess level? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ 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 Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital -- 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 Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital --
[Freesurfer] Manual editing of skull strip and mri_segstats
Hi, I'm new to Freesurfer and am trying to process some data for the first time. I have two questions: 1. I have done some manual editing of the brainmask for skullstripping, saving the edits using 'Save As' and the default names. This seems to create a new group of files separate from the brianmask, in the mri subdirectory. Are these edits incorporated in the brainmask when autorecon2 and autorecon3 are run? I ask because the pial surfaces viewed using tkmedit after processing is complete often extends into the dura and unstripped skull that remains visible on the brainmask, even though it was removed in manual editing. Should I be using 'Save' instead of 'Save as' after editing? 2. For then initial analysis of my data, I would like to create a table of intracranial volume, brain parenchymal volume, gray matter volume and white matter volume. I've tries using the following command line: mri_segstats --sum TableFileName.sum --pv $SUBJECTS_DIR/Subject/mri/norm.mgz --ctab-default --surf-ctxgmwm --etiv $SUBJECTS_DIR/Subject/mri/transforms/talairach.xfm However, this fails with the error: unknown option --surf-ctxgmwm. What have I missed? Can you recommend another way to get this information? I have also tried asegstats2table as well, but intracranial volume was not included in the table. Thank you for any assistance or suggestions. Kind regards, Cheryl ___ 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] Manual editing of skull strip and mri_segstats
Hi Cheryl, 1) Yes, just use save not save as 2) this information is already generated and can be found in the aseg.stats in each subject's stats dir. Some of the information is at the top of that file. On Mon, 31 Jan 2011, Cheryl McCreary wrote: Hi, I'm new to Freesurfer and am trying to process some data for the first time. I have two questions: 1. I have done some manual editing of the brainmask for skullstripping, saving the edits using 'Save As' and the default names. This seems to create a new group of files separate from the brianmask, in the mri subdirectory. Are these edits incorporated in the brainmask when autorecon2 and autorecon3 are run? I ask because the pial surfaces viewed using tkmedit after processing is complete often extends into the dura and unstripped skull that remains visible on the brainmask, even though it was removed in manual editing. Should I be using 'Save' instead of 'Save as' after editing? 2. For then initial analysis of my data, I would like to create a table of intracranial volume, brain parenchymal volume, gray matter volume and white matter volume. I've tries using the following command line: mri_segstats --sum TableFileName.sum --pv $SUBJECTS_DIR/Subject/mri/norm.mgz --ctab-default --surf-ctxgmwm --etiv $SUBJECTS_DIR/Subject/mri/transforms/talairach.xfm However, this fails with the error: unknown option --surf-ctxgmwm. What have I missed? Can you recommend another way to get this information? I have also tried asegstats2table as well, but intracranial volume was not included in the table. Thank you for any assistance or suggestions. Kind regards, Cheryl ___ 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] loading data to matlab?
Hi everyone, A sort of continuation of an old topic: I am able to load data into matlab (actually, I now plot the patches in Matlab, in order to be able to control the color myself, works great), but now I want to be able to get the x, y, z coordinates of the original data back. For example, if my functional was 64 x 64 x 18, I want to know the mapping from that space to my flattened/inflated brain. The reason I want to know this is because I have some additional info per voxel, which I want to be able to show/pop up if I click at a spot in the flattened/inflated representation. So, I have all the files already in matlab, now I just need to know how this conversion works. Specifying -noreshape apparently isn't the entire story. Thanks a lot in advance, kind regards, Frank ___ 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.
