Re: [Freesurfer] Volume in hippocampus and its subfields
Hi Zih-Kai, the subfield and main FreeSurfer streams are different and therefore give different results. On average, the volumes estimated by the subfield stream will be lower, but very highly correlated with those from the main FreeSurfer stream. I hope this helps! /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: 高子凱 clandestine1...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, January 16, 2015 5:24:40 AM Subject: [Freesurfer] Volume in hippocampus and its subfields Dear All, I recently begin to use the latest FreeSurfer version to segment subcortical and hippocampus subfields in human brain of MR image. The result shows left hippocampus volume is 4332.6 mm^3 and volumeInVoxels of hippocampus subfields as below: Left-Hippocampus: 3017.11 left_presubiculum: 4103.92 left_CA1: 2247.6 left_CA2_3: 6919.65 left_fimbria: 597.982 left_subiculum: 5209.91 left_CA4_DG: 3914.19 left_hippocampal_fissure: 327.23 After I sum of the voxels and divided it by 8 ( each voxel is of the size 0.5x0.5x0.5mm^3 ), the result (3929.199 mm^3) is not equal to the hippocampus volume (4332.6 mm^3). I am quite confused how to do so. It would be great if you could advice me. Thanks a lot for your help. I really appreciate it. Beat Regard, ZK -- Zih-Kai Kao Clinical Research Assistant Psychiatry Department of Taipei Veterans General Hospital No.201, Sec. 2, Shipai Rd., Beitou District, Taipei City, Taiwan 11217, R.O.C. tel:+886-2-28712121#2912 fax:+886-2-28742421 ___ 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] Freesurfer Calculation of Vertex-Wise Area
Hi Bronwyn the surface area at each vertex (I assume you mean vertex and not voxel) is simply the average of the area of the triangles it is attached to. cheers Bruce On Fri, 16 Jan 2015, Bronwyn Overs wrote: Dear Mailing List, I would like to understand how freesurfer calculates the surface area at each voxel to be used in the GLM procedure. Is there a key methods paper that describes this process, and can this method be explained in simple terms? ___ 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] Apply alignment transformation to a surface?
Thanks! I will give this a go. Andrea On Thu, Jan 15, 2015 at 10:16 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: use mri_surf2surf. If you run it with --help you will see several examples. See example 4. You will need a registration which you should already have if can map the volumes. doug On 01/15/2015 11:08 AM, Andrea Grant wrote: Hello, I am comparing segmentations from subjects who have been scanned at 7T and 3T. I'd like to be able to view the T1 image collected at 3T with the surfaces from both the 3T and 7T segmentations. For a given subject, I know how to align the 3T and 7T volume images (e.g., brainmask or T1) and apply the transformation matrix to the cortical and subcortical volume labels (e.g., wmparc.mgz), but I can't figure out how to apply that transformation to the surface files. Do I need to convert the surface files to volume with mri_surf2vol, transform that, and then convert back? I'm interested in ?h.pial, ?h.white in particular, and I use FSL flirt to align the volumes. Thanks, Andrea - Andrea Grant Visual Neuroimaging Technologist Center for Magnetic Resonance Research, University of Minnesota 2021 6th St. SE, Minneapolis, MN 55455, 612-626-4948 gran0...@umn.edu mailto:gran0...@umn.edu umn.edu/~gran0260 http://umn.edu/%7Egran0260 ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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] Problem with a recon edit
Hi Freesurfer team We have been struggling with editing recon for one patient, see the 2 slices attached. The problem is that the surface don't go all the way up to the bottom of the sulci. I had this some times before but usually managed to fix it with editing the wm and the aseg, but this time I couldn't have it work correctly. Would you have a clue to help me on that? I can put the data in some folders if you want to take a look at the entire volumes. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ 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] Viewing QDEC results in tksurfer
Hi Doug, I have set up and run the usual Group Analysis through the command line. I have then run mri_concat output-of-preproc.mgh --mean --o mean.output-of-preproc.mgh to obtain a mean thickness for all subjects included in the preprocessing. I'm now having a problem with visualising this with tksurfer, getting ERROR: could not read header info from T1 or orig in /home/k1204763/images/BRCATLAS/FREESURFER.v5.3.0/GroupAnalysis/mri Presumably this is because all of the T1/orig are stored in each subjects data file and I'm not trying to look at a specific subject. Is there a way to get around this problem? Best wishes, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve gr...@nmr.mgh.harvard.edu Sent: 15 January 2015 16:56 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer QDEC will not produce mean maps for each group. If this is something you want to do, you will need to do it in the command-line group analysis stream. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis On 01/15/2015 05:25 AM, Worker, Amanda wrote: Hi, I am currently only able to open a thickness map for a single subject using tksurfer SUBJECT lh inflated. I can use the analysis figures from qdec, but I'd really like to plot the mean thickness for a particular group to compare to others visually. Is this possible? Thanks, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve gr...@nmr.mgh.harvard.edu Sent: 14 January 2015 23:46 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer what is your tksurfer command line? On 01/13/2015 07:12 AM, Worker, Amanda wrote: Hi, Is it possible to view the results of a qdec analysis (correlation with a single continuous group) in tksurfer? I am currently unable to open it and I'm getting an error saying could not open file */mri/transforms/talairach.xfm ..no such file or directory . Is this a file that is not created with qdec? I'm also trying to visualise group mean thickness' in different colours to allow difference between groups, that are not significant in the analysis to be visualised. I cannot find any advice on how to do this, is this something it's possible to do using either freeview of tksurfer? Thanks, Amanda ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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
Re: [Freesurfer] Problem with a recon edit
Hi Celine hard to tell from the slices. Are there voxels labeled ventricle there? If so, you need to correct the aseg. If not, it's probably a topological defect that is fixed incorrectly. If you upload the subject we'll take a look Bruce On Fri, 16 Jan 2015, Celine Louapre wrote: Sorry forgot the attachement :-) Hi Freesurfer team We have been struggling with editing recon for one patient, see the 2 slices attached. The problem is that the surface don't go all the way up to the bottom of the sulci. I had this some times before but usually managed to fix it with editing the wm and the aseg, but this time I couldn't have it work correctly. Would you have a clue to help me on that? I can put the data in some folders if you want to take a look at the entire volumes. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ 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] help-convert vome index to vertex numbe in surface
hello I have some points defined in volume (RAS coordination) and now I want to see these locations (vertex number) on surface. I don't know how to do it. I can see one point using tkmedit, input the coordination and save point and then in tksurfer, go to saved point, so I can get the vertex number. However, now i have so many subjects, and so many points defined in volume, how can i find these vertex numbers soon? Thanks in advance! Meiling ___ 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] Problem with a recon edit
Thanks Bruce The aseg is correct, no ventricule labeled there (I was used to that) that I could see. I couldn't find the topological defect indeed, and what is strange if that the wrong surface on the right hemisphere were correct after autorecon2 but incorrect after autorecon3. The problem on the left hemisphere was already present after autorecon2. I have uploaded the recon directory there: https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/32464/1/2115a25100be43906c26359fbbd1ed08 Thank you again :-) Celine On Fri, 2015-01-16 at 11:03 -0500, Bruce Fischl wrote: Hi Celine hard to tell from the slices. Are there voxels labeled ventricle there? If so, you need to correct the aseg. If not, it's probably a topological defect that is fixed incorrectly. If you upload the subject we'll take a look Bruce On Fri, 16 Jan 2015, Celine Louapre wrote: Sorry forgot the attachement :-) Hi Freesurfer team We have been struggling with editing recon for one patient, see the 2 slices attached. The problem is that the surface don't go all the way up to the bottom of the sulci. I had this some times before but usually managed to fix it with editing the wm and the aseg, but this time I couldn't have it work correctly. Would you have a clue to help me on that? I can put the data in some folders if you want to take a look at the entire volumes. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ 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 ___ 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] Convert volume index to vertex number in surface
hello I have some points defined in volume (RAS coordination) and now I want to see these locations (vertex number) on surface. I don't know how to do it. I can see one point using tkmedit, input the coordination and save point and then in tksurfer, go to saved point, so I can get the vertex number. However, now i have so many subjects, and so many points defined in volume, how can i find these vertex numbers soon? Thanks in advance! Meiling ___ 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] Convert volume index to vertex number in surface
Hi Meiling to go from volume points to the surface you pretty much have to search. We speed this up internally by compiling the surface into a spatial lookup table then only searching through the vertices that are in each bin, but there is no easy external interface to that code (although you are welcome to write such a thing). cheers Bruce On Sat, 17 Jan 2015, Meiling Li wrote: hello I have some points defined in volume (RAS coordination) and now I want to see these locations (vertex number) on surface. I don't know how to do it. I can see one point using tkmedit, input the coordination and save point and then in tksurfer, go to saved point, so I can get the vertex number. However, now i have so many subjects, and so many points defined in volume, how can i find these vertex numbers soon? Thanks in advance! Meiling ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon failed with aseg.mgz
Hi All, The recon-all stopped at the step of mri_normalize. The command is: mri_normailze -mprage -noconform -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz. The error massege: assuming input volume is MGH (Van der Kouwe) MP-RAGE. not interpolating and embedding volume to be 256^3… using segmentation for initial intensity normalization, using MR volume brainmask.mgz to mask input volume. reading from norm.mgz, reading from aseg.mgz, mdi_normalize: aseg volume aseg.mgz must be conformed. The aseg.mgz is conformed to minimum voxel size with matrix size: 320 X 320 X 320. Also, the aseg.mgz looks right. any suggestions? thanks in advance. Xiaomin ___ 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] Convert volume index to vertex number in surface
You can create a label with your coordinates in them and then use the --paint feature of mri_label2label doug On 01/16/2015 01:52 PM, Bruce Fischl wrote: Hi Meiling to go from volume points to the surface you pretty much have to search. We speed this up internally by compiling the surface into a spatial lookup table then only searching through the vertices that are in each bin, but there is no easy external interface to that code (although you are welcome to write such a thing). cheers Bruce On Sat, 17 Jan 2015, Meiling Li wrote: hello I have some points defined in volume (RAS coordination) and now I want to see these locations (vertex number) on surface. I don't know how to do it. I can see one point using tkmedit, input the coordination and save point and then in tksurfer, go to saved point, so I can get the vertex number. However, now i have so many subjects, and so many points defined in volume, how can i find these vertex numbers soon? Thanks in advance! Meiling ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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] Viewing QDEC results in tksurfer
what is your command line? On 01/16/2015 11:02 AM, Worker, Amanda wrote: Hi Doug, I have set up and run the usual Group Analysis through the command line. I have then run mri_concat output-of-preproc.mgh --mean --o mean.output-of-preproc.mgh to obtain a mean thickness for all subjects included in the preprocessing. I'm now having a problem with visualising this with tksurfer, getting ERROR: could not read header info from T1 or orig in /home/k1204763/images/BRCATLAS/FREESURFER.v5.3.0/GroupAnalysis/mri Presumably this is because all of the T1/orig are stored in each subjects data file and I'm not trying to look at a specific subject. Is there a way to get around this problem? Best wishes, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve gr...@nmr.mgh.harvard.edu Sent: 15 January 2015 16:56 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer QDEC will not produce mean maps for each group. If this is something you want to do, you will need to do it in the command-line group analysis stream. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis On 01/15/2015 05:25 AM, Worker, Amanda wrote: Hi, I am currently only able to open a thickness map for a single subject using tksurfer SUBJECT lh inflated. I can use the analysis figures from qdec, but I'd really like to plot the mean thickness for a particular group to compare to others visually. Is this possible? Thanks, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve gr...@nmr.mgh.harvard.edu Sent: 14 January 2015 23:46 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer what is your tksurfer command line? On 01/13/2015 07:12 AM, Worker, Amanda wrote: Hi, Is it possible to view the results of a qdec analysis (correlation with a single continuous group) in tksurfer? I am currently unable to open it and I'm getting an error saying could not open file */mri/transforms/talairach.xfm ..no such file or directory . Is this a file that is not created with qdec? I'm also trying to visualise group mean thickness' in different colours to allow difference between groups, that are not significant in the analysis to be visualised. I cannot find any advice on how to do this, is this something it's possible to do using either freeview of tksurfer? Thanks, Amanda ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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 -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Re: [Freesurfer] Freesurfer Calculation of Vertex-Wise Area
I don't have a core paper on the area mapping (which is more complicated than mapping thickness). Anderson Winkler wrote a paper on the subject, but we are not using his method. Our method is relatively simple. Each vertex in fsaverage is mapped back to the individual to find the closest vertex. The thickness or area at this vertex is then assigned to the vertex in fsaverage. There will be some fsaverage vertices that map to the same vertex in the individual. For thickness, this is not a problem. For area or volume, we divide the value by the number of fsaverage vertices that share the individual vertex to preserve the total. This may leave some vertices in the individual that were never a closest vertex. We loop through these vertices and do a reverse map back to fsaverage to find the closest vertex. These fsaverage vertices will then have multiple vertices from the individual. For thickness, we compute the mean of the source vertices. For area or volume we compute the sum (must preserve the total). make sense? doug On 01/16/2015 12:00 AM, Bronwyn Overs wrote: I meant that as well as the mapping of the area to the average space. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 16/01/2015 3:58 pm, Douglas Greve wrote: The computation is pretty simple, it is just the average of the area of the surrounding triangle. Is that what you mean or do you mean the mapping of said area to the average space? doug On 1/15/15 11:37 PM, Bronwyn Overs wrote: Dear Mailing List, I would like to understand how freesurfer calculates the surface area at each voxel to be used in the GLM procedure. Is there a key methods paper that describes this process, and can this method be explained in simple terms? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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
Re: [Freesurfer] Freesurfer Calculation of Vertex-Wise Area
Yes that makes perfect sense. Thanks very much. On 17 Jan 2015, at 7:01, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I don't have a core paper on the area mapping (which is more complicated than mapping thickness). Anderson Winkler wrote a paper on the subject, but we are not using his method. Our method is relatively simple. Each vertex in fsaverage is mapped back to the individual to find the closest vertex. The thickness or area at this vertex is then assigned to the vertex in fsaverage. There will be some fsaverage vertices that map to the same vertex in the individual. For thickness, this is not a problem. For area or volume, we divide the value by the number of fsaverage vertices that share the individual vertex to preserve the total. This may leave some vertices in the individual that were never a closest vertex. We loop through these vertices and do a reverse map back to fsaverage to find the closest vertex. These fsaverage vertices will then have multiple vertices from the individual. For thickness, we compute the mean of the source vertices. For area or volume we compute the sum (must preserve the total). make sense? doug On 01/16/2015 12:00 AM, Bronwyn Overs wrote: I meant that as well as the mapping of the area to the average space. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 16/01/2015 3:58 pm, Douglas Greve wrote: The computation is pretty simple, it is just the average of the area of the surrounding triangle. Is that what you mean or do you mean the mapping of said area to the average space? doug On 1/15/15 11:37 PM, Bronwyn Overs wrote: Dear Mailing List, I would like to understand how freesurfer calculates the surface area at each voxel to be used in the GLM procedure. Is there a key methods paper that describes this process, and can this method be explained in simple terms? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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
