[Freesurfer] mesh_vertex_nearest and white matter segmentation
Hi list, I've got to questions: 1) mesh_vertex_nearest matlab script takes the vertices from a surface a matrix of points in 3D Cartesian coordinates system. Is it correct if I choose points in the Scanner RAS Space as input for this script? I cannot figure out by the description of the tool. 2) I've some points in the brain volume and I'd like to understand if they belongs to white or to grey matter is it possible to classify them (white against grey) using some freesurfer tool? I can find anything in previous email in the list. I'm sorry if the questions has been previously answered. Cheers, g. -- In a world without wall, how needs WINDOWS?? ___ 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] best orientation of t1 images for recon-all
Dear all, we acquired mprage images of a Siemens tim-Trio scanner and converted the DICOMs into nifti-Format for VBM and manual Morphometry. Nifti images were automatically co-registered with the MNI Standard brain in SPM8 by changing the header information. No reslicing was performed. We noticed differences in volumes in the aseg_stats_tables depending on the initial orientation of the individual brain. Is there a standard procedure to optimally reorient the images before processing the recon-all analysis? Is it better to use reoriented images that have been resliced or is it sufficient to change only the header information? Is it advisable to reorient the anatomical images manually to AC-PC before running recon-all? Thanks in advance for your help, Simon ___ 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] best orientation of t1 images for recon-all
Hi Simon We did a study of this with the Oasis data and found it didn't make much difference Bruce On Feb 9, 2011, at 6:16 AM, simon maier wrote: > Dear all, > > we acquired mprage images of a Siemens tim-Trio scanner and converted > the DICOMs into nifti-Format for VBM and manual Morphometry. Nifti > images were automatically co-registered with the MNI Standard brain in > SPM8 by changing the header information. No reslicing was performed. We > noticed differences in volumes in the aseg_stats_tables depending on the > initial orientation of the individual brain. Is there a standard > procedure to optimally reorient the images before processing the > recon-all analysis? Is it better to use reoriented images that have been > resliced or is it sufficient to change only the header information? Is > it advisable to reorient the anatomical images manually to AC-PC before > running recon-all? > > Thanks in advance for your help, > > Simon > ___ > 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] Bad orientation/registration in the motion correction step
Hi! I am having some trouble with the motion correction step when having two volumes (NIFTI files). The average volume has not been determined correctly due to a wrong orientation/registration of the two original volumes (see http://freesurfer.nikolasborrel.com/bad_registration.tif). Is the problem caused by wrong information in the qform matrix in the header of the NIFTI file or by a bad registration in the mri_robust_template or mri_convert functions in the motion correction step? Kind regards Nikolas Borrel-Jensen ___ 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 TrackVis Transforms
Dears expert, I would like to know how can i get the transformation from trackvis to a space Freesurfer?. I have here a link http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms But i don't understand what mean this command, how I could load the file .dtk trk_verts_crs.xyz = trk_verts.xyz / (trkHeader.voxel_size[0], trkHeader.voxel_size[1], trkHeader.voxel_size[2]) and then I have a problem with this command trk_verts_tkreg = CRS2XYZtkreg * trk_verts_crs Could you give an example using a file .dtk? Many thanks Pablo > ___ 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] reg-feat2anat: a problem!
Dear Doug, The determinant sign is negative for both example_func and orig.mgz (-73.6 and -1, respecitively). The files differed also in their format, type, vox2ras-fsl and orientation, but I guess it is ok. My feeling was that flirt is unable to fit the brain given the maximum angle of rotation 90, so I doubled this using: re-feat2anat --dof 6 --maxangle 180 --feat run1.feat --subject xx I tried this on several subjects and the registration looks very good: I would not make it better manually. Can I assume it works now? Cheers, Aga -Ursprüngliche Nachricht- Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Gesendet: Mo 2011-02-07 19:36 An: Burzynska, Aga Cc: 'freesurfer@nmr.mgh.harvard.edu' Betreff: Re: [Freesurfer] reg-feat2anat: a problem! That is not a problem. By "anatomical" I meant the FreeSurfer anatomical (eg, orig.mgz) doug Agnieszka Burzynska wrote: > Dear Doug, > Thank you a lot! > Our feat data is always nifti, but anatomical FSL data is sometimes in the > analyze format. Is this already a problem? > > I will now check the rest. > > Thank you, cheers, > Aga > > > On 2/7/11 4:35 PM, "Douglas N Greve" wrote: > > >> Hi Aga, are you using nifti? If analyze, that could be the problem. Do >> your functionals and anatomicals have a different sign to their >> determinants (you can check with mri_info). In principle, reg-feat2anat >> should handle this but in some cases it does not. The 5.1 version will >> handle it properly. If they do have the same sign, then look through the >> log file and find the flirt command. Run that command by itself (you may >> need to run reg-feat2anat with --nocleanup to keep it from deleting the >> files). If that fails, then contact the FSL people >> >> doug >> >> Agnieszka Burzynska wrote: >> >>> Dear all, >>> I am using the command reg-feat2anat to transform functional data >>> pre-processed in FSL to the anatomical image in Freesurfer. >>> >>> As suggested, I check the registration with reg-feat2anat --feat >>> run2.feat >> >>> I have 3 runs of functional data for each subject. Surprisingly, some >>> runs are registered well but others not (even of the same subject, so >>> using the same reference anatomical images: see the attached image. >>> Upper row: bad registration of one run and lower row: good >>> registration of another run). >>> >>> I have no problem to manually correct the registrations, it works >>> well, but as I have many subjects, I wonder if there may be a way to >>> change some options of reg-feat2anat to make it work better? Can you >>> see from the attached image what is the problem with my images? (I >>> viewed the functional and anatomical data of a few subjects, some woth >>> good and some with bad registration and see no difference or flip) >>> >>> Thanks a lot for your help! >>> Aga >>> >>> >>> >>> >>> >>> ___ >>> 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 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] FreeSurfer TrackVis Transforms
Do you mean .trk file? The format is described in detail here: http://trackvis.org/docs/?subsect=fileformat Ruopeng On 2/9/11 10:04 AM, pablo maturana wrote: Dears expert, I would like to know how can i get the transformation from trackvis to a space Freesurfer?. I have here a link http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms But i don't understand what mean this command, how I could load the file .dtk trk_verts_crs.xyz = trk_verts.xyz / (trkHeader.voxel_size[0], trkHeader.voxel_size[1], trkHeader.voxel_size[2]) and then I have a problem with this command trk_verts_tkreg = CRS2XYZtkreg * trk_verts_crs Could you give an example using a file .dtk? Many thanks Pablo ___ 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] reg-feat2anat: a problem!
Yea, though I might just go to 179 to make sure there's not a flip. doug Burzynska, Aga wrote: > > Dear Doug, > The determinant sign is negative for both example_func and orig.mgz > (-73.6 and -1, respecitively). > > The files differed also in their format, type, vox2ras-fsl and > orientation, but I guess it is ok. > > My feeling was that flirt is unable to fit the brain given the maximum > angle of rotation 90, so I doubled this using: > re-feat2anat --dof 6 --maxangle 180 --feat run1.feat --subject xx > > I tried this on several subjects and the registration looks very good: > I would not make it better manually. > > Can I assume it works now? > > Cheers, > Aga > > > > > > -Ursprüngliche Nachricht- > Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Gesendet: Mo 2011-02-07 19:36 > An: Burzynska, Aga > Cc: 'freesurfer@nmr.mgh.harvard.edu' > Betreff: Re: [Freesurfer] reg-feat2anat: a problem! > > That is not a problem. By "anatomical" I meant the FreeSurfer anatomical > (eg, orig.mgz) > doug > > Agnieszka Burzynska wrote: > > Dear Doug, > > Thank you a lot! > > Our feat data is always nifti, but anatomical FSL data is sometimes > in the > > analyze format. Is this already a problem? > > > > I will now check the rest. > > > > Thank you, cheers, > > Aga > > > > > > On 2/7/11 4:35 PM, "Douglas N Greve" wrote: > > > > > >> Hi Aga, are you using nifti? If analyze, that could be the problem. Do > >> your functionals and anatomicals have a different sign to their > >> determinants (you can check with mri_info). In principle, reg-feat2anat > >> should handle this but in some cases it does not. The 5.1 version will > >> handle it properly. If they do have the same sign, then look > through the > >> log file and find the flirt command. Run that command by itself > (you may > >> need to run reg-feat2anat with --nocleanup to keep it from deleting the > >> files). If that fails, then contact the FSL people > >> > >> doug > >> > >> Agnieszka Burzynska wrote: > >> > >>> Dear all, > >>> I am using the command reg-feat2anat to transform functional data > >>> pre-processed in FSL to the anatomical image in Freesurfer. > >>> > >>> As suggested, I check the registration with reg-feat2anat --feat > >>> run2.feat >>> > >>> I have 3 runs of functional data for each subject. Surprisingly, some > >>> runs are registered well but others not (even of the same subject, so > >>> using the same reference anatomical images: see the attached image. > >>> Upper row: bad registration of one run and lower row: good > >>> registration of another run). > >>> > >>> I have no problem to manually correct the registrations, it works > >>> well, but as I have many subjects, I wonder if there may be a way to > >>> change some options of reg-feat2anat to make it work better? Can you > >>> see from the attached image what is the problem with my images? (I > >>> viewed the functional and anatomical data of a few subjects, some woth > >>> good and some with bad registration and see no difference or flip) > >>> > >>> Thanks a lot for your help! > >>> Aga > >>> > >>> > > >>> > >>> > > >>> > >>> ___ > >>> 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 > > > > 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. > > -- 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] reg-feat2anat: a problem!
Good point, I will do that! But so far when I looked, the L-R flip did not happen. Thank you! Aga Aga Burzynska Max Planck Institute for Human Development Neurocognition of Decision Making Lentzeallee 94 14195 Berlin Ph: + 49 30 82406 335 -Ursprüngliche Nachricht- Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Gesendet: Mi 2011-02-09 17:11 An: Burzynska, Aga Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: AW: [Freesurfer] reg-feat2anat: a problem! Yea, though I might just go to 179 to make sure there's not a flip. doug Burzynska, Aga wrote: > > Dear Doug, > The determinant sign is negative for both example_func and orig.mgz > (-73.6 and -1, respecitively). > > The files differed also in their format, type, vox2ras-fsl and > orientation, but I guess it is ok. > > My feeling was that flirt is unable to fit the brain given the maximum > angle of rotation 90, so I doubled this using: > re-feat2anat --dof 6 --maxangle 180 --feat run1.feat --subject xx > > I tried this on several subjects and the registration looks very good: > I would not make it better manually. > > Can I assume it works now? > > Cheers, > Aga > > > > > > -Ursprüngliche Nachricht- > Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Gesendet: Mo 2011-02-07 19:36 > An: Burzynska, Aga > Cc: 'freesurfer@nmr.mgh.harvard.edu' > Betreff: Re: [Freesurfer] reg-feat2anat: a problem! > > That is not a problem. By "anatomical" I meant the FreeSurfer anatomical > (eg, orig.mgz) > doug > > Agnieszka Burzynska wrote: > > Dear Doug, > > Thank you a lot! > > Our feat data is always nifti, but anatomical FSL data is sometimes > in the > > analyze format. Is this already a problem? > > > > I will now check the rest. > > > > Thank you, cheers, > > Aga > > > > > > On 2/7/11 4:35 PM, "Douglas N Greve" wrote: > > > > > >> Hi Aga, are you using nifti? If analyze, that could be the problem. Do > >> your functionals and anatomicals have a different sign to their > >> determinants (you can check with mri_info). In principle, reg-feat2anat > >> should handle this but in some cases it does not. The 5.1 version will > >> handle it properly. If they do have the same sign, then look > through the > >> log file and find the flirt command. Run that command by itself > (you may > >> need to run reg-feat2anat with --nocleanup to keep it from deleting the > >> files). If that fails, then contact the FSL people > >> > >> doug > >> > >> Agnieszka Burzynska wrote: > >> > >>> Dear all, > >>> I am using the command reg-feat2anat to transform functional data > >>> pre-processed in FSL to the anatomical image in Freesurfer. > >>> > >>> As suggested, I check the registration with reg-feat2anat --feat > >>> run2.feat >>> > >>> I have 3 runs of functional data for each subject. Surprisingly, some > >>> runs are registered well but others not (even of the same subject, so > >>> using the same reference anatomical images: see the attached image. > >>> Upper row: bad registration of one run and lower row: good > >>> registration of another run). > >>> > >>> I have no problem to manually correct the registrations, it works > >>> well, but as I have many subjects, I wonder if there may be a way to > >>> change some options of reg-feat2anat to make it work better? Can you > >>> see from the attached image what is the problem with my images? (I > >>> viewed the functional and anatomical data of a few subjects, some woth > >>> good and some with bad registration and see no difference or flip) > >>> > >>> Thanks a lot for your help! > >>> Aga > >>> > >>> > > >>> > >>> > > >>> > >>> ___ > >>> 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 > > > > 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. > > -- 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@nm
Re: [Freesurfer] Bad orientation/registration in the motion correction step
I'm not sure about the mri_robust_template issue, but you can check the orientation by loading it in tkmedit. If the axial is axial with (nose up) and the sag is sag (with nose to the right), then the qform is right (assuming that LR is ok, which you can't check based on the direction of the nose:). doug Nikolas Borrel-Jensen wrote: > Hi! > > I am having some trouble with the motion correction step when having > two volumes (NIFTI files). The average volume has not been determined > correctly due to a wrong orientation/registration of the two original > volumes (see > http://freesurfer.nikolasborrel.com/bad_registration.tif). Is the > problem caused by wrong information in the qform matrix in the header > of the NIFTI file or by a bad registration in the mri_robust_template > or mri_convert functions in the motion correction step? > > Kind regards > Nikolas Borrel-Jensen > > > ___ > 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] roisummary-sess from binary mask
You have to make it work with func2roi-sess. One way to do this is to create a label file then use the -labelfile option to func2roi-sess. You can create a label from a binary mask with mri_cor2label. Spec "--id 1" doug Emily Ward wrote: > Hello, > > I am trying to get a summary of beta value activation for a hand-drawn > binary mask. This mask is a sphere, so it does not correspond to a > particular anatomical label or functional contrast. Is there any way > to apply roisummary-sess to this type fo binary mask (in nii or mgz > format)? If not, can I specify my mask as an roi so that the > roisummary-sess function will work? Or is there another command I > should be using to get a summary of beta values for a particular mask? > > Thank you, > > Emily > ___ > 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] Three starting questions
Tetiana Dadakova wrote: > Dear FreeSurfer community, > > You were very helpful for my last question, thank you. > > Now I have three basic questions. > > 1. I would like to check the segmentation by loading T1.mgz and > aseg.mgz as an -aux volume, so that I can switch between them. How can > I do this? ( gives some king of > black and white segmentation instead of colorful one). > Use "tkmedit subject T1.mgz -seg aseg.mgz" (instead of -aux). See the examples on the wiki tutorial. > 2. When I press View -> View configuration, I have three options there > (Single view, Multiple orientations, and Mosaic). How can I view just > 3 orientations or 2 (e.g. sagittal and transverse)? > No, you're limited to 1, 3, or mosaic. > 3. Do MacOS users have problems with mouse? When I try to edit > segmentation or surfaces with Edit Tools, my mouse doesn't seem to > work. I mean, when I click on the pixel with any of three buttons, > nothing changes. I saw similar problem on the mailing list, but there > was no answer. > You may need to configure the interface to allow the type of edits that you want. See the tutorial on the wiki. doug > Thank you for your time, > Tanja. > ___ > 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] Slice Order
For Siemens with an even number of slices, it is generally 2,4,6,..30,1,3,...29. This changes if there is an odd number of slices. doug Rita Loiotile wrote: > If my BOLD scan has 30 slices in "interleaved" series, can I assume > the slice order is 1,3,5,7,9...29,2,4,6,8..30? In other words, > 1:2:30,2:2:30? > ___ > 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] Abblocked Setup
Chindhuri Selvadurai wrote: > Dear Doug, > > Thanks for your response! > > Our stimuli starts with the null condition, but abblocked assumes it's the > ON condition. Is there a way to invert this? > No, not currently, though you can tell tkmedit/tksurfer to invert the color scale. Or you can do it by hand by multiplying the image by -1 (with fscalc). > When we look at the sig maps, how do we know what the contrast is? Which > condition does it think is null/task, negative/positive? From what I > understand from your first e-mail, this is the opposite of what we want. > > I tried looking at the surface-based analysis using tksurfer, but since > there is no constrast file for abblocked, I specified all contrasts, but > how do you differentiate if you have more than one? > > tksurfer-sess -s PBMST08 -hemi -lh -analysis mandy_mst_v_mct_lh -call > You can just specify "-c fund" etc. doug > I think perhaps it would be better for us to switch to the block design to > make things "simpler"? > > Thanks!! > > Chindhuri > > >> sfa-sess is depricated now (should not even be in there). Use >> selxavg3-sess. >> >> doug >> >> Chindhuri Selvadurai wrote: >> >>> Hi Doug, >>> >>> For some reason, our mkanalysis-sess command only created an >>> analysis.info file and not a .cfg file, so we can't run the abblocked >>> analysis using sfa-sess. Do you know what might cause this? >>> >>> We are using: >>> >>> freesurfer v5 >>> >>> our subjects directory: /cluster/manoach/milton/subjects >>> >>> command that was run: >>> mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 >>> -runlistfile task -surface fsaverage lh >>> >>> output that was given: >>> >>> # FSBUILD freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110202 >>> # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.8 2011/01/18 17:08:22 greve >>> Exp $ >>> # MKACMD /usr/local/freesurfer/stable5/fsfast/bin/mkanalysis-sess >>> -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile >>> task >>> -surface fsaverage lh >>> # DATE Fri Feb 4 14:36:01 EST 2011 >>> analysis mandy_mst_v_mct_lh >>> mcstem fmcpr >>> fsd bold >>> runlistfile task >>> TR 3 >>> RegDOF 6 >>> RawSpace surface fsaverage lh >>> mask brain >>> RawFWHM 8 >>> RawSTC none >>> inorm 100 >>> acfbins 0 >>> fixacf 1 >>> acffwhm 20 >>> acfsvd 0 >>> designtype abblocked >>> nskip 0 >>> polyfit 2 >>> HPFCutoffHz 0 >>> period 30 >>> >>> >>> The contrasts are going to be created automatically. These will be: fund >>> - stands for "fundamental" - this is the F-test of the sine and cosine >>> components, probably what you want >>> >>> fund-sin -- t-test of the sine component (this may also be useful) >>> fund-cos -- t-test of the cosine component (think of this like the >>> derivative when you assume a shape) >>> >>> harm -- F test on the harmonics (probably not too useful) It is going to assume that the first condition is ON. This does not >>> matter for the F-tests above, but will affect the sign of the sine >>> component. >>> >>> doug Chindhuri Selvadurai wrote: > Hello, > We are trying to set up the analysis for a periodic design alternating > > >>> between 30s rest and 30s active condition. Because abblocked doesn't >>> require a paradigm file, how do we specify which condition comes first >>> (rest or active)? We understand that abblocked expects that the >>> conditions will be alternating. >>> >>> > Also, how do we set up the -a and -c weighting conditions if we are > > >>> using >>> >>> > abblocked, since it doesn't have a paradigm file? How do we specify > > >>> the >>> >>> > arguments for this command? Should we instead be using the -ncond and > > >>> -wcond commands? >>> >>> > Best, > Chindhuri Selvadurai > Psychiatric Neuroimaging, Manoach Lab > Martinos Center for Biomedical Imaging, MGH > Phone: (617)726-0307 > ___ > 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 >>> Best, >>> >>> Chindhuri Selvadurai >>> >>> Psychiatric Neuroimaging, Manoach Lab >>> Martinos Center for Biomedical Imaging, MGH >>> Phone: (617)726-0307 >>> >>> >>> >>> >>> >>> >>> >>> >> -- >> 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.har
Re: [Freesurfer] two vol fields for retinotopic analysis?
I don't know what you mean by 3D coordinates or a 1d array of corresponding phase values. In any case, use the mri.vol. This should be in voxel-for-voxel correspondence with your input data. doug Jason Connolly wrote: > Dear freesurfer experts: > > I noticed that there are two 'vol' fields when I use MRIread. > > 1) mri.vol > 2) mri.analyzehdr.vol > > My question is: > > I have two arrays, one with 3D coordinates and a second 1 dimensional array > with corresponding phase values. > > Which 'vol' field do I put the 3D coordinates in and which do I put the phase > values in? > > Many thanks! > > -jason. > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] testing FreeSurfer
Hi FreeSurfer's user, I'm new using this software, I try to install on Ubuntu and to set up following the recommendation of the webpage. Then I tried to test but any commmand seems to be recognized, also when I started a new terminal a warning is shown: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist FREESURFER_HOME /home/cvalencia/Descargas/freesurfer FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects MNI_DIR /home/cvalencia/Descargas/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 Thanks in advance for the support, Best regards, cvalencia ___ 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] phase data overlay using fsaverage
First, make sure that the volume you created is in register with the template functional. Eg, tkmedit -f f.nii -ov f_LH12.mgz where f.nii is the functional that f_LH12.mgz was derived from. Once that is correct, run bbregister with the actual subject as the target (not fsaverage), spec the --mov as f.nii, and use --init-fsl instead of --init-header The vol2surf cmd is correct, though it will sample it on the subject's surface (not that of fsaverage; you can change this with --trgsubject). The tksurfer cmd is correct, just make sure to use the correct subject. doug Jason Connolly wrote: > > Dear freesurfer experts, > > I have used the mri.vol and mri.analyzehdr.vol fields to encode my > coordinates and phase values using MRIread and MRIwrite (f_LH12.mgz). > > I then brought these data into freesurfer using the following: > > > bbregister --s fsaverage --mov > /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg > register12.dat --bold --init-header —t2 > > mri_vol2surf --mov > /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg > /Applications/freesurfer/subjects/fsaverage/surf/register12.dat --hemi > lh --surf white --o > /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh > > tksurfer fsaverage lh sphere --overlay > /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh > > However, I do not see anything on the sphere (or fsaverage for that > matter) … > > Can you provide any hints? > > The phase values are normalized and range from 4 – 5 and I have > converted to RAS space properly (I hope) … > > Any tips would be a big help! > > Best wishes, > > Jason. > > > > ___ > 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] Whole brain gray matter image
Do you want cortical and subcortical or just cortical? doug caoaize wrote: > Hello FS Experts, > > I am trying to generate the whole brain gray matter image, I use > aparc_aseg.mgz - wm.mgz for gray matter mask, then use this mask for > gray matter. Is it correct? What is the difference between aseg.mgz > and ribbon.mgz? Hope your help. Thanks. > > Aize > > > > ___ > 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] surfaces to voxelspace
The --vox2ras-tkr transform will take you to voxel space in the conformed coordinates (not the raw input). Is this good enough? doug Steffen Bollmann wrote: > Dear freesurfer experts, > > I would like to display freesurfer surfaces in the voxelspace of the > original subject image using matlab. > > Which coordinate transformation do I have to apply to get the > vertex-coordinates to the RAS space and finally to the original > voxelspace of the subject? (i guess for RAS2Vox I can use the matrix I > can obtain with mri_info ... but I cannot find a way from > vertex-coordinates to RAS) > > Thank you for any hint > Best Regards > Steffen Bollmann > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] RA position available at VA Boston
Preliminary Announcement for Neuroimaging Research Assistant Position National Center for Posttraumatic Stress Disorder (Boston) The Behavioral Science Division of the National Center for PTSD, located at the VA Boston Healthcare System, anticipates an opening for a research assistant who will work on projects related to neuroimaging of posttraumatic stress disorder and memory disorders. Responsibilities for this position include: Collecting behavioral and neuroimaging data from healthy and clinical subjects, entering data and managing databases, performing statistical analyses, and assisting in the preparation of grants, manuscripts, and professional presentations. Applicants should have a B.A./B.S. (concentration in Cognitive Neuroscience/Psychology is preferred), experience working in an imaging laboratory and running functional magnetic resonance imaging (fMRI) experiments, proficiency with UNIX and MATLAB, FSL, and/or SPM, and the maturity and interpersonal sensitivity necessary for working in a clinical setting. Openings are expected for June 2011. Salary and benefits are highly competitive with similar positions at institutions in the Boston area. A two year commitment typically is required. Official job postings and formal application instructions are expected to appear in early March 2011, but potential candidates are encouraged to submit the following materials prior to formal application: 1) a letter describing their interest in a position and related career goals, 2) a resume, 3) a current transcript, and 4) at least two letters of recommendation. Materials can be sent electronically or by mail to: Andrea Carney National Center for PTSD (116B-2) VA Boston Healthcare System 150 South Huntington Ave. Boston, MA 02130-4817 andrea.car...@va.gov Further information can be obtained via e-mail or by phone at (857) 364-4143, or visit the websites: http://www.bu.edu/traumamemorylab/ http://www.bu.edu/brainlab/ -- Scott M. Hayes, Ph.D. Memory Disorders Research Center Neuroimaging Research Center VA Boston Healthcare System Assistant Professor Department of Psychiatry Boston University School of Medicine ___ 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] roisummary-sess from binary mask
Hi Doug, I've been running: mri_cor2label --c s105/rois/RhFFA_sphere.nii.gz --id 1 --l s105/labels/RhFFA_sphere.label to generate my label from my nifiti file. And then putting it through: func2roi-sess -sesslabel RhFFA_sphere -s s105 -roidef RhFFA_8rad_sphere -analysis repetitionAnalysis and viewing it like this: tkmedit-sess -s s105 -a repetitionAnalysis -c RhFFA_sphere -map mask -fthresh .5 When I compare the label mask to the nifiti file, the label appears much more inferior than the nifti file and has holes in it. Since this is a sphere, it has a pre-specified number of voxels comprising it, but when I run roisummary-sess, the number of voxels varies from person to person. I just want an average beta value for all the voxels in the sphere for the conditions in my analysis. Is there something I'm missing? Thank you, Emily On Wed, Feb 9, 2011 at 11:18 AM, Douglas N Greve wrote: > You have to make it work with func2roi-sess. One way to do this is to create > a label file then use the -labelfile option to func2roi-sess. You can create > a label from a binary mask with mri_cor2label. Spec "--id 1" > > doug > > Emily Ward wrote: >> >> Hello, >> >> I am trying to get a summary of beta value activation for a hand-drawn >> binary mask. This mask is a sphere, so it does not correspond to a >> particular anatomical label or functional contrast. Is there any way >> to apply roisummary-sess to this type fo binary mask (in nii or mgz >> format)? If not, can I specify my mask as an roi so that the >> roisummary-sess function will work? Or is there another command I >> should be using to get a summary of beta values for a particular mask? >> >> Thank you, >> >> Emily >> ___ >> 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 > > > > 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] roisummary-sess from binary mask
Try to load the label on RhFFA_sphere.nii.gz in tkmedit to make sure they line up. And what space is your binary mask in? It needs to be in anatomical space to use with a label. It's a little crazy, but you can map it to anatomical space if you need to. Emily Ward wrote: > Hi Doug, > > I've been running: > > mri_cor2label --c s105/rois/RhFFA_sphere.nii.gz --id 1 --l > s105/labels/RhFFA_sphere.label > > to generate my label from my nifiti file. And then putting it through: > > func2roi-sess -sesslabel RhFFA_sphere -s s105 -roidef > RhFFA_8rad_sphere -analysis repetitionAnalysis > > and viewing it like this: > > tkmedit-sess -s s105 -a repetitionAnalysis -c RhFFA_sphere -map mask -fthresh > .5 > > When I compare the label mask to the nifiti file, the label appears > much more inferior than the nifti file and has holes in it. Since this > is a sphere, it has a pre-specified number of voxels comprising it, > but when I run roisummary-sess, the number of voxels varies from > person to person. > > I just want an average beta value for all the voxels in the sphere for > the conditions in my analysis. Is there something I'm missing? > > Thank you, > > Emily > > > > > > > > > > > > On Wed, Feb 9, 2011 at 11:18 AM, Douglas N Greve > wrote: > >> You have to make it work with func2roi-sess. One way to do this is to create >> a label file then use the -labelfile option to func2roi-sess. You can create >> a label from a binary mask with mri_cor2label. Spec "--id 1" >> >> doug >> >> Emily Ward wrote: >> >>> Hello, >>> >>> I am trying to get a summary of beta value activation for a hand-drawn >>> binary mask. This mask is a sphere, so it does not correspond to a >>> particular anatomical label or functional contrast. Is there any way >>> to apply roisummary-sess to this type fo binary mask (in nii or mgz >>> format)? If not, can I specify my mask as an roi so that the >>> roisummary-sess function will work? Or is there another command I >>> should be using to get a summary of beta values for a particular mask? >>> >>> Thank you, >>> >>> Emily >>> ___ >>> 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 >> >> >> >> 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. >> >> >> > > > -- 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
