[Freesurfer] Flip brain
Hi Dear FS experts, Doug sent these links, but I can't download them. Do you have the new links? Download these filesftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfregftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemiregftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preprocftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.tar.gzftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.mcc.tar.gzftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.linux Thank you. Regards, Tadeu ___ 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] Flip brain
Thank you Doug! Tadeu On Mon, Jul 16, 2012 at 1:31 PM, Douglas N Greve wrote: > Hi Tadeu, I have updated the files. The only difference is that the > "mcc" file below is now > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor.tar.gz > < > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.mcc.tar.gz > > > > doug > > On 07/10/2012 09:25 AM, Tadeu Kubo wrote: > > Hi Dear FS experts, > > > > Doug sent these links, but I can't download them. Do you have the new > > links? > > > > Download these files > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemireg > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.tar.gz > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.mcc.tar.gz > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.linux > > > > Thank you. > > > > Regards, > > Tadeu > > > > > > > > > > ___ > > 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 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] TRACULA - Error: bvecs and bvals don't have the same number of entries
Dear FS Experts, I'm trying to work with the DTI Siemens (non MGH) and is not working. An error occurs in step "Tensor Fit”. II tried a solution that have worked as substitute bvecs values before this step manual (by original bvecs) and it works great (is meant by: continued)!. Surely I'm doing something wrong, but not yet identified. I would like your help. Sorry for the basic question, but I’m starting with TRACULA. Attached files: .log bvecs.txt bvals.txt trac-all.log Description: Binary data dmrirc.tracula_teste Description: Binary data 0 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 9000 0 0 0.170354783535 -0.5811995267868 0.79573011398315 0.22868627309799 0.5909623503685 -0.77360594272613 0.44574096798896 0.25920024514198 -0.85681402683258 -0.3914169371128 0.76478457450866 -0.51175904273986 -0.21208196878433 0.95597493648529 -0.20281316339969 0.86269807815551 -0.50134819746017 0.0663471892476 0.71906572580337 -0.53749132156372 0.44050827622413 -0.36056712269783 0.24018001556396 -0.90127962827682 0.69824856519699 -0.21267391741275 0.68353396654129 -0.68143260478973 0.69373673200607 0.23319295048713 -0.35334324836731 0.92088252305984 0.16469347476959 -0.38041466474533 0.44053542613983 0.81315016746521 -0.69361215829849 0.45392537117004 0.5593335032463 0.9876697063446 -0.14244417846202 -0.06494748592376 0.88434565067291 -0.11212377250194 -0.45316770672798 -0.05546042323112 0.66819763183593 0.74191373586654 -0.04059650376439 0.9087147116661 0.41543886065483 0.60757118463516 0.4832566678524 0.63033348321914 0.26992079615593 0.4560355246067 0.84804147481918 -0.25474265217781 0.08677887171506 0.96310728788375 0.143529728055 0.09476573765277 0.98509830236435 0.6191736459732 0.7234011888504 0.30547451972961 0.29175463318824 0.93595695495605 0.19713911414146 0.18853455781936 0.96447527408599 -0.18504625558853 0.41298800706863 0.78297990560531 -0.46517023444175 0.76158994436264 0.24580234289169 -0.59963482618331 0.73748731613159 0.57036411762237 -0.36165890097618 0.8407550741 0.54103332757949 0.02050634659826 0.82337826490402 0.15177546441555 0.54682028293609 -0.96726638078689 -0.18701308965683 -0.17152798175811 ___ 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] Flip brain
Dear FS experts, How can I flip hemispheres? I read the mail list and Doug said that (2010): The problem with this is that you will get different results when you use the left hemi and the right-flipped-to-left hemi as compared to the right hemi and the left-flipped-to-right hemi. You'll actually get different areas that appear to be significant. This is because the right-flipped-to-left is registered to the left template target and it does not register as well as the left registered to the left template target (and the same in the other direction). I'm sure it means something, but I don't know how to interpret it. doug I'm specially interesting because we're studying MTS. The status of this procedure remains the same or it is possible to do it ? Thank you, Tadeu ___ 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] Flip brain
Hi Doug Thank you! Tadeu On Wed, May 16, 2012 at 5:02 PM, Douglas N Greve wrote: > Hi Tadeu, It will be available in 5.2. If you can't wait until then, > then follow the instructions here: > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html > doug > > On 05/16/2012 03:51 PM, Tadeu Kubo wrote: > > Dear FS experts, > > > > How can I flip hemispheres? I read the mail list and Doug said that > > (2010): > > The problem with this is that you will get different results when you > > use the left hemi and the right-flipped-to-left hemi as compared to the > > right hemi and the left-flipped-to-right hemi. You'll actually get > > different areas that appear to be significant. This is because the > > right-flipped-to-left is registered to the left template target and it > > does not register as well as the left registered to the left template > > target (and the same in the other direction). I'm sure it means > > something, but I don't know how to interpret it. > > > > doug > > > > I'm specially interesting because we're studying MTS. The status of > > this procedure remains the same or it is possible to do it ? > > > > Thank you, > > Tadeu > > > > > > > > > > > > ___ > > 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 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] frontal lobe volume
Me too... Best wishes, Tadeu Kubo. On Fri, Sep 19, 2008 at 4:18 AM, dfwang <[EMAIL PROTECTED]> wrote: > Dear all, > > I would like to calculate the frontal lobe volume from the outputs of > freesrufer. Could any body here please tell me the way to do this? > > Any comments are welcome! > > Best wishes, > Vincent > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Tadeu Takao Almodovar Kubo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Talairach x MNI 152
Hi, I've been using FS, in which the Talairach transform is applied as a standard space for registration. Instead of the Talairach transformation i would like to use the MNI 152 as it is done in FSL and SPM. Does anybody have some experience with this? What would be the impact on the results of the cortical or subcortical structures? I would appreciate it if somebody could help me out with this. Thanks in advance, Tadeu Kubo ___ 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] ICV volume and 1.5T x 3.0T
Hi FS, I have two important doubts... Is it the CSF volume included in the ICV volume (aseg.stats)? Is it possible include in the same group patient acquired from 1.5T and 3.0T? Do you have an article about this topic? TK ___ 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] ICV volume and 1.5T x 3.0T
Thanks Doug. I'll do it! TK On Fri, Aug 20, 2010 at 7:08 PM, Douglas N Greve wrote: > The ICV is not computed based on a sum of the volumes of individual > structures. It is a summary measure computed from the registration to > talairach space. See the wiki and Randy Buckner's paper for more info. As > for combining across field strengths, that would not be highly recommended. > If you want to do this, make sure to include a regressor for field strength > in your GLM. Try looking at the Han paper. > > doug > > Tadeu Kubo wrote: > >> Hi FS, >> >> I have two important doubts... >> >> Is it the CSF volume included in the ICV volume (aseg.stats)? >> >> Is it possible include in the same group patient acquired from 1.5T and >> 3.0T? Do you have an article about this topic? >> >> >> >> >> TK >> >> >> >> >> >> ___ >> 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.
