[Freesurfer] fsaverage aseg
Hi all, How was the fsaverage aseg.mgz (in the 4.5 distribution, if it differs) created? I can't seem to find this information anywhere on the Freesurfer website. Thanks! Mike ___ 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] Need admin rights to run FS on mac?
Hi, This is Kumar. I am a grad student at the Dept of Biomedical Engineering, University of Florida. I would like to bring to your notice a problem that I am facing when I am running FreeSurfer on my mac at the lab. I am testing the freesurfer installation as documented on the Free Surfer Wiki. I was able to run the first few commands without an issue other than it saying "cannot create.xdebug_tkmedit"but it ends up running well. When I try to run the recon-all command, it says I do not have admin rights to make a directory and so I used "sudo" to boost the privileges. This time it says, FREESURFER_HOME: Undefined Variable Can you please help me in this regard? Thank you. -- Aditya Kumar. K Grad Student, Department of BME UF. ___ 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] Freesurfer to DTI space
Hello all, I am using surface tracking in FSL to align my freesurfer surfaces to my diffusion data. I am wondering if it were possible to use the freesurfer2fa.mat registration file as the registration input for mri_label2vol. The freesurfer2fa.mat was generated using FLIRT in FSL by registering the freesurfer conformed structural space to diffusion space. Ultimately I want to align the gyri and sulci volumes to the diffusion images I have. Is this a viable solution? Thanks in advance, Tina Jeon ___ 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] Question about getting fusiform stats
Hi Brian I don't know which parcellation you are using, but in the sulco-gyral parcellation (aparc.a2009s.annot), the fusiform appears as "G_oc- temp_lat-fusifor" cheers -CD Le 8 juin 10 à 21:56, Weisinger, Brian (NIH/OD) [E] a écrit : Hello I am trying to retrieve the fusiform volumes of a sample. I looked in the subject output files but didn't see any mention of the fusiform and when I searched the website so far all I could find involved fsl and functional data which mine is not. If it is possible to do could you please point me in the right direction to figure this out. Thank you for your help ___ 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] Question about getting fusiform stats
Hello I am trying to retrieve the fusiform volumes of a sample. I looked in the subject output files but didn't see any mention of the fusiform and when I searched the website so far all I could find involved fsl and functional data which mine is not. If it is possible to do could you please point me in the right direction to figure this out. Thank you for your help ___ 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] [Fwd: Re: Different slices number for control group]
Sorry, my initial reply went to just to Laura, and not the list. -MH Forwarded Message From: Laura Verga To: Michael Harms Subject: Re: [Freesurfer] Different slices number for control group Date: Tue, 8 Jun 2010 17:13:14 +0200 Hi MIchael, thanks so much for your answer. Firstly: you're absolutely right about the number of slices. My mistake. I meant 150. I will surely contact my physicist. Thanks again and sorry for being imprecise. 2010/6/8 Michael Harms Hi Laura, What do you mean in saying that the images of the control group are taken from a "different acquisition session"? Different subjects are always scanned in a different "session"... Assuming that all subjects were scanned on the same scanner, the differing number of slices in the acquisitions for the two groups could still be a major confound for a group comparison, depending on the sequence used. For example, with an MPRAGE acquisition, many k- space lines are acquired during each "TR", so changing the number of slices will in principle change the contrast and spatial filtering properties of the acquisition, even if all other parameters are identical. In your case, the change in the number of slices is quite dramatic. You probably need to talk to your local MR physicist regarding the sequence that you used, the details of how it is implemented on the Philips scanner, and whether a change in number of slices will affect the contrast and spatial filtering due to the manner in which the Philips sequence loops through k-space. BTW: 128 sagittal slices of 1 mm thickness is only 128 mm, which is not enough to cover the L/R dimension of a human head. Were those really the parameters? cheers, -MH On Tue, 2010-06-08 at 10:50 +0200, pik...@tin.it wrote: > Hi freesurfers! > > We want to estimate the differences of cortical thickness between two > groups. The images of the control group are taken from a different > acquisition session. the only differences would be the number of > slices (200 vs 128). > It is still possible to compare the two groups? > > Images were acquired on the sagittal plane on a 3T Phillips scanner, > SENSE coil, voxels 1x1x1, matrix 256x256, T1 MPR. > > Thanks so much for your time > > Laura > ___ > 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] Different slices number for control group
Is there total overlap between group and number of slices? Sounds not very good. I don't have a feel for what the MR on this and whether changing the number of slices would create systematic differences in SNR or contrast. Maybe Andre would like to weih in. doug On Tue, 8 Jun 2010, pik...@tin.it wrote: > Hi freesurfers! > > We want to estimate the differences of cortical thickness between two groups. > The images of the control group are taken from a different acquisition > session. the only differences would be the number of slices (200 vs 128). > It is still possible to compare the two groups? > > Images were acquired on the sagittal plane on a 3T Phillips scanner, SENSE > coil, voxels 1x1x1, matrix 256x256, T1 MPR. > > Thanks so much for your time > > Laura > -- 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] brain regions
Yes I do see values for cc in the stats file thank you! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Allison Stevens Sent: 08 June 2010 12:29 To: Ahmed, F, Me Cc: Freesurfer Mailing List; Doug Greve Subject: Re: [Freesurfer] brain regions You'll also find it listed in the aseg.stats file in the stats dir as cc-anterior, cc-posterior, etc. (labeled as the same when viewing the aseg.mgz in tkmedit). do you see values for the cc in the stats file? On Jun 8, 2010, at 4:56 AM, "Ahmed, F, Me " wrote: > Thank you for that Doug, I just had a look in the aseg.mgz file, but unless > I'm blind, I can't seem to see it...could you tell me what it's labelled as > please? > > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Doug Greve > Sent: 08 June 2010 10:53 > To: Ahmed, F, Me > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] brain regions > > > The corpus collosum is labeld in the auotmatic volume segmenation > (aseg.mgz). The prefrontal cortex is subdivided into a number of > regions in the auotmatic surface parcellation (lh.aparc.annot or > rh.aparc.annot) > > doug > > > > On Tue, 8 Jun 2010, Ahmed, F, Me wrote: > >> Hello FS experts, >> >> A quick question, I'm looking for specific brain regions, but I can't seem >> to find them in the files once processing has been completed, I'm just >> wondering if FS does processing for areas including prefrontal cortex and >> corpus collosum? >> >> Thanks, >> Fatima >> >> >> >> > > -- > 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 > > ___ 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] brain regions
You'll also find it listed in the aseg.stats file in the stats dir as cc-anterior, cc-posterior, etc. (labeled as the same when viewing the aseg.mgz in tkmedit). do you see values for the cc in the stats file? On Jun 8, 2010, at 4:56 AM, "Ahmed, F, Me " wrote: > Thank you for that Doug, I just had a look in the aseg.mgz file, but unless > I'm blind, I can't seem to see it...could you tell me what it's labelled as > please? > > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Doug Greve > Sent: 08 June 2010 10:53 > To: Ahmed, F, Me > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] brain regions > > > The corpus collosum is labeld in the auotmatic volume segmenation > (aseg.mgz). The prefrontal cortex is subdivided into a number of > regions in the auotmatic surface parcellation (lh.aparc.annot or > rh.aparc.annot) > > doug > > > > On Tue, 8 Jun 2010, Ahmed, F, Me wrote: > >> Hello FS experts, >> >> A quick question, I'm looking for specific brain regions, but I can't seem >> to find them in the files once processing has been completed, I'm just >> wondering if FS does processing for areas including prefrontal cortex and >> corpus collosum? >> >> Thanks, >> Fatima >> >> >> >> > > -- > 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 > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] brain regions
cmd line? On Tue, 8 Jun 2010, Ahmed, F, Me wrote: > I'm running version 4.3.1 > > > -Original Message- > From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu] > Sent: 08 June 2010 11:01 > To: Ahmed, F, Me > Cc: Freesurfer Mailing List > Subject: RE: [Freesurfer] brain regions > > > How did you look at it (what was your command-line)? You should load it as a > segmentation in > tkmedit. What version of FS are you using? Older versions did not have > CC defined, but it would have to be pretty old. > > doug > > > > On Tue, 8 Jun 2010, Ahmed, F, Me wrote: > >> Thank you for that Doug, I just had a look in the aseg.mgz file, but unless >> I'm blind, I can't seem to see it...could you tell me what it's labelled as >> please? >> >> >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Doug Greve >> Sent: 08 June 2010 10:53 >> To: Ahmed, F, Me >> Cc: Freesurfer Mailing List >> Subject: Re: [Freesurfer] brain regions >> >> >> The corpus collosum is labeld in the auotmatic volume segmenation >> (aseg.mgz). The prefrontal cortex is subdivided into a number of >> regions in the auotmatic surface parcellation (lh.aparc.annot or >> rh.aparc.annot) >> >> doug >> >> >> >> On Tue, 8 Jun 2010, Ahmed, F, Me wrote: >> >>> Hello FS experts, >>> >>> A quick question, I'm looking for specific brain regions, but I can't seem >>> to find them in the files once processing has been completed, I'm just >>> wondering if FS does processing for areas including prefrontal cortex and >>> corpus collosum? >>> >>> Thanks, >>> Fatima >>> >>> >>> >>> >> >> > > -- 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] brain regions
I'm running version 4.3.1 -Original Message- From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: 08 June 2010 11:01 To: Ahmed, F, Me Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] brain regions How did you look at it (what was your command-line)? You should load it as a segmentation in tkmedit. What version of FS are you using? Older versions did not have CC defined, but it would have to be pretty old. doug On Tue, 8 Jun 2010, Ahmed, F, Me wrote: > Thank you for that Doug, I just had a look in the aseg.mgz file, but unless > I'm blind, I can't seem to see it...could you tell me what it's labelled as > please? > > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Doug Greve > Sent: 08 June 2010 10:53 > To: Ahmed, F, Me > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] brain regions > > > The corpus collosum is labeld in the auotmatic volume segmenation > (aseg.mgz). The prefrontal cortex is subdivided into a number of > regions in the auotmatic surface parcellation (lh.aparc.annot or > rh.aparc.annot) > > doug > > > > On Tue, 8 Jun 2010, Ahmed, F, Me wrote: > >> Hello FS experts, >> >> A quick question, I'm looking for specific brain regions, but I can't seem >> to find them in the files once processing has been completed, I'm just >> wondering if FS does processing for areas including prefrontal cortex and >> corpus collosum? >> >> Thanks, >> Fatima >> >> >> >> > > -- 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] brain regions
How did you look at it (what was your command-line)? You should load it as a segmentation in tkmedit. What version of FS are you using? Older versions did not have CC defined, but it would have to be pretty old. doug On Tue, 8 Jun 2010, Ahmed, F, Me wrote: > Thank you for that Doug, I just had a look in the aseg.mgz file, but unless > I'm blind, I can't seem to see it...could you tell me what it's labelled as > please? > > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Doug Greve > Sent: 08 June 2010 10:53 > To: Ahmed, F, Me > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] brain regions > > > The corpus collosum is labeld in the auotmatic volume segmenation > (aseg.mgz). The prefrontal cortex is subdivided into a number of > regions in the auotmatic surface parcellation (lh.aparc.annot or > rh.aparc.annot) > > doug > > > > On Tue, 8 Jun 2010, Ahmed, F, Me wrote: > >> Hello FS experts, >> >> A quick question, I'm looking for specific brain regions, but I can't seem >> to find them in the files once processing has been completed, I'm just >> wondering if FS does processing for areas including prefrontal cortex and >> corpus collosum? >> >> Thanks, >> Fatima >> >> >> >> > > -- 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] brain regions
Thank you for that Doug, I just had a look in the aseg.mgz file, but unless I'm blind, I can't seem to see it...could you tell me what it's labelled as please? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Doug Greve Sent: 08 June 2010 10:53 To: Ahmed, F, Me Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] brain regions The corpus collosum is labeld in the auotmatic volume segmenation (aseg.mgz). The prefrontal cortex is subdivided into a number of regions in the auotmatic surface parcellation (lh.aparc.annot or rh.aparc.annot) doug On Tue, 8 Jun 2010, Ahmed, F, Me wrote: > Hello FS experts, > > A quick question, I'm looking for specific brain regions, but I can't seem to > find them in the files once processing has been completed, I'm just wondering > if FS does processing for areas including prefrontal cortex and corpus > collosum? > > Thanks, > Fatima > > > > -- 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
Re: [Freesurfer] brain regions
The corpus collosum is labeld in the auotmatic volume segmenation (aseg.mgz). The prefrontal cortex is subdivided into a number of regions in the auotmatic surface parcellation (lh.aparc.annot or rh.aparc.annot) doug On Tue, 8 Jun 2010, Ahmed, F, Me wrote: > Hello FS experts, > > A quick question, I'm looking for specific brain regions, but I can't seem to > find them in the files once processing has been completed, I'm just wondering > if FS does processing for areas including prefrontal cortex and corpus > collosum? > > Thanks, > Fatima > > > > -- 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] Different slices number for control group
Hi freesurfers! We want to estimate the differences of cortical thickness between two groups. The images of the control group are taken from a different acquisition session. the only differences would be the number of slices (200 vs 128). It is still possible to compare the two groups? Images were acquired on the sagittal plane on a 3T Phillips scanner, SENSE coil, voxels 1x1x1, matrix 256x256, T1 MPR. Thanks so much for your time Laura ___ 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] Label files for the Cortical Ribbon
How did you create the .label files? mri_label2vol (your last step) does not produce them. Maybe with mri_cor2label run on the output of mri_label2vol? doug On Mon, 7 Jun 2010, Tina Jeon wrote: > Hello freesurfers! > > After creating some labeling files from aparc.a2005s.annot, I noticed that my > sulci and gyri volumes generated from the .label files (i.e., after running > mri_annotation2label and mri_label2vol) were only representing the outer > layer of the white surface. Is there any way to generate .label files that > include the entire cortical ribbon? > > Thanks, any help would be appreciated. > > Tina Jeon > > ___ > 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] brain regions
Hello FS experts, A quick question, I'm looking for specific brain regions, but I can't seem to find them in the files once processing has been completed, I'm just wondering if FS does processing for areas including prefrontal cortex and corpus collosum? Thanks, Fatima ___ 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.
