Freesurfer

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30132 discussions

Cortical statistical maps
by 传玺 23 Jun '13

23 Jun '13

Dear FS expert： I have complete those three steps of FS,then how can I get the Cortical statistical maps? as follows: thank you for your help!

2 1

TRACULA - tract volume and length
by Fred Sanders 22 Jun '13

22 Jun '13

Dear DTI experts, I am trying to understand how to interpret tract length & volume measurements that TRACULA provides. For example, let’s say a clinical population differs from a control group in mean FA of a particular tract, and tract length & volume are comparable across the 2 groups. I think this would support the notion that the tract’s diffusion properties are indeed different across the two groups and that the FA finding are unlikely to be an artifact of probabilistic tractography. Is this a correct interpretation? Conversely, if group differences in tract volumes were detected, would you recommend comparing mean FA across the two group while covarying for tract volume? Thanks!

2 1

Possible to generate connectivity map using FS and Tracula
by Salil Soman 22 Jun '13

22 Jun '13

Dear Doug, Is there a way to use the Freesurfer and Tracula output to compute connectivity maps? Thanks! Sal

3 2

check orientation
by Brigitte Dahmen 22 Jun '13

22 Jun '13

Dear Freesurfer experts, is there a command in Freesurfer to check for correct orientation (LAS vs. PSR) of T1 images (similar to "fslhd" in FSL)? Thank you very much! Brigitte

5 9

retinotopic mapping selxavg3-sess error
by Bianca van Kemenade 21 Jun '13

21 Jun '13

Dear Freesurfers, I'm setting up freesurfer to do retinotopic mapping. I use a PC with Windows XP, so I installed Freesurfer using the VirtualBox (with Xubuntu). I managed to get through the initial steps for retinotopic mapping, but I get stuck at the actual analysis. The point where I get stuck is: selxavg3-sess -a rtopy.self.lh -s P2_BK It starts the analysis, but runs into problems at the stage "Using FSL's BET to extract brain" and gives the following error output: # ---------- Using FSL's BET to Extract Brain------------------ # /home/virtualuser/freesurfer/ shared/P2_BK/bold bet.fsl /tmp/mkbrainmask_4425/in.nii /tmp/mkbrainmask_4425/brain -m -f 0.1 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found [: 158: =: unexpected operator /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found /bin/rm: cannot remove `_tmp*': Protocol error ERROR: bet failed I tried updating FSL in case that is the problem, but it is only available for Ubuntu 10.04 and up, whereas the Ubuntu system that is provided to install the Freesurfer virtual disk image is 9.04. If anyone has an idea how to proceed let me know, any help is much appreciated. Thanks, Bianca

2 1

use mri_convert to flip A/P labels
by Ray, Siddharth 21 Jun '13

21 Jun '13

Hi, I have niftii files of some subjects where A/P labels are flipped. Is there anyway I can flip those labels using mri_convert, like mri_convert -left-right-reverse for flipping L/R labels. Thanks, -Siddharth

2 1

Fwd: missing surfaces
by Deirdre O Shea 21 Jun '13

21 Jun '13

---------- Forwarded message ---------- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date: Fri, Jun 21, 2013 at 11:33 AM Subject: Re: [Freesurfer] missing surfaces To: Deirdre O Shea <deirdreoshea84(a)gmail.com> Hi Deirdre can you cc the list so that others can answer? Bruce On Fri, 21 Jun 2013, Deirdre O Shea wrote: Hi Doug and Bruce, > > I have an error.logs file which shows only this message for one of the > subjects.. > > mrisReadTriangleFile(/share/**users/doshea/WHICAP_PET/** > W32714V2/3DT1/FreeSurfer/surf/**rh.pial): surface > doesn't match /share/users/doshes/WHICAP_**PET/w32714v2/3dt1/ > > > > > On Fri, Jun 21, 2013 at 9:57 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > Hi Deirdre > > can you send us the recon-all.log, or at least the last 100 lines of > it? > cheers > Bruce > > On Thu, 20 Jun 2013, Deirdre O Shea wrote: > > Dear FreeSurfers, > > I have been using FreeSurfer for editing for the past year now > and I have > recently come across an > issue that I have not seen before in a new dataset. The pial > surfaces are > missing in the right > hemisphere following the first run of Freesurfer (before any > edits). There > are also some without > white matter surfaces. However, not all my subjects have shown > this and are > just fine. Any > suggestions on how i can fix this? > > Thanks, > Deirdre > > > > > 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<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. > > > > >

1 0

Corrected thickness values?
by Jackie Lam 21 Jun '13

21 Jun '13

Hi there, I was wondering if the cortical thickness values of the ROIs in ?h.aparc.a2009s.stats or ?h.aparc.stats have been corrected based on the subject's whole brain volume or the template volume or if it is just the thickness measures without correction. Thanks, Jack

2 1

missing surfaces
by Deirdre O Shea 21 Jun '13

21 Jun '13

Dear FreeSurfers, I have been using FreeSurfer for editing for the past year now and I have recently come across an issue that I have not seen before in a new dataset. The pial surfaces are missing in the right hemisphere following the first run of Freesurfer (before any edits). There are also some without white matter surfaces. However, not all my subjects have shown this and are just fine. Any suggestions on how i can fix this? Thanks, Deirdre

3 2

problem bbregister onto longitudinal pipeline
by Daniel Garcia 21 Jun '13

21 Jun '13

Dear Freesurfer Users, I'm having a problem to register my PET images into the longitudinal pipeline of freesurfer (version 5.1). I have use bbregister without any problem to put the PET image into the crossectional images but it fails to register to the long version of it. Someone can tell me if I'm doing something wrong? bbregister -s P09_TA --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz This last command works perfectly, but bbregister -s P09_TA.long.P09 --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz Fails completely. My objective is to project my pet cortex into the surface in longitudinal that is why I'm interested in this processing. Maybe you can tell my another way of doing this. Thank you very much. Daniel

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