Re: [Freesurfer] coregistration - FA to Freesurfer

Dear Bruce and Anastasia, Thanks for the quick reply! I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all. This is the comand i used: bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg /home/joana/FA/CN01/registe

Re: [Freesurfer] coregistration - FA to Freesurfer

Hi Joana, You should use the lowb volume as the moving volume for the registration and then apply the output registration matrix to your FA volume. You can also add the --o flag to your below command so that the resampled and registered volume gets written out at the end. You would want that a

Re: [Freesurfer] trac-all results

Hi Ping-Hong, Yes, you can set usemaskanat = 0 in your dmrirc, and then the brain mask will be extracted from the DWI data by the bet tool, instead of using the aparc+aseg. But, and this is a big but, TRACULA uses the aparc+aseg to constrain the tractography solutions, i.e. the aparc+aseg i

Re: [Freesurfer] Incorrect pial surface

Hi Jordan, it's hard to tell from a single slice but it looks like that might be amygdala, in which case you shouldn't worry about it. In any case, you can upload and we'll take a look cheers Bruce On Fri, 14 Oct 2011, Jordan Pierce wrote: Here's an image (if I attach this correctly) of a p

Re: [Freesurfer] mkcontrasts & retinotopy cannot find eccen error

do you have matlab installed? What is the result of the "getmatlab" command? Jodie Davies-Thompson wrote: > Hi Doug, > > Thanks for your reply. I tried running the contrast you suggested and > still get the same error as shown below. I'm guessing it's a problem > with my command? What have I do

[Freesurfer] Image Filtering

Bruce and others, Are there any spatial filters applied during the segmentation process other than a bias field correction? For example, a spatially adaptive non-linear means filter (e.g VBM8)? If not, do you think denoising filters will improve the accuracy and/or reduce manual editting? Thanks

Re: [Freesurfer] Image Filtering

Hi Don there is a nonlinear offset filter (Fischl and Schwartz, 1999, IEEE PAMI) applied during the segmentation process internally, but no filtered images are ever written to disk. You can try it out with mri_nlfilter. In general I would rather incorporate the information in the filtering into

Re: [Freesurfer] Incorrect pial surface

Yes, it looks like amygdala. Here are instructions for uploading the case: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange Allison On Fri, 14 Oct 2011, Bruce Fischl wrote: Hi Jordan, it's hard to tell from a single slice but it looks like that might be amygdala, in which case you

Re: [Freesurfer] Incorrect pial surface

How do I upload the subject file?___ 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 belie

Re: [Freesurfer] Automatic corrections log/diary and questions about Tkmedit color options

Hi Bruce, >From your last response, does that mean then that we can add the voxels back >to extend the pial surface that we mistakenly retracted in the previous edit? Best, Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563

Re: [Freesurfer] Automatic corrections log/diary and questions about Tkmedit color options

sure On Fri, 14 Oct 2011, Vy Dinh wrote: > Hi Bruce, > > From your last response, does that mean then that we can add the voxels back > to extend the pial surface that we mistakenly retracted in the previous edit? > > Best, > > Vy T.U. Dinh > Research Assistant, Neurological Sciences > Rush Unive

[Freesurfer] hippo-subfields not creating some files

Hi Bruce et al., I have a problem with the -hippo-subfields segmentation not creating some files for the left side when I run it on our Linux box located at the Martinos Center, with Freesurfer sourced to /usr/local/freesurfer/nmr-stable51-env. Specifically, it runs to apparent completion and

Re: [Freesurfer] hippo-subfields not creating some files

Hi Inge I think this is a question for Koen (ccd) cheers Bruce On Fri, 14 Oct 2011, Inge Knudson wrote: > Hi Bruce et al., > > I have a problem with the -hippo-subfields segmentation not creating some > files for the left side when I run it on our Linux box located at the > Martinos Center, w

[Freesurfer] Hippocampal Sub-Field Segmentation -Appropriate Scan Protocol to Use

Dear Experts, I've been collecting hi-res hippocampal scans with a 32 ch coil on a 3T Siemens Trio to manually segment hippocampal subfields. However, I wonder whether the protocol is appropriate for use with the new Freesurfer subfield segmentation tool. Specifically, our hi-res scan does not ca

[Freesurfer] Suggested longitudinal processing stream for already skull stripped images

Hi, We are attempting to use FreeSurfer in order to process a longitudinal T1 series. Our input data is partly simulated and already skull stripped. When running $ recon-all -autorecon1 on one of these images, the check of the Talairach transformation fails. Using the option -notal-check resul

[Freesurfer] CVS or MNI registration

Hi Bruce, I will be very grateful if you can give me an advise regarding registration. In TBSS there is recommended if the subjects are  young children (the adult-derived FMRIB58_FA target is inappropriate), to  identify the "most representative" one, and use this as the target image. This target