[Freesurfer] TRACULA preprocessing: bvector rotation, negative eigenvalues

Dear all, Do you have suggestions/ideas for me please? Thank you, Barbara Original Message Subject:TRACULA preprocessing: bvector rotation, negative eigenvalues Date: Tue, 07 Oct 2014 19:09:00 +0100 From: Barbara Kreilkamp To: Freesurfer support list Dear F

Re: [Freesurfer] pial vs. aseg

Ezra, The labeling of gm and wm that you see in the aseg.mgz file is not used to produce the cortical statistics found in the .stats files. The aseg.mgz grey matter appears this way because the aseg.mgz file is produced prior to running our 'surface stream', which produces the accurate gm/wm surf

[Freesurfer] TRACULA dwi flipping

Dear all, Would you please explain why TRACULA is flipping the data so often? And what does the flip4fsl command do? The data I have is already in the right (radiological) orientation. fslswapdim does not seem to have an effect either, as the parameters are just set to 'x y z'. Are these comman

[Freesurfer] watershed error again

Hi all, I posted this problem earlier, but did not get an answer, so I am posting it again, sorry! --- recon-all runs smoothly for all my subjects but one. It throws the error "mri_watershed Error: indices out of bounds" and finishes (see https://www.dropbox.com/s/4del0uy8g1qw5az/recon-all.

[Freesurfer] unpacksdcmdir

Hi , The command is only used to unpack Siemens DICOM files, How can I unpack the non Siemens DICOMs? Thanks, Moahmad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informat

[Freesurfer] bbregister / mri_vol2vol with nifti file header

Dear Freesurfer users, I wanted to see if anyone knows what part of the file NIFIT header mri_vol2vol or mri_convert uses to write transform information from register.dat acquired from bbregister? I used the following commands to register the anatiomcal brain.mgz to the last time point of my EPI

Re: [Freesurfer] T1 white matter segmentation

first you have to run recon-all with the T1 On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote: > Hi Bruce, > The T2 is very good and better than T1 So I will use the T2 image in the > following command line > recon-all -subjid subjid -T2pial > > Is this correct? > Thanks > > Mohamad > > __

Re: [Freesurfer] T1 white matter segmentation

Hi Bruce, The T2 is very good and better than T1 So I will use the T2 image in the following command line recon-all -subjid subjid -T2pial Is this correct? Thanks Mohamad From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.e

Re: [Freesurfer] T1 white matter segmentation

Hi Mohamad recon-all requires a T1, so use it. If the T2 is good quality you can use it to avoid dura in a subsequent invocation of recon-all with the -T2pial flag cheers Bruce On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote: Hi FS Experts, The T1 and T2 images in my data set are as the

Re: [Freesurfer] problem with gyrification index extraction

However, I'm afraid I still have a problem with my stats files. So my pipeline at the moment is: - creation of a manual label (i.e. rh.MRQI_Tmppole.label) with QDEC - automatic creation of the corresponding label (i.e. *subj_1*/label/rh.MRQI_Tmppole.label) for each subject with File > Map Label to