[Freesurfer] bad magic number

Hi, I'm getting a bad magic number error using mri_convert. I'm trying to convert a .nii file to a .mgz file. I've searched all over and all I can find is that you can use python in another program to delete this number, and it is related to the file extension. I've tried using the .nifti1 exte

Re: [Freesurfer] bad magic number

Jennifer can MRIcro read it? Usually that means it is corrupted Bruce On Tue, 9 Jun 2015, Kriegel, Jennifer Lynn Sarai wrote: > > Hi, > >   > > I’m getting a bad magic number error using mri_convert. I’m trying to > convert a .nii file to a .mgz file. I’ve searched all

Re: [Freesurfer] bad magic number

06/09/2015 04:03 PM, Kriegel, Jennifer Lynn Sarai wrote: > MRIcro opens it, and so does SPM 8. > > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Tuesday,

Re: [Freesurfer] bad magic number

roblem as we experienced. We don't know the origin of this extra byte, but most likely it is a bug in the conversion software that is affecting only some of the scans. Regards, Jalmar > On 09 Jun 2015, at 22:21, Kriegel, Jennifer Lynn Sarai > wrote: > > mri

[Freesurfer] sagittal slices

I used the following command to convert a sagittal slice from analyze to mgz format. The original was acquired in an anterior to posterior/right to left angle of slices. However, while it is converting to an mgz properly, it seems to be giving me a flip upside down, and reverting to transverse o

Re: [Freesurfer] Skullstrip problems

Hi Paul, >From my understanding, that's the stuff that can interfere with your surfaces. >I've run g-cut skullstrip on volumes where the surface of the pial is seen as >the white matter, and the dura is seen as the cortical/pial surface. I think >in terms of cortical measures, such as cortical

Re: [Freesurfer] Skullstrip problems

rerun the skullstrip with different watershed-parameters so as to prevent the skullstrip to be overly aggressive and "bite" these chunks out of the dura? Or would you leave it like it is? Thanks again! Best, Paul Quoting "Kriegel, Jennifer Lynn Sarai" : > Hi Paul, >

[Freesurfer] surface lines in manual edits

Hi, I'm hand editing brains to get the most accurate cortical thickness analysis possible, and ran into a bit of a problem with surface lines. One issue is with the original structural reconstructions from the hdr files, and the other deals with the manual edits I've made when the recon was re-

Re: [Freesurfer] surface lines in manual edits

Of Kriegel, Jennifer Lynn Sarai Sent: Wednesday, August 19, 2015 10:44 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] surface lines in manual edits Hi, I'm hand editing brains to get the most accurate cortical thickness analysis possible, and ran into a bit of a problem

Re: [Freesurfer] surface lines in manual edits

freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Kriegel, Jennifer Lynn Sarai Sent: Thursday, August 20, 2015 7:08 AM To: Freesurfer support list Subject: Re: [Freesurfer] surface lines in manual edits Hi Freesurfer experts, I asked this question yester

Re: [Freesurfer] surface lines in manual edits

r subject > data (the entire subject directory) and we will take a look? > > cheers > Bruce > > > > On Mon, 24 Aug 2015, Kriegel, Jennifer Lynn Sarai wrote: > >> >> Hi, >> >>   >> >> I apologize for asking this question again, but I’m

Re: [Freesurfer] surface lines in manual edits

Thanks Lee. I'll see how this works. I hope these examples make me an expert too. Best, Jennifer -Original Message- From: Lee Tirrell [mailto:ltirr...@nmr.mgh.harvard.edu] Sent: Saturday, August 29, 2015 5:50 PM To: Kriegel, Jennifer Lynn Sarai Cc: Freesurfer support list Subjec