Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

This fixed everything! Thank you! Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Wed, Aug 10, 2011 at 2:43 PM, Douglas N Greve wrote: > One thing you can try is to look at th

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

One thing you can try is to look at the current orientation with mri_info --orientation f.img This will print out a 3-letter string like LPS or LSA. Create a new string by replacing the A with a P or P with an A. then mri_convert f.img --in_orientation NewString f.new.nii where NewString is th

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Hi Chris, that won't work for us. We assume it's in an ras coordinate system. I think you can do it with mri_convert, Doug probably knows how, but if you can't tell left from right it's going to be a problem forever. It's not worth running it through recon-all until the .img files comes up wit

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Hi Bruce, We tried to reverse A/P by reversing it the Talairach transform since recon-all wasn't able to do it automatically. I'm actually not sure how to reverse it in the IMG and HDR files. Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Bra

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Hi Chris, when I bring that one up in freeview it looks like the a/p axis is still reversed (i.e. 'P' is at the front of the head) Bruce On Wed, 10 Aug 2011, Christopher Luna wrote: Okay, I've uploaded them as cdluna_whitematter_002.img and *.hdr. Thanks, Christopher Luna MIT Brain and Cog

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Okay, I've uploaded them as cdluna_whitematter_002.img and *.hdr. Thanks, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Tue, Aug 9, 2011 at 11:02 PM, Bruce Fischl wrote: > E

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Eek, that looks awful! Can you upload this subject so we can figure out what is going on? On Aug 9, 2011, at 4:09 PM, Christopher Luna wrote: > Hello, > > On this topic again, we tried fixing the coordinate system (we flipped A/P) > as much as we could until we heard back from our colleague

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Hi Bruce, Thank you very much! We'll get in contact with them. Best, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Mon, Aug 1, 2011 at 2:52 PM, Bruce Fischl wrote: > Hi Chr

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Hi Chris, they are front/back reversed (a/p), which is why everything fails. I don't know how you are ever going to know left from right though. You should talk to whoever got you this data and see if they have some way to tell. cheers Bruce On Mon, 1 Aug 2011, Christopher Luna wrote: I

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

I've uploaded the IMG and HDR files, they are named after my email address. Thank you kindly, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Mon, Aug 1, 2011 at 12:40 PM, Bruc

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange?highlight=%28ftp%29 On Mon, 1 Aug 2011, Christopher Luna wrote: Ah, I forgot about the left/right orientation. Where should I upload these files? Thanks, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGo

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Ah, I forgot about the left/right orientation. Where should I upload these files? Thanks, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Mon, Aug 1, 2011 at 12:23 PM, Bruce Fi

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

how do you know left/right is correct? In any case, if you upload the subject we'll take a look. Things very rarely fail that badly On Mon, 1 Aug 2011, Christopher Luna wrote: > Hi Bruce, > The orientations are correct - they weren't at first so I had to do a lot of > work in tkregister2 to ge

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Hi Bruce, The orientations are correct - they weren't at first so I had to do a lot of work in tkregister2 to get the orientations correct. Unfortunately I only have access to the *.IMG and sometimes the *.HDR file for each subject. Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Hi Christopher, are you sure that the orientations are correct? That is, when you bring the orig.mgz up in tkmedit does the coronal view actually show the brain coronally? Img is a dangerous format to use as it doesn't contain orientation info. Do you have access to the data in some other forma

[Freesurfer] Large White Matter Areas Ignored In Surface Detection

Hello Freesurfers, I'm putting *.IMG files into the program and after correcting talaraich transformations for them, I notice that when the reconstructions have completed, that there are entire lobes of white matter absent from the surfaces detected and from the wm.mgz file. I went through my hand