There is some white matter there being excluded as well. If you include that,
the pial surface will likely grow out and include that gm.
On Aug 1, 2011, at 7:37 AM, _andre...@sapo.pt wrote:
> Dear FS experts,
>
> I'm correcting the pial surface when it includes more than it is supposed,
> but
Hi Andreia
it's tough to tell from one slice. There appear to be some bright stuff
in the superficial gray matter, which may be messing stuff up, not sure
what it is, or it could be something happening through-plane that we
can't see. If you want to upload the dataset I'll take a look
cheers
B
Dear all,
I am trying to make group level analysis of functional data on the surface and
add per-vertex regressors (PVR, here: cortical thickness) into the design. When
I view the results I have the feeling that the PVR is not really included in
the model:
I am using the command:
mri_glmfit --
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
Hi Hiroyuki
can you send us the mris_flatten command and all it's output?
cheers
Bruce
On Mon, 1 Aug
2011, Oya, Hiroyuki (UI Health Care) wrote:
Dear all,
A patch created by mris_flatten looked odd (see attached image) . Any
suggestion for this problem?
Original patch (before flatteni
thanks. Nick: any idea?
On Mon, 1 Aug 2011, joanna floria wrote:
Hi Bruce,
Yes, please find two log files attached. I renamed one with label 2. These
were for two different datasets and I think the error was the same.
Thanks
Joanna
On Fri, Jul 29, 2011 at 3:34 PM, Bruce Fischl
wrote:
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
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
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
Hi Bruce,
So for the following command:
bbregister --s bert --mov func.nii --init-fsl --reg register.dat
tkregister2 --mov func.nii --reg register.dat --surf
In the case of a retinotopy analysis, which files are register.dat and
func.nii?
Quoting Bruce Fischl :
[Hide Quoted Text]
Hi Michelle
func.nii is the functional data you want to register, and the
register.dat is the output of bbregister.
cheers
Bruce
On Mon, 1 Aug 2011, Michelle Umali wrote:
> Hi Bruce,
> So for the following command:
> bbregister --s bert --mov func.nii --init-fsl --reg register.dat
>
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
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
Hi,
I am also getting the error where the txt files cannot be opened because they
were not created beforehand. Where does the trac-all -prior step take place?
Does it appear within the trac-all -prep script?
Thank you,
Ammar Moiyadi, BS
Professional Research Assistant
Department of Psychiatry
U
Hi Ammar - Yes, -prior is the last step included in -prep. Are the text
files missing for all tracts, or specifically for lh.cst?
Thanks,
a.y
On Mon, 1 Aug 2011, Moiyadi, Ammar wrote:
> Hi,
> I am also getting the error where the txt files cannot be opened because they
> were not created befo
Hi Ping,
This is an issue with the mac build, that we are currently working on
fixing. Anastasia, (cc'd) is working on a patch that you can download to
resolve this issue.
As far as the nb0 value is concerned you're correct, it assumes that the
first 7 volumes are b0, but it uses that to compute
Hi Branka
those are really big bias fields in your data that are causing the
problems. Can you tell us about the acquisitions? What field strength?
Scanner? Coil? Sequence?
thanks
Bruce
On Mon, 1 Aug 2011, Branka Milivojevic wrote:
> Hi,
>
> I'm a relatively new user of freesurfer, so I don
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
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
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
Dear Sir/Madam,
I would like to use freesurfer for cortical flattening, working with the nii
format. When I try to load the nii.gz file as described on
http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html, I get the following error:
student@BMT-PC125:~$ tkmedit -f t1.nii.gz
niiRead(): error open
hmmm, that should have worked. Do you want to email us the t1.nii.gz
volume and we'll take a look?
On Mon, 1 Aug 2011, Tax, C.M.W. wrote:
> Dear Sir/Madam,
>
> I would like to use freesurfer for cortical flattening, working with the nii
> format. When I try to load the nii.gz file as described
But of course, Bruce says the .nii.gz format should have worked, so it does not
need to be type mgz format. I would trust Bruce. Sorry for not cc'ing the
mailing list earlier.
Thanks,
John
John Drozd
Post-Doctoral Fellow
Robarts Research Institute
University of Western Ontario
London, Ontario,
Hi:
In the web page "FSTutorial/TroubleshootingData - Free Surfer Wiki"
appears "Try using an xopts script first to change the intensity
thresholds being used"... What is a xopts script ?... How can I use a
xopts script to change the intensity thresholds ?...
Sincerely,
Gonzalo Rojas Co
Hi,
I am using mri_label2vol to generate some volume ROIs from surface labels. I
noticed that the results contain "holes", by which I mean voxels that aren't
label and are surrounded by labeled voxels. This seems to happen regardless of
the step size I specify after the "--proj" option of mri_labe
I would like to run FreeSurfer just up to the point it creates the aseg file,
and no further. I believe this would be steps 1 through 11. Is there any way
other than making a copy of the recon-all script and removing everything after
step 11. Not sure I know exactly where this is.
-Jeff
___
26 matches
Mail list logo
