Hi Doug
Thanks.
Generated a new one.. its ok now..
Cheers
Rajeev
*Thu Aug 16 11:18:49 EDT 2012*
Hi Rajeev, did you look in that file to see if there is anything in it?
You can try regenerating the file with
recon-all -s subject -segstats
doug
On 08/16/2012 08:19 AM, rajeev krishnadas
Dear all,
We are designing a study based on clinical data. We want to work with a
MPRAGE sequence but subjects have been given 4 different sets of parameters:
- TR: 1900; TE: 4,38; TI: 1100; flip angle: 15
- TR: 1900; TE: 3,55; TI: 1100; flip angle: 15
- TR: 1900; TE: 3,39; TI: 900; flip angle:
Hi Daniel
those are pretty big differences in flip angle. I'll cc Andre van der Kouwe
on this so he can comment, but I would be hesitant. The increased TE will
have a big effect on dura (darkening it), but will also reduce gray/white
contrast.
cheers
Bruce
On Fri, 17 Aug 2012, Daniel
Hi Alex
when you say it is in the native anatomical space can you elaborate? How
did you create the mask?
Bruce
On Fri, 17 Aug 2012, Alex Kell wrote:
hi freesurfers,
i'm trying to move a volume from a subject's native anatomical space
to that subject's surface space, and i'm running into
hi bruce,
the mask was generated by morphing a binary mask from CVS space back to the
subject's anatomical space. the cvs mask was generated from a functional
parcellation algorithm our lab uses.
if it's useful -- the registration header in the anatomical-space mask is
identical to the
Hi Knut - Does merged_ph1samples.nii.gz exist in your dmri.bedpostX
directory? It's one of the bedpostx output files. If not, it means
bedpostx did not finish running properly. You can try running bedpostx
directly on the dmri directory, not through trac-all -bedp.
Output files of bedpostx
does it align with say the orig.mgz when viewed in tkmedit?
On Fri, 17 Aug
2012, Alex Kell wrote:
hi bruce,
the mask was generated by morphing a binary mask from CVS space back to the
subject's anatomical space. the cvs mask was generated from a functional
parcellation algorithm our lab
Hi Anastasia
This files do not exist in dmri.bedpostX directory. I am now running
bedpostx on the directory.
Knut J
On 08/17/2012 05:35 PM, Anastasia Yendiki wrote:
Hi Knut - Does merged_ph1samples.nii.gz exist in your dmri.bedpostX
directory? It's one of the bedpostx output files. If
Hi Alex
I think Doug is the one to help you. Hopefully he has enough info at this
point
Bruce
On Fri, 17 Aug 2012, Alex Kell wrote:
i don't really use tkmedit. with freeview it's right where it should be --
e.g., see attached.
alex
On Fri, Aug 17, 2012 at 11:43 AM, Bruce Fischl
sorry, it fell through the cracks. Please feel free to resend if I don't
get back in a reasonable amount of time... Try this command instead
mri_segstats --annot subjectname lh aparc --sum lh.sulc.sum --i surf/lh.sulc
the output will be lh.sulc.sum
doug
On 08/16/2012 07:02 PM, Hugh Pemberton
Hi Alex, does the output of mri_vol2surf look ok on the surface? When
you run mri_cor2label, you should use the white or pial surface instead
of inflated, but I don't think that is the problem here. Another thing
to look at is
tkregister2 --mov volumetric-mask --regheader --reg junk.dat --s
Hi Sam, it sounds like what you are doing is correct. Another possible
solution would be to use mri_binarize, something like
mri_binarize EXAMPLE.nii.gz --match 17 --o left.hippo.nii.gz
This matches the number rather than doing a thresholding. It seems like
the thresholding should work, but
Dear freesurfers,
Do I need to normalize volumes (MNI space or Tailarach) from aseg.stats and
aparc.stats before entering data in another statistical programme?
Thanks
Alfredo
___
Freesurfer mailing list
Not really, but you might want to account for total brain size or
(estimated) ICV.
doug
On 08/17/2012 02:13 PM, Alfredo Damasceno wrote:
Dear freesurfers,
Do I need to normalize volumes (MNI space or Tailarach) from
aseg.stats and aparc.stats before entering data in another statistical
hi doug,
i can't visualize it. when i try to use tksurfer (or even mris_info) i get
the following error messages repeatedly (like 100 times and keeps going
until i interrupt the call).
freadFloat: fread failed
No such file or directory
i tried mri_vol2surf using the white surface instead of
what is your command line? You have to load it as an overlay, it isn't a
surface just a scalar field over the surface
On Fri, 17 Aug 2012, Alex Kell
wrote:
hi doug,
i can't visualize it. when i try to use tksurfer (or even mris_info) i get
the following error messages repeatedly (like 100
Ah, I did not see that you had used inflated in your original vol2surf
command. That is definitely the source of the misplaced label. The
surf_name.mgz file is not a surface, it is an overlay. If you are trying
to load it as a surface in tksurfer (or getting info from mris_info),
then it will
Hi Maria, unpacksdcmdir is for Siemens dicoms only. Try using dcmunpack
instead.
doug
On 08/16/2012 03:47 PM, iac...@nmr.mgh.harvard.edu wrote:
Hi,
I've been trying to sort some dicom and to convert them into nifti volumes.
I am using the command:
unpacksdcmdir -src $source -targ $target
ah, thanks -- i didn't realize the distinction.
also, i think i've figured out what was wrong. i shouldn't sample to the
inflated surface -- i should sample to the white surface.
the call that lead to misplacement:
mri_vol2surf --mov volumetric_mask --regheader subj_id --hemi rh
--inflated --o
Sure, glad it worked out
Bruce
On Aug 17, 2012, at 3:03 PM, Alex Kell alexk...@mit.edu wrote:
ah, thanks -- i didn't realize the distinction.
also, i think i've figured out what was wrong. i shouldn't sample to the
inflated surface -- i should sample to the white surface.
the call
Hello,
The corpus callosum (CC) segmentation in my aparc+aseg.mgz file is not OK. It has included the fornix and ventricular areas within the CC. I erased with edit tool in the tkmedit and saved the new segmentation.
How do I do to reprocess the subject and correct the stats (volume, etc)? Is
21 matches
Mail list logo
