Hi Doug,
Thanks for your reply. Here are the message:
ERROR:
/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm
is not a dicom file or some other problem
Entering IsDICOM
(/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm)
Opening
/hom
Hi Freesurfer experts,
We’ve been collecting structural (1mm isotropic) and functional (2.75x2.75x3mm)
data on a Philips 3T scanner using an 8-channel head coil. We are
reconstructing each subject’s surface and mapping functional data processed in
FSL’s FEAT to the surface. For some subjects, w
Hello again,
In Qdec we get a plot of the data for a particular vertex showing the variable
and the thickness in the x, y axis respectively. Is there a way to get the same
plot when using glmfit? Where do I find the data for the plot? Thank you!
Jeni Chen
__
Hi Doug.
The missing files are NOT in $FREESURFER_HOME/bin; So, I guess that's
why they are not found even though the path is set up in the system
PATH variable.
Suggestions?
Fidel
Are the missing files in $FREESURFER_HOME/bin and is that path in your
system PATH variable?
On 07/26/2012 01:
Hi Jeni, usually you smooth with surf2surf and include a mask or label
to indicate that it should only be smoothed inside the mask/label.
mri_glmfit will create a mask from non-zero voxels; if you ask glmfit to
smooth, then it will only smooth inside of the mask. If you smooth using
surf2surf,
Mostly yes. The one in mri_glmfit will also do smoothing within a given
mask by default, but basically they do the same thing.
doug
On 7/29/12 11:15 PM, Jeni Chen wrote:
> So essentially the -fwhm option in mri_glmfit does the same thing as
> mri_surf2surf --fwhm ? Just want to make sure... Tha
So essentially the -fwhm option in mri_glmfit does the same thing as
mri_surf2surf --fwhm ? Just want to make sure... Thanks again!
Jeni
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can you send us the output of that command?
On Sun, 29 Jul 2012, Douglas
Greve wrote:
> what do you mean a "document file"?
>
> On 7/29/12 7:58 PM, Skyler Gabriel Shollenbarger wrote:
>> Hi,
>>
>> Trying to convert a file to mgz and keep getting a 'document file' instead
>> of the freesurfer mgz
what do you mean a "document file"?
On 7/29/12 7:58 PM, Skyler Gabriel Shollenbarger wrote:
> Hi,
>
> Trying to convert a file to mgz and keep getting a 'document file' instead of
> the freesurfer mgz file. This is the command I used:
> mri_convert -ot mgz -anat+orig.BRIK freesurfer/mri/o
Hi,
Trying to convert a file to mgz and keep getting a 'document file' instead of
the freesurfer mgz file. This is the command I used:
mri_convert -ot mgz -anat+orig.BRIK freesurfer/mri/orig/001.mgz
Any suggestions? Thanks!
Skyler
--
Skyler G. Shollenbarger
Graduate Student - UWM Br
Hi Jeni, yes that means you would be double smoothing your data.
doug
On 7/29/12 6:03 PM, Jeni Chen wrote:
> Hello Freesurfer experts,
>
> Just a question about smoothing. I did recon-all -qcache to get pre-smoothed
> fsaverage surface at 0, 5, 10, 15, 20 and 25mm FWHM, so for mris_preproc I
> u
Hello Freesurfer experts,
Just a question about smoothing. I did recon-all -qcache to get pre-smoothed
fsaverage surface at 0, 5, 10, 15, 20 and 25mm FWHM, so for mris_preproc I used
the "--cache-in" option (eg. for the *10mm.fsaverage file). When I run
mri_glmfit, I see the option "--fwhm". I
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