r/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz --o
> t-in-mni152.nii
>
> doug
>
>
> On 07/31/2014 11:05 AM, jaco...@nmr.mgh.harvard.edu wrote:
>> Hello Doug,
>>
>> Ideally, I am trying to take subject tstat maps from FsFast (stable3
>> environment)
;m not sure what you are trying to do, but that command line looks
like
>> things are not set up properly. What is t_000.bfloat? (And why are you
using bfloats?)
>> doug
>> On 7/17/14 1:14 PM, jaco...@nmr.mgh.harvard.edu wrote:
>>> Hello again Doug,
>>> Thank y
Thank you for the heads up Bruce.
> Hi Jacob
>
> Doug is on vacation for a couple of weeks, so you should probably repost
> in early August.
>
> cheers
> Bruce
> On Mon, 21 Jul 2014, jaco...@nmr.mgh.harvard.edu wrote:
>
>> Hello Doug,
>>
>> Ideally
;m not sure what you are trying to do, but that command line looks
like
>> things are not set up properly. What is t_000.bfloat? (And why are you
using bfloats?)
>> doug
>> On 7/17/14 1:14 PM, jaco...@nmr.mgh.harvard.edu wrote:
>>> Hello again Doug,
>>> Thank y
'm not sure what you are trying to do, but that command line looks like
> things are not set up properly. What is t_000.bfloat? (And why are you
> using bfloats?)
> doug
>
>
> On 7/17/14 1:14 PM, jaco...@nmr.mgh.harvard.edu wrote:
>> Hello again Doug,
>>
>&g
Hello Freesurfer Experts,
I am trying to view stats generated with FsFast in fslview/MNIspace, and
in doing so I have run mni152reg to generate the registration matrix.
That said, mni152reg did not complete correctly and below I have pasted
the terminal output:
Thu Jul 17 09:58:10 EDT 2014
sete
Thank you Doug, that seems to solve the issue!
> Try this instead
>
> mri_vol2vol --inv --targ M4_LH_orig.mgz --mov
> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o M4_LH_orig_MNI152.nii.gz
> --interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat
>
> On 07/1
Hello Freesurfer,
I am attempting to take label files generated in fsaverage surface space
and transform them into MNI152 volume space.
Using the commands below, I am able to view the final output image with
fslview in the the same space as the MNI brain. However, the registration
is very off. Ad
10:34 AM, "jaco...@nmr.mgh.harvard.edu"
>> wrote:
>>
>> I have not tried dev version. Can you please let me know how I can load
>> that?
>>
>>> Have you tried dev version?
>>>
>>> On May 6, 2014, at 10:15 AM, "jaco...@nmr.mgh.har
I have not tried dev version. Can you please let me know how I can load that?
> Have you tried dev version?
>
> On May 6, 2014, at 10:15 AM, "jaco...@nmr.mgh.harvard.edu"
> wrote:
>
>> Hello All,
>>
>> Any idea why freeview fails to open? Below I ha
Hello All,
Any idea why freeview fails to open? Below I have included the terminal
output.
I have checked my quota and I have plenty of available memory. I also
tried running the 2 options (-start_in_debugger and
-on_error_attach_debugger), but these were not recognized. I was next
going to atte
Thank you Doug!
>
> On 5/1/14 3:59 PM, jaco...@nmr.mgh.harvard.edu wrote:
>> Hello Freesurfer Experts,
>>
>> Using func2roi (in stable3), we constrained our functional data with
>> specific surface labels and t thresholds, and over-threshold masks were
>> o
Hello Freesurfer Experts,
Using func2roi (in stable3), we constrained our functional data with
specific surface labels and t thresholds, and over-threshold masks were
outputted as .bfloat files. Does this mean these masks are in volume
format and that the volumetric functional data was mapped to t
No worries, thank you for the help!
> oops, sorry, that is an option to mri_vol2vol, not vol2surf. Just
> exclude that option
>
> On 04/30/2014 02:48 PM, jaco...@nmr.mgh.harvard.edu wrote:
>> Hello Doug,
>>
>> Thank you for such a quick reply and for your insight.
output file with extension. Try the cmd
> below
>
> mri_vol2surf --mov /.../tstat2.nii.gz --fstarg
>--mni152reg --hemi rh
> --surf white --o /.../stats/output.mgh
>
>
> On 04/30/2014 11:55 AM, jaco...@nmr.mgh.harvard.edu wrote:
>> Hello Freesurfer Experts,
>&
Hello Freesurfer Experts,
I was wondering if someone can help me understand which options I need to
include with mri_vol2surf for the following situation?
I am trying to take group stats generated within FEAT that are in
MNI152_2mm space and registrar/project those to fsaverage inflated
surface.
Thank you, much appreciated!
>
> Is this the same question posted yesterday on martinos-tech? I answered
> it as below
>
> Yes, those are in the sig.nii.gz file (these are -log10(p)). The DOF is
> related to the number of TRs
> doug
>
> On 04/29/2014 04:49 PM, jaco..
-- Forwarded message --
Hello Doug et al.,
I was wondering if anyone could give me some information about whether a p
value can be associated with t maps generated in individual subjects
(across one or two runs) for fMRI data. When doing group contrasts an
uncorrected p value can b
Hello again,
It seems the issue was being caused by a change we had made to our
director structure that did not account for a reference document to some
of the outputs from earlier processing.
Thank you,
Jacob
> Hello Freesurfer experts,
>
> We are trying to run func2roi-sess in stable 3 (this
Hello Freesurfer experts,
We are trying to run func2roi-sess in stable 3 (this command still exists
in stable 3). However, we get an error that says it can't find the
analysis.info file, even though it is definitely there (not to mention
that we previously ran this analysis for the same subjects u
20 matches
Mail list logo
