sorry
try:
cd Users/sampada/Desktop/
mkdir test
cd test
mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii
sampada/Desktop/test/s400a1001.mgz
Hth,
shantanu
On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote:
> You don't need the quotation marks in your path
> also, it seems you don't hav
You don't need the quotation marks in your path
also, it seems you don't have a directory called
/Users/sampada/Desktop/test/org
try something like:
cd Users/sampada/Desktop/
mkdir test
cd test
mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii
sampada/Desktop/test/s400a1001.nii
Hth,
shan
I want to use surf2vol to get volume files of gray thickness.And
the --volreg
Contains the matrix that maps XYZ
in the reference anatomical to XYZ in the functional volume. So I use
bbregister.Why I need not invert the BBR registration matrix with
surf2vol?I mean , the BBR registration matrix
Hello Shantanu,
Many thanks for your reply! This is my exact commandline which I give to
free surfer for the 1st of the eight nii files. When i am able to convert
this nii to mgz then i will ask how to convert all the eight files at one
go.
mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001
but are there holes in the cortex label irrespective of what is
happening in the fMRI?
On 5/6/14 4:44 PM, Cesar Echavarria wrote:
I looked at the surface mask and it seems those 0-valued vertices are
0-valued in the mask as well (image attached). Is there a way to
correct this? To reiterate
Hi Virendra,
There are tools embedded in the process of surfaces' creation in FreeSurfer
which are correcting the topology and prevent the surface to have holes in it.
So if you use the pial surface that you get from the recon-all process, you'll
be safe for inputing them to the lGI computatio
can you send your exact mri_convert commandline?
On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote:
> *Hello freesurfer*
>
> *Sorry for the personal message Shantanu. *
>
> *I managed to convert my dicom to nifti using mricron software, though had
> to make some changes to the preferences. *
>
*Hello freesurfer*
*Sorry for the personal message Shantanu. *
*I managed to convert my dicom to nifti using mricron software, though had
to make some changes to the preferences. *
*About the dcmunpack: The user manual on dcmunpack on fs site says that the
unpackdcmdir is used only to unpack Sie
Hi Marie,
Following your advice, I want to compute IGI for pial surface and
mris_euler_number gives me 68 holes. What is the procedure to fill these holes?
Thank you,
Sincerely,
Virendra
From: Marie Schaer [mailto:marie.sch...@unige.ch]
Sent: Wednesday, April 30, 2014 7:50 PM
To: Virendra Mis
To add to my previous e-mail, it seems the surface masks differ from run to
run. The run whose registration we revised manually seems to have no
problem. We then use the registration from this run as the initial point
for the registration of subsequent runs. These later runs do show those
"holes" o
Dear FS list,
I have structural data from a learning study (pre&post-training scans, with
3 groups). Although the training was only one week, I'm guessing from an
analysis point of view, this still qualifies as longitudinal. I want to
check for
- the main within-subjects effect of time point (
Is the cortex label 0 in the same locations where you have 0s in the
surface mask?
On 05/06/2014 12:07 PM, Cesar Echavarria wrote:
> Hi Doug,
>
> Me and Shahin have looked at the registration and it looks fine. I
> know the activation is 0 because when I click on those vertices it
> tells me t
You have to pass the label to mri_glmfit. The mask is created there.
--cache-label to mri_glmfit-sim assumes that you are using pre-computed
results with the given label, eg, the cortex label pre-computed results
are be found here
$FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex. It
Thanks for the replies Bruce and Doug. Do either of you know of any
publications (or posters) that address the issue of editing effects in healthy
controls?
Also do you know where I could find some examples of "bad" reconstructions? I
have seen screenshots/images on the wiki, but I am looking f
Hi Doug,
Me and Shahin have looked at the registration and it looks fine. I know the
activation is 0 because when I click on those vertices it tells me the
tksconcat.nii value is "**0.00**". I looked at the cortex.label file
and found the 0-valued vertices within the file. We have scanned the
Thank you for the source details for dev. I just tried running freeview
under the dev environment and I still received the same error message.
Any other ideas on what may be going on?
Thank you!
> Just run:
> source /usr/local/freesurfer/nmr-dev-env
>
>> On May 6, 2014, at 10:34 AM, "jaco...@nmr
Just run:
source /usr/local/freesurfer/nmr-dev-env
> On May 6, 2014, at 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.harv
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 have included the terminal
>> output.
>>
>> I have
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 have included the terminal
> output.
>
> I have checked my quota and I have plenty of available memory. I also
> tried running the 2 opti
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
Hi Jason
it's hard to say a priori, particularly since this probably isn't even
really an mp-rage (given that it's a GE scanner) and that you are using
an 8 channel array. I guess I would say try it out and see.
As far as a pedi atlas, I'm not sure, perhaps Avi can comment?
Bruce
On Tue, 6
If you don't see an effect of gender, then it is ok to leave it out of
the model. I could be affecting the power as you suspect.
doug
On 5/6/14 3:55 AM, Anna Jonsson wrote:
thank you. I have another question; I am getting several significant
clusters for group, when correcting for multiple c
What command lines are you using? You don't need to invert the BBR
registration matrix with surf2vol
doug
On 5/5/14 10:54 PM, ??? wrote:
Dear Freesurfer:
I have some problems with using mri_surf2vol .I'd like to ask if
you could help me with this.--volreg Contains the matrix that maps
Hi there,
I am working on a project that involves pediatric data, ages 3-12. We are
using Freesurfer to generate cortical surfaces. Information regarding the
T1 acquisition is listed below. Is it appropriate to use the -3T and
mprage flags for such data? Is there an alternative, pediatric atlas, t
Hi Gabor
we do partial volume correction when we compute the aseg.stats
cheers
Bruce
On Tue, 6 May
2014, Gabor Perlaki wrote:
> Dear all,
>
> I've loaded the mri/aseg.mgz in slicer3D and done a label statistics
> on the image. The left caudate was reported to be 4005 mm^3 and the
> right caudat
Dear all,
I've loaded the mri/aseg.mgz in slicer3D and done a label statistics
on the image. The left caudate was reported to be 4005 mm^3 and the
right caudate to be 4011 mm^3 by Slicer3D. However, these numbers are
somewhat different from the values reported in aseg.stats: 3757 mm^3
and 3901 mm^
thank you. I have another question; I am getting several significant
clusters for group, when correcting for multiple comparisons and total
brain size and age, but when I enter sex in, msot of these disappear, but i
do not understand whether this is a power issue (as qdec automatically
incorporates
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