hi Doug,
I am sorry but I still don't get it.
If:
label vector lookup of annotation values for
corresponding vertex index.
and label contains some 0 and 0 is not a valid id in colortable.table(:, 5)
what should I do with my vertices whose label is 0?
thanks
Alex
On Mon, A
sure, if you send it we will try to take a look
Bruce
On Tue, 27 Aug 2013, Yuval
Harpaz wrote:
Dear Team
I tried to convert AFNI BRIK file to mgz using mri_convert. the MRI was
shifted strangely.
I overcame it by converting the MRI to nii using afni command (3dcopy) and
from there to mgz wi
Dear FS experts,I am contacting you to report an error after launching recon
-all for one of my subjects (see below). I am using a macbook pro with snow
leopard version 10.6.8.
I would greatly appreciate if you could advise me which step/s should I take to
correct this.Thank you for your attent
Nope, there's no flipping in tracula. But, *both* the gradient vectors and
the DWIs are converted to LAS orientation as the first step in the
preprocessing. This makes the FSL tools that are run later in the
preprocessing (dtifit and bedpostx) run smoothly without any flipping.
On Mon, 26 Au
Hi FS Commuity,
I am using the stable version 5.3 of FS to recon-all a subject of mine,
but the job is aborted and gives the following message:
The command that I ran is: recon-all -all -subjid
/cluster/ichresearch/Petechial/MEG/CAA_022_struc
Subject Stamp: freesurfer-Linux-centos6_x86_64-st
Hi Pablo
have you visually inspected the talairach xform to see if it is indeed
incorrect? What input format did you start with? Most of these occur
because people start with analyze, which doesn't have the direction
cosines, and so the data is oriented incorrectly
cheers
Bruce
On Tue, 27
try this instead
recon-all -all -subjid CAA_022_struc
On 08/27/2013 11:23 AM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS Commuity,
>
> I am using the stable version 5.3 of FS to recon-all a subject of mine,
> but the job is aborted and gives the following message:
>
> The command that I ran is: r
Hello,
I am having a few issues with editing the pial surface in freeview. It appears
as though the edits I make to the brainmask are not being taken into account
when I re-run recon-all. I work on a MacBook Pro and have been using
"shift+click" to delete voxels at a brush value of 1 and then s
Hi Heidi, the problem is being caused by the interaction column. Try
demeaning the ed_log and MMSE before multiplying them together to get
the interaction. Do the demeaning on the entire data set, not on a group
by group basis.
doug
On 08/27/2013 02:04 AM, Jacobs H (NP) wrote:
> Sure, her
Thank you very much for your input. Yes, I did start with analyze format and
also I have visually inspected the images. Almost all my scans consistently
show an extended whole in the prefrontal area (with a few exception of some
scans showing this in posterior locations).
I am assuming the best
yes, definitely. The dicoms are best
On Tue, 27 Aug 2013, pablo najt wrote:
Thank you very much for your input. Yes, I did start with analyze format and
also I have visually inspected the images. Almost all my
scans consistently show an extended whole in the prefrontal area (with a few
excepti
I think the 0s represent "unknown" areas. In this case, vertices that
were not part of any cluster. Does that make sense?
doug
On 08/27/2013 07:47 AM, Alexandre Gramfort wrote:
> hi Doug,
>
> I am sorry but I still don't get it.
>
> If:
>
> label vector lookup of annotation
Hi Doug,
The same error message comes up.
Panos
> try this instead
>
> recon-all -all -subjid CAA_022_struc
>
> On 08/27/2013 11:23 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi FS Commuity,
>>
>> I am using the stable version 5.3 of FS to recon-all a subject of mine,
>> but the job is aborted an
Can you run it with -debug as the first option and send me the terminal
output?
On 08/27/2013 12:36 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> The same error message comes up.
>
> Panos
>
>> try this instead
>>
>> recon-all -all -subjid CAA_022_struc
>>
>> On 08/27/2013 11:23 AM, pfot..
Sure thing, I have attached it.
Best,
Panos
> Can you run it with -debug as the first option and send me the terminal
> output?
> On 08/27/2013 12:36 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> The same error message comes up.
>>
>> Panos
>>
>>> try this instead
>>>
>>> recon-all -al
It did not generate the error because the IsRunning file still exists.
Can you delete this file
/autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/
scripts/IsRunning.lh+rh
and re-run, capturing the output to send to me?
doug
On 08/27/2013 12:47 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Sur
Hi I have one last question. I just noticed that my images are in Philips
format. Would you recommend to convert to DICOM anyway? Or should I used
NIFTI?Thanks,Pablo
Date: Tue, 27 Aug 2013 12:31:09 -0400
From: fis...@nmr.mgh.harvard.edu
To: pablon...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.ed
Hi again,I still have a doubt about how to proceed with the processing of my
images. Correcting my original response to the format of my images: I ran recon
-all -all with NIFTI images (but converted from analyze format). I have
converted this by opening them with MRIron and saving as NIFTI.gz (
hi doug,
this helps thanks. A next question is why can we have in the colortable
a structureID that has no corresponding vertex with this label?
In my example it was 3834223 but I get the same thing with
"fsaverage/label/lh.aparc.annot"
that has a 3294840 structureID not present in the label arra
It looks like there might be some3ting wrong with this file
/autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/mri/orig/001.mgz
how was it created? Can you open it in tkmedit (eg, tkmedit -f 001.mgz)
doug
On 08/27/2013 01:43 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Yes, sorry about that.
Hi Pablo
once you go through analyze format the direction cosines are lost. Can you
get the data before they were converted to analyze? If not, how will you
ever tell left from right?
Bruce
On Tue, 27 Aug 2013, pablo najt wrote:
Hi again,I still have a doubt about how to proceed with the pro
For aparc, that is the corpus callosum. It just means that it was in the
color table when the annotation file was created. It is not necessary
that it be in the annotation itself. Can you ignore it?
doug
On 08/27/2013 03:33 PM, Alexandre Gramfort wrote:
> hi doug,
>
> this helps thanks. A next
> For aparc, that is the corpus callosum. It just means that it was in the
> color table when the annotation file was created. It is not necessary
> that it be in the annotation itself. Can you ignore it?
now that I have your approval to ignore it yes :)
thanks all clear.
Alex
__
Dear Supporter
I am new to freesurfer and have started to download tutorial data for
tracula.There is an error saying: "hostname: Host name lookup failure"
what shall I do?
Regards
Leyla___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https:
Dear All,
I would like to upgrade my freesurfer distribution to the latest
version - Is there an automated procedure to do this?
My current version is
linux-gnu-stable5-20110522
Many thanks!
Otto
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Dear Zeke,
Thank you very much!
My problem was eventually solved by downloading the whole freesurfer
package.
Sincerely,
Ye
On Fri, Aug 16, 2013 at 3:51 PM, Z K wrote:
> Ye,
>
> Freesurfer is a fairly large and complex software bundle that contains
> plenty of dependencies if you are going t
Hello,
Is there a way to apply a label to a mgh file? I would like to show a gray
brain with values from an mgh shown only in the significant areas (ie only
within my label). Is there a way to do this?
I have a set of mgh files with beta values from a regression. I also have a
set of labels for t
you can convert the label to a binary mask with mri_label2label with the
--outmask option
You can then apply it to your mgh file with mri_mask
doug
On 8/27/13 7:46 PM, Sarah Madsen wrote:
Hello,
Is there a way to apply a label to a mgh file? I would like to show a
gray brain with values fr
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