Re: [Freesurfer] Missing Insula and mri_label2vol

Thanks Doug,

now it works!!

for mac use

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.mac < ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux32

...

doug

On 12/05/2012 05:11 AM, Jos? ?ngel Pineda wrote:

...

Hi again,

Sure I did set the permissions for execution, and also for this new one I am still having the same error. "/Exec format error. Binary file not executable/". I tried this on two macs (OSX Snow Leopard). I am still thinking that this is a compilation issue of the script, that is just compiled for linux.

Thanks for your help

Try this one

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux32

...

On 12/04/2012 12:13 PM, Sarosh, Cyrus wrote:
> Doug,
>
> I am unsure if Jose did this in his attempts to get it to work,
but I ran this command after downloading and receiving this error
initially and even after running this command I still receive the
same error in the Windows virtual machine version of FreeSurfer.
Any other ideas?
>
> Thanks,
>
> Cyrus
>
> -----Original Message-----
> From: freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
[mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] On Behalf Of
Douglas N Greve
> Sent: Tuesday, December 04, 2012 11:58 AM
> To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] (no subject)
>
> Hi Jose, did you set the permissions to be executable?
> chmod a+x mri_label2vol
> doug
>
>
> On 12/04/2012 11:34 AM, Sarosh, Cyrus wrote:
>> Doug,
>>
>> I am also curious about this mri_label2vol upgrade. Will this
work on
>> the Windows virtual machine version of FreeSurfer? I downloaded

and

...

>> placed it in the FREESURFER/bin directory, but when trying to
run it I
>> receive an error that states: Exec format error. Binary file not
>> executable. Thanks for your help.
>>
>> Cyrus
>>
>> *From:*freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] *On Behalf Of *Jos?
>> ?ngel Pineda
>> *Sent:* Tuesday, December 04, 2012 9:07 AM
>> *To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
>> *Subject:* [Freesurfer] (no subject)
>>
>> Thanks Doug,
>>
>> I already downloaded the new script for mri_label2vol, but it
seems it
>> is just compiled for linux, as I cannot execute it in my Mac.
If it is
>> so, could you please upload another compiled for mac, or source.
>> Thanks
>>
>> Jose
>>
>>      For the missing insula problem, try using a newer version of
>>      mri_label2vol
>>
>>

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_labe

...

>> l2vol
>>
>>      The 2nd problem is not so easy to fix. You might be better
off using
>>      aparc+aseg.mgz as input to mri_label2vol instead of the
surface
>>      annotation.
>>      doug
>>
>>
>>      On 12/3/12 10:35 AM, Jos? ?ngel Pineda wrote:
>>      > Dear experts,
>>      >
>>      > I am registering cortical labels from Talairach
coordinates to my
>>      > native T1. For doing this, I have run the next script

lines:

...

>>      >
>>      >
>>      > tkregister --targ brainmask.mgz --mov
highres_brain.nii.gz --reg
>>      > T1FS2Highres.dat --regheader --noedit
>>      >
>>      > mri_label2vol --annot rh.aparc.annot --temp
highres_brain.nii.gz
>>      --reg
>>      > T1FS2Highres.dat --o rh_aparc.nii.gz --hemi rh --subject
FS --proj
>>      > frac 0 1 .1 --fillthresh .3
>>      >
>>      > and the same for the left hemi.
>>      >
>>      > However I am finding two problems at the result. First
Insula is
>>      > missing for both hemispheres, and second the cortical
ROIs have the
>>      > shape of the figure attached, e.g. there are many voxels
empty
>>      >
>>      > Im?genes integradas 1
>>      >
>>      > I found in previous topics, that the mri_label2vol, was
updated
>>      as it
>>      > left last volume from the list out of the conversion. I
tried to
>>      > download it, but it is just compiled for linux, and
since Im working
>>      > with mac I am not able to run it. Could you please give
me any
>>      > comments to solve the problem with the missing voxels.
>>      > About the problem with the insula, the other option is
to just
>>      extract
>>      > it with mri_annotation2label, but if I could get the
mri_label2vol
>>      > working correctly it would be better.
>>      >
>>      > Thanks a lot
>>      >
>>      > Jose