New subject: Mssing Insula and mri_label2vol script

5 Dec 2012

      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] On Behalf Of Douglas N Greve
...
Sent: Tuesday, December 04, 2012 11:58 AM
To: 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] *On Behalf Of *Jos?
?ngel Pineda
*Sent:* Tuesday, December 04, 2012 9:07 AM
*To:* 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

--
José Angel Pineda Pardo
Center of Biomedical Technology (CTB)
Parque Científico y Tecnológico de la UPM
Campus de Montegancedo
28223 Pozuelo de Alarcón, Madrid, ES

Re: [Freesurfer] Mssing Insula and mri_label2vol script