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_label2volftp://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 offusing
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 havethe
> 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 Imworking
> 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 themri_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