Re: [Freesurfer] (no subject)

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 *José Ángel 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

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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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