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-boun...@nmr.mgh.harvard.edu > > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu > > <mailto:freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu > > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > > >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu > > <mailto:freesurfer-boun...@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 > >
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