Thanks Doug, The mri_label2vol for linux32 works for the Windows virtual machine version of FreeSurfer.
Cyrus -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, December 05, 2012 10:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mssing Insula and mri_label2vol script 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, José Ángel 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_labe > l2vol.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 > > -- > > 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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. 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