Thanks Doug,
The mri_label2vol for linux32 works for the Windows virtual machine version of FreeSurfer.
Cyrus
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 oneftp://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-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto: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 <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-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >> [mailto: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 <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
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