Hi Francesca
your output is a volume not an ROI, so you need to load it as a volume in freeview to check it
cheers Bruce
On Thu, 3 Dec 2015, Francesca Strappini wrote:
Thanks! I run this command:
mri_label2vol --label lh.V1dorsalLG_MNI.label --temp /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --regheader /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o lh.V1dorsalLG_MNI.nii.gz
but unfortunately, it gave me the same big downward shift (I checked it with fslview).
But if I try to open the ROI with freeview it gives me this error: freeview.bin: empty label LabelRead failed freeview.bin: empty label
2015-12-03 16:57 GMT+02:00 Douglas Greve greve@nmr.mgh.harvard.edu: Use --regheader /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz instead of --identity
On 12/3/15 8:46 AM, Francesca Strappini wrote: Thank you!I run the recon-all on the MNI brain and now the first step, label2label, produced a label which is perfectly mapped on the surface of the MNI template. I tried to run the second step, mapping the new label to the volume, but I still got the shift downward.
mri_label2vol --label lh.V1dorsalLG_MNI.label --temp /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o lh.V1dorsalLG_MNI.nii.gz --identity
Best Francesca
2015-12-01 20:26 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu: Try adding --invertmtx to the mri_label2vol command. I don't think the label2label command does anything, does it? Also, you might have better alignment if you run recon-all on the mni152 brain, then use mri_label2label to map the label from the individual into the 152 space using the surface transform, then convert that to the volume.
On 11/30/2015 10:13 AM, Francesca Strappini wrote: > Dear FreeSurfer experts, > > I'm trying to convert some retinotopic labels I created on the surface > of each individual subject to MNI305 space for FSL. > > I run the following commands, but the output is not registered > correctly. It seems to be shifted downward. > > mni152reg --s LG > > mri_label2label --srclabel lh.V1dorsalLG.label --s LG --regmethod > surface --trglabel lh.V1dorsalLG_new.label --hemi lh > > mri_label2vol --label lh.V1dorsalLG_new.label --reg > /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg --temp > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o > lh.V1dorsalLG_new_MNI.nii.gz > > Thanks for your help, > Francesca > > -- > Francesca Strappini, Ph.D. > Neurobiology Department > Weizmann Institute of Science > 234 Herzl Street, Rehovot 7610001 Israel > Tel.: +972 58 444 2584 > E-mail: francesca.strappini@weizmann.ac.ilmailto:francesca.strappini@weizmann.ac.il
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-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini@weizmann.ac.il
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini@weizmann.ac.il