Hi Doug So I tried running mni152reg and had the following error:
mni152reg --s icbm-102_test setenv SUBJECTS_DIR /data-01/trisanna/freesurfer cd /home/trisanna /usr/local/freesurfer-5.3//bin/mni152reg --s icbm-102_test fslregister --mov /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --s icbm-102_test --reg /data-01/trisanna/freesurfer/icbm-102_test/mri/transforms/reg.mni152.2mm.dat --dof 12 mkdir: cannot create directory ‘/usr/share/fsl/5.0/data/standard/tmp.fslregister.11061’: Permission denied I spoke with our IT guy and he says that of course I cannot be writing to fsl/5.0/data. I then did a web search and found that someone else was having this problem https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41276.html How might I fix this? Let me know if I should send the log file that was created. best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Apr 8, 2016 at 1:33 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > not sure, mni152reg uses $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz > > You can always just run the following command directly > > fslregister --mov icbm.nii.gz --s $subject --reg > $SUBJECTS_DIR/subject/transforms/icbm.reg.dat --dof 12 > --lta $SUBJECTS_DIR/subject/transforms/icbm.reg.lta > > This will use a linear (12 dof) registration which might not be > particularly accurate > > > On 04/08/2016 01:27 PM, Trisanna Sprung-Much wrote: > > thanks, Doug. I'll get started on running all brains using recon-all. > > > > The MNI has several ICBM templates now: > > > > ICBM152 linear > > ICBM152 nonlinear symmetric VI > > ICBM152 nonlinear 2009 > > > > Do you know which one mni152reg is using? > > > > Trisanna > > > > -- > > Ph.D. Candidate > > McGill University > > Integrated Program in Neuroscience > > Psychology > > > > > > On Fri, Apr 8, 2016 at 12:47 PM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > > > On 04/07/2016 03:50 PM, Trisanna Sprung-Much wrote: > > > thanks, Doug. I am still extremely confused, however. *Am I meant > to > > > run recon-all first? *I was told in a previous email that I > > should do > > > this first, however, I thought that Freesurfer takes the volumes > and > > > does a linear registration to MNI305 template, which would not work > > > for my scans that are linearly registered to ICBM152 nonlinear 2006 > > > template... > > run recon-all first, otherwise you won't have surfaces. recon-all > > computes the transform matrix to the mni305 but keeps all the data in > > the native anatomical space. I think the ICBM152 is the same as the > > MNI152. Is that right? If so, you can use mni152reg to compute the > > registration to 152 space. If not, then we'll have to workout > > something > > else. > > > > > > When you have a moment, could you please outline in a step by step > > > manner the steps I should run to take my labels.mnc and my volumes > > > such that I can generate surfaces for those 50 volumes, overlay the > > > labels (for which I thought I was using mri_vol2surf) and then edit > > > those labels to make them more accurate? > > so you want to transfer the labels from labels.mnc to the surfaces of > > your individual 50 subjects? Start by running recon-all on the 50. > > > *The idea is that I want to generate some sulcal probability maps > > > using surface-based registration, as I can already generate > > > probability maps using volumetric registration quite easily.* > > > > > > many thanks > > > > > > Trisanna > > > > > > > > > > > > > > > > > > > > > -- > > > Ph.D. Candidate > > > McGill University > > > Integrated Program in Neuroscience > > > Psychology > > > > > > > > > On Wed, Apr 6, 2016 at 2:43 PM, Douglas Greve > > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > > > For the 152, you can run mni152reg --s subject, then specify > > > $SUBJECTS_DIR/subject/mri/transform/mni152reg.dat (or .lta) for > > > the argument to --reg. I'll need to figure out how to generate > a > > > .dat/.lta for the 305. > > > > > > > > > > > > On 4/6/16 12:50 PM, Trisanna Sprung-Much wrote: > > >> Any ideas? > > >> > > >> Trisanna > > >> > > >> -- > > >> Ph.D. Candidate > > >> McGill University > > >> Integrated Program in Neuroscience > > >> Psychology > > >> > > >> > > >> On Tue, Apr 5, 2016 at 9:37 PM, Trisanna Sprung-Much > > >> <trisanna.sprung-m...@mail.mcgill.ca > > <mailto:trisanna.sprung-m...@mail.mcgill.ca> > > >> <mailto:trisanna.sprung-m...@mail.mcgill.ca > > <mailto:trisanna.sprung-m...@mail.mcgill.ca>>> wrote: > > >> > > >> Hi Dr. Fischl > > >> > > >> I have a mixture - some of the labels were painted in the > > >> MNI305 space (older ones) and the more recent ones are > > >> registered to the ICBM152 nonlinear symmetric VI (2006) > > template. > > >> > > >> Best > > >> > > >> Trisanna > > >> > > >> -- > > >> Ph.D. Candidate > > >> McGill University > > >> Integrated Program in Neuroscience > > >> Psychology > > >> > > >> > > >> On Tue, Apr 5, 2016 at 6:34 PM, Bruce Fischl > > >> <fis...@nmr.mgh.harvard.edu > > <mailto:fis...@nmr.mgh.harvard.edu> > > >> <mailto:fis...@nmr.mgh.harvard.edu > > <mailto:fis...@nmr.mgh.harvard.edu>>> wrote: > > >> > > >> Hi Trisanna > > >> > > >> what space are your labels in? > > >> > > >> cheers > > >> Bruce > > >> On Tue, 5 Apr 2016, Trisanna Sprung-Much > > >> wrote: > > >> > > >> > Hi Freesurfer > > >> > > > >> > I have some labels (.mnc) that are painted voxels > > >> generated from a Montreal > > >> > Neurological Institute software. I am trying to > > project > > >> the labels onto the > > >> > surfaces generated from recon-all that I applied > > to the > > >> corresponding MRI > > >> > volumes. > > >> > > > >> > I used mri_vol2surf: > > >> > > > >> > mri_vol2surf --src labels.mnc --out test.mgz > --srcreg > > >> talairach.auto.xfm > > >> > --hemi lh > > >> > > > >> > and got the following error: > > >> > > > >> > Error reading inplaneres from talairach.auto.xfm > > >> > > > >> > > > >> > Do I need a .dat file? If so, how can I attain it? > > >> Essentially, what is the > > >> > registration file that I am supposed to be using? > > >> > > > >> > Many thanks! > > >> > > > >> > Trisanna > > >> > > > >> > -- > > >> > Ph.D. CandidateMcGill University > > >> > Integrated Program in Neuroscience > > >> > Psychology > > >> > > > >> > > > >> > > > >> > > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> > > >> > > >> 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. > > >> > > >> > > >> > > >> > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > 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. > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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