13 Apr
2016
13 Apr
'16
5:06 p.m.
this is a known bug. Try this version instead ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg
On 04/13/2016 01:06 PM, Trisanna Sprung-Much wrote:
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca> > <mailto:trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>> > >> <mailto:trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca> > <mailto:trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@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 > >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@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>> > >> <mailto: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>> > >> <mailto: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>> > <mailto: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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> > <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> <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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@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
greve@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/