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. Candidate McGill University Integrated Program in Neuroscience Psychology
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
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 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 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.
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> 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 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 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.
Hi Trisanna
sorry, we are in the middle of given a FreeSurfer course so response times will be longer than usual. Doug will probably have more insight, but you should be able to use the talaiarch.xfm file to map at least the MNI305 ones to your individual subject using mri_vol2vol (if they are stored as a volume of labels) or mri_label2label (if they are stored in our label format). Note that this mapping is unlikely to be terribly accurate as linear transforms don't do a very good job at aligning the cortex across subjects. Not sure about the nonlinear space or how you align your individual subject data to it.
cheers Bruce
On Wed, 6 Apr 2016, Trisanna Sprung-Much wrote:
Any ideas?
Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 5, 2016 at 9:37 PM, Trisanna Sprung-Much 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. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 5, 2016 at 6:34 PM, Bruce Fischl 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 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.
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> 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>> 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> 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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...
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? *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 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.catrisanna.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.edufischl@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 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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
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> 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>> 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>> 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> 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_______________________________________________ Freesurfer mailing list 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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> 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>> 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>> 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>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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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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/
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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> 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>>> 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>>> 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>>> 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 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
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 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> wrote:
On 04/07/2016 03:50 PM, Trisanna Sprung-Much wrote: > thanks, Doug. I am still extremely confused, however. *Am I meantto
> run recon-all first? *I was told in a previous email that I should do > this first, however, I thought that Freesurfer takes the volumesand
> 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>>> 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 generatea
> .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>>> 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>>> 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 forthe
>> 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 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
thanks, Doug. *Unfortunately, I got a different error this time:*
trisanna@kaplan:~$ mni152reg --s icbm-102 /usr/local/freesurfer-5.3//sources.csh: No such file or directory.
What does this mean?
After doing some thinking about the command, *I am now confused about why I need to generate a .dat in the first place. here is my thinking:*
my labels and my icbm volumes are either registered to MNI305 or MNI152 template - i.e. when I painted my voxels to generate my labels, the volumes were already registered to either of these templates when using an in-house software.
So, why do I want to do ANOTHER registration of mni152reg to generate a .dat file that is then needed for mri_vol2surf? Why can't I simply create my surfaces in Freesurfer and then overlay my labels onto those surfaces if, as I have found online,* Freesurfer does not change the space of the input volumes?* My understanding is that it calculates an MNI305 transformation but does not alter the actual input space. Therefore, I do not want to do any further transformations since my labels and volumes are already in sync. If mri_vol2surf really needs a .dat to run, *shouldn't I be creating a registration matrix that does absolutely nothing to ensure my labels don't change?* Some clarification would be greatly appreciated!
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Apr 13, 2016 at 5:06 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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 tryingto
> 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 sentto
> 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry, that is something we put in for version 6 to be able to run under newer versions of mac. Edit the file and remove the following line source $FREESURFER_HOME/sources.csh
On 04/14/2016 10:31 AM, Trisanna Sprung-Much wrote:
thanks, Doug. *Unfortunately, I got a different error this time:*
trisanna@kaplan:~$ mni152reg --s icbm-102 /usr/local/freesurfer-5.3//sources.csh: No such file or directory.
What does this mean?
After doing some thinking about the command, *I am now confused about why I need to generate a .dat in the first place. here is my thinking:*
my labels and my icbm volumes are either registered to MNI305 or MNI152 template - i.e. when I painted my voxels to generate my labels, the volumes were already registered to either of these templates when using an in-house software.
So, why do I want to do ANOTHER registration of mni152reg to generate a .dat file that is then needed for mri_vol2surf? Why can't I simply create my surfaces in Freesurfer and then overlay my labels onto those surfaces if, as I have found online,*Freesurfer does not change the space of the input volumes?* My understanding is that it calculates an MNI305 transformation but does not alter the actual input space. Therefore, I do not want to do any further transformations since my labels and volumes are already in sync. If mri_vol2surf really needs a .dat to run, *shouldn't I be creating a registration matrix that does absolutely nothing to ensure my labels don't change?
Some clarification would be greatly appreciated!
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Apr 13, 2016 at 5:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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> <mailto: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>> > <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: > > > > > > > > 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>>> > > <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 <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>>> > > >> <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 <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>>> > > >> <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 <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>>> > > >> <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 <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>>> > > >> <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 <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>>> > > <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 <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 > > > > -- > > 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>> > <mailto: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>> > <tel: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>> <tel: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> > > <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> > > <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>> > <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>> > > 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 Fax: 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
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will try this, thanks.
In the meantime
After doing some thinking about the command, *I am now confused about why I need to generate a .dat in the first place. here is my thinking:*
my labels and my icbm volumes are either registered to MNI305 or MNI152 template - i.e. when I painted my voxels to generate my labels, the volumes were already registered to either of these templates when using an in-house software.
So, why do I want to do ANOTHER registration of mni152reg to generate a .dat file that is then needed for mri_vol2surf? Why can't I simply create my surfaces in Freesurfer and then overlay my labels onto those surfaces if, as I have found online,* Freesurfer does not change the space of the input volumes?* My understanding is that it calculates an MNI305 transformation but does not alter the actual input space. Therefore, I do not want to do any further transformations since my labels and volumes are already in sync. If mri_vol2surf really needs a .dat to run, *shouldn't I be creating a registration matrix that does absolutely nothing to ensure my labels don't change?* Some clarification would be greatly appreciated!
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Thu, Apr 14, 2016 at 11:33 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Sorry, that is something we put in for version 6 to be able to run under newer versions of mac. Edit the file and remove the following line source $FREESURFER_HOME/sources.csh
On 04/14/2016 10:31 AM, Trisanna Sprung-Much wrote:
thanks, Doug. *Unfortunately, I got a different error this time:*
trisanna@kaplan:~$ mni152reg --s icbm-102 /usr/local/freesurfer-5.3//sources.csh: No such file or directory.
What does this mean?
After doing some thinking about the command, *I am now confused about why I need to generate a .dat in the first place. here is my thinking:*
my labels and my icbm volumes are either registered to MNI305 or MNI152 template - i.e. when I painted my voxels to generate my labels, the volumes were already registered to either of these templates when using an in-house software.
So, why do I want to do ANOTHER registration of mni152reg to generate a .dat file that is then needed for mri_vol2surf? Why can't I simply create my surfaces in Freesurfer and then overlay my labels onto those surfaces if, as I have found online,*Freesurfer does not change the space of the input volumes?* My understanding is that it calculates an MNI305 transformation but does not alter the actual input space. Therefore, I do not want to do any further transformations since my labels and volumes are already in sync. If mri_vol2surf really needs a .dat to run, *shouldn't I be creating a registration matrix that does absolutely nothing to ensure my labels don't change?
Some clarification would be greatly appreciated!
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Apr 13, 2016 at 5:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
this is a known bug. Try this version insteadftp://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 someoneelse
> 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 filethat
> 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> <mailto: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> <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: > > > > > > > > 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 takesthe
> 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-allon
> 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> > <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 <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>>> > > >> <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 <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>>> > > >> <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 <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>>> > > >> <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 <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> > >> 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>>> > > >> <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 <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>>> > > <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 <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 > > > > -- > > 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> <mailto: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>
> <tel: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>> <tel: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> > > <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> > > <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>> > <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>> > > 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 Fax: 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/
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Hi there
Just to reiterate my point above, when I open a surface created in Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no transformations have been performed) I get the following snapshot #1.* Clearly, my original labels are aligned with the surface, as they should be since Freesurfer did not alter the space.* So, how can I use mrivol2surf to resample the surface such that the vertices carry the label info? What output format should I use in mrivol2surf? How can I open this output in Freeview?
For instance, when I try a .dat that creates no transformation and save the output as .mgz and use Overlay in Freeview, I get snapshot #2. So, something is going wrong in my mrivol2surf command.
My apologies for the questions Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Thu, Apr 14, 2016 at 12:08 PM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
will try this, thanks.
In the meantime
After doing some thinking about the command, *I am now confused about why I need to generate a .dat in the first place. here is my thinking:*
my labels and my icbm volumes are either registered to MNI305 or MNI152 template - i.e. when I painted my voxels to generate my labels, the volumes were already registered to either of these templates when using an in-house software.
So, why do I want to do ANOTHER registration of mni152reg to generate a .dat file that is then needed for mri_vol2surf? Why can't I simply create my surfaces in Freesurfer and then overlay my labels onto those surfaces if, as I have found online,* Freesurfer does not change the space of the input volumes?* My understanding is that it calculates an MNI305 transformation but does not alter the actual input space. Therefore, I do not want to do any further transformations since my labels and volumes are already in sync. If mri_vol2surf really needs a .dat to run, *shouldn't I be creating a registration matrix that does absolutely nothing to ensure my labels don't change?* Some clarification would be greatly appreciated!
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Thu, Apr 14, 2016 at 11:33 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Sorry, that is something we put in for version 6 to be able to run under newer versions of mac. Edit the file and remove the following line source $FREESURFER_HOME/sources.csh
On 04/14/2016 10:31 AM, Trisanna Sprung-Much wrote:
thanks, Doug. *Unfortunately, I got a different error this time:*
trisanna@kaplan:~$ mni152reg --s icbm-102 /usr/local/freesurfer-5.3//sources.csh: No such file or directory.
What does this mean?
After doing some thinking about the command, *I am now confused about why I need to generate a .dat in the first place. here is my thinking:*
my labels and my icbm volumes are either registered to MNI305 or MNI152 template - i.e. when I painted my voxels to generate my labels, the volumes were already registered to either of these templates when using an in-house software.
So, why do I want to do ANOTHER registration of mni152reg to generate a .dat file that is then needed for mri_vol2surf? Why can't I simply create my surfaces in Freesurfer and then overlay my labels onto those surfaces if, as I have found online,*Freesurfer does not change the space of the input volumes?* My understanding is that it calculates an MNI305 transformation but does not alter the actual input space. Therefore, I do not want to do any further transformations since my labels and volumes are already in sync. If mri_vol2surf really needs a .dat to run, *shouldn't I be creating a registration matrix that does absolutely nothing to ensure my labels don't change?
Some clarification would be greatly appreciated!
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Apr 13, 2016 at 5:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
this is a known bug. Try this version insteadftp://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 someoneelse
> 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 filethat
> 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> <mailto: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 notbe
> 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> <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: > > > > > > > > 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 takesthe
> 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 keepsall
> 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 50volumes,
> 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 tothe
> surfaces of > > your individual 50 subjects? Start by running recon-allon
> 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> > <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 <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>>> > > >> <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 <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>>> > > >> <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 <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 thatI
> 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>>> > > >> <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 <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> > > >> > > >> The information in this e-mail isintended
> 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> > >> 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>>> > > >> <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 <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>>> > > <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 <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 > > > > -- > > 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> <mailto: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>
> <tel: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>> <tel: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> > > <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> > > <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>> > <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>> > >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 Fax: 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>
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-- 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/
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Hi Trisanna
you can give the transformation "file" named identity.nofile and it will assume that the transform is the identity. You can then use mri_vol2label to sample the label onto the surface and visualize it with:
freeview -f lh.inflated:label=lh.labels.label
or some such
cheers Bruce
On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:
Hi there
Just to reiterate my point above, when I open a surface created in Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no transformations have been performed) I get the following snapshot #1. Clearly, my original labels are aligned with the surface, as they should be since Freesurfer did not alter the space. So, how can I use mrivol2surf to resample the surface such that the vertices carry the label info? What output format should I use in mrivol2surf? How can I open this output in Freeview?
For instance, when I try a .dat that creates no transformation and save the output as .mgz and use Overlay in Freeview, I get snapshot #2. So, something is going wrong in my mrivol2surf command.
My apologies for the questions Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Thu, Apr 14, 2016 at 12:08 PM, Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca wrote: will try this, thanks.
In the meantime
After doing some thinking about the command, I am now confused about why I need to generate a .dat in the first place. here is my thinking:
my labels and my icbm volumes are either registered to MNI305 or MNI152 template - i.e. when I painted my voxels to generate my labels, the volumes were already registered to either of these templates when using an in-house software.
So, why do I want to do ANOTHER registration of mni152reg to generate a .dat file that is then needed for mri_vol2surf? Why can't I simply create my surfaces in Freesurfer and then overlay my labels onto those surfaces if, as I have found online, Freesurfer does not change the space of the input volumes? My understanding is that it calculates an MNI305 transformation but does not alter the actual input space. Therefore, I do not want to do any further transformations since my labels and volumes are already in sync. If mri_vol2surf really needs a .dat to run, shouldn't I be creating a registration matrix that does absolutely nothing to ensure my labels don't change?
Some clarification would be greatly appreciated!
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Thu, Apr 14, 2016 at 11:33 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: Sorry, that is something we put in for version 6 to be able to run under newer versions of mac. Edit the file and remove the following line source $FREESURFER_HOME/sources.csh
On 04/14/2016 10:31 AM, Trisanna Sprung-Much wrote: > thanks, Doug. *Unfortunately, I got a different error this time:* > > trisanna@kaplan:~$ mni152reg --s icbm-102 > /usr/local/freesurfer-5.3//sources.csh: No such file or directory. > > > What does this mean? > > After doing some thinking about the command, *I am now confused about > why I need to generate a .dat in the first place. here is my thinking:* > > my labels and my icbm volumes are either registered to MNI305 or > MNI152 template - i.e. when I painted my voxels to generate my labels, > the volumes were already registered to either of these templates when > using an in-house software. > > So, why do I want to do ANOTHER registration of mni152reg to generate > a .dat file that is then needed for mri_vol2surf? Why can't I simply > create my surfaces in Freesurfer and then overlay my labels onto those > surfaces if, as I have found online,*Freesurfer does not change the > space of the input volumes?* My understanding is that it calculates an > MNI305 transformation but does not alter the actual input space. > Therefore, I do not want to do any further transformations since my > labels and volumes are already in sync. If mri_vol2surf really needs a > .dat to run, *shouldn't I be creating a registration matrix that does > absolutely nothing to ensure my labels don't change? > * > Some clarification would be greatly appreciated! > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Wed, Apr 13, 2016 at 5:06 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > 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.d at > > --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><mailto: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>
> <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: > > > > > > > > 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>>
> > <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 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>> > > >>
<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 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>> > > >> <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 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>> > > >>
<mailto:Freesurfer@nmr.mgh.harvard.edu
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contact the
Partners > > > Compliance HelpLine at > > > http://www.partners.org/complianceline . If
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information, please
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> > > > -- > > 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>
> <mailto: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>
> <tel: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> <tel: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
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https://gate.nmr.mgh.harvard.edu/filedrop2
> >
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>
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >
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> > -- > 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
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tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >
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http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu
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thanks Bruce
I could not find identity.nofile anywhere, when I ran mri_vol2surf I got the following error
trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz srcreg = identity.nofile srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): No such file or directory Could not open identity.nofile
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Trisanna
you can give the transformation "file" named identity.nofile and it will assume that the transform is the identity. You can then use mri_vol2label to sample the label onto the surface and visualize it with:
freeview -f lh.inflated:label=lh.labels.label
or some such
cheers Bruce
On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:
Hi there
Just to reiterate my point above, when I open a surface created in Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no transformations have been performed) I get the following snapshot #1. Clearly, my original labels are aligned with the surface, as they should be since Freesurfer did not alter the space. So, how can I use mrivol2surf to resample the surface such that the vertices carry the label info? What output format should I use in mrivol2surf? How can I open this output in Freeview?
For instance, when I try a .dat that creates no transformation and save the output as .mgz and use Overlay in Freeview, I get snapshot #2. So, something is going wrong in my mrivol2surf command.
My apologies for the questions Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Thu, Apr 14, 2016 at 12:08 PM, Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca wrote: will try this, thanks.
In the meantime
After doing some thinking about the command, I am now confused about why I need to generate a .dat in the first place. here is my thinking:
my labels and my icbm volumes are either registered to MNI305 or MNI152 template - i.e. when I painted my voxels to generate my labels, the volumes were already registered to either of these templates when using an in-house software.
So, why do I want to do ANOTHER registration of mni152reg to generate a .dat file that is then needed for mri_vol2surf? Why can't I simply create my surfaces in Freesurfer and then overlay my labels onto those surfaces if, as I have found online, Freesurfer does not change the space of the input volumes? My understanding is that it calculates an MNI305 transformation but does not alter the actual input space. Therefore, I do not want to do any further transformations since my labels and volumes are already in sync. If mri_vol2surf really needs a .dat to run, shouldn't I be creating a registration matrix that does absolutely nothing to ensure my labels don't change?
Some clarification would be greatly appreciated!
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Thu, Apr 14, 2016 at 11:33 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: Sorry, that is something we put in for version 6 to be able to run under newer versions of mac. Edit the file and remove the following line source $FREESURFER_HOME/sources.csh
On 04/14/2016 10:31 AM, Trisanna Sprung-Much wrote: > thanks, Doug. *Unfortunately, I got a different error this time:* > > trisanna@kaplan:~$ mni152reg --s icbm-102 > /usr/local/freesurfer-5.3//sources.csh: No such file or directory. > > > What does this mean? > > After doing some thinking about the command, *I am now confused about > why I need to generate a .dat in the first place. here is my thinking:* > > my labels and my icbm volumes are either registered to MNI305 or > MNI152 template - i.e. when I painted my voxels to generate my labels, > the volumes were already registered to either of these templates when > using an in-house software. > > So, why do I want to do ANOTHER registration of mni152reg to generate > a .dat file that is then needed for mri_vol2surf? Why can't I simply > create my surfaces in Freesurfer and then overlay my labels onto those > surfaces if, as I have found online,*Freesurfer does not change the > space of the input volumes?* My understanding is that it calculates an > MNI305 transformation but does not alter the actual input space. > Therefore, I do not want to do any further transformations since my > labels and volumes are already in sync. If mri_vol2surf really needs a > .dat to run, *shouldn't I be creating a registration matrix that does > absolutely nothing to ensure my labels don't change? > * > Some clarification would be greatly appreciated! > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Wed, Apr 13, 2016 at 5:06 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > 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.d at > > --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
<mailto: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 commanddirectly
> > fslregister --mov icbm.nii.gz --s $subject --reg > $SUBJECTS_DIR/subject/transforms/icbm.reg.dat --dof12
> --lta$SUBJECTS_DIR/subject/transforms/icbm.reg.lta
> > This will use a linear (12 dof) registration whichmight not be
> particularly accurate > > > On 04/08/2016 01:27 PM, Trisanna Sprung-Much wrote: > > thanks, Doug. I'll get started on running allbrains 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.edumailto: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: > > > > > > > > On 04/07/2016 03:50 PM, Trisanna Sprung-Muchwrote:
> > > thanks, Doug. I am still extremely confused, however. *Am > I meant to > > > run recon-all first? *I was told in aprevious email
that I > > should do > > > this first, however, I thought thatFreesurfer takes the
> volumes and > > > does a linear registration to MNI305template, which
would > not work > > > for my scans that are linearly registered toICBM152
> nonlinear 2006 > > > template... > > run recon-all first, otherwise you won't havesurfaces.
> recon-all > > computes the transform matrix to the mni305but keeps all
> the data in > > the native anatomical space. I think theICBM152 is
the same > as the > > MNI152. Is that right? If so, you can usemni152reg to
> compute the > > registration to 152 space. If not, then we'llhave to
workout > > something > > else. > > > > > > When you have a moment, could you pleaseoutline in
a step > by step > > > manner the steps I should run to take mylabels.mnc
and my > volumes > > > such that I can generate surfaces for those50 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 fromlabels.mnc to the
> surfaces of > > your individual 50 subjects? Start by runningrecon-all on
> the 50. > > > *The idea is that I want to generate somesulcal
> probability maps > > > using surface-based registration, as I canalready
generate > > > probability maps using volumetricregistration quite
easily.* > > > > > > many thanks > > > > > > Trisanna > > > > > > > > > > > > > > > > > > > > > -- > > > Ph.D. Candidate > > > McGill University > > > Integrated Program in Neuroscience > > > Psychology > > > > > > > > > On Wed, Apr 6, 2016 at 2:43 PM, DouglasGreve
> > > <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.edumailto: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 <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > > > For the 152, you can run mni152reg --ssubject, then
> specify > > >$SUBJECTS_DIR/subject/mri/transform/mni152reg.dat (or
> .lta) for > > > the argument to --reg. I'll need tofigure out
how to > generate a > > > .dat/.lta for the 305. > > > > > > > > > > > > On 4/6/16 12:50 PM, Trisanna Sprung-Muchwrote:
> > >> 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>>> > > >><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 <mailto:trisanna.sprung-much@mail.mcgill.ca>>>>> wrote: > > >> > > >> Hi Dr. Fischl > > >> > > >> I have a mixture - some of thelabels were
> painted in the > > >> MNI305 space (older ones) and themore 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>>> > > >> <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 <mailto:fischl@nmr.mgh.harvard.edu>>>>> wrote: > > >> > > >> Hi Trisanna > > >> > > >> what space are your labels in? > > >> > > >> cheers > > >> Bruce > > >> On Tue, 5 Apr 2016, TrisannaSprung-Much
> > >> wrote: > > >> > > >> > Hi Freesurfer > > >> > > > >> > I have some labels (.mnc)that are
painted > voxels > > >> generated from a Montreal > > >> > Neurological Institutesoftware. I am
trying to > > project > > >> the labels onto the > > >> > surfaces generated fromrecon-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 amsupposed
to be > using? > > >> > > > >> > Many thanks! > > >> > > > >> > Trisanna > > >> > > > >> > -- > > >> > Ph.D. CandidateMcGillUniversity
> > >> > Integrated Program inNeuroscience
> > >> > Psychology > > >> > > > >> > > > >> > > > >> > > > >>
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> > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu>
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freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas Greve -
Douglas N Greve
-
Trisanna Sprung-Much