Thanks for the response! I seem to be getting better results.

I was wondering if there was any way the same resampling can be achieved using Freesurfer 4.5 since a lot of analysis (including analysis with other tasks) has already been done in it, or if it is okay to use JUST the reg.2mm.mni152.dat file from Freesurfer 5.1 and keep the rest of the analysis the same as before?

Thank you once again for this help!

Regards,

Balaji Goparaju

On Tue, Jun 14, 2011 at 11:46 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu

wrote:

To go from mni152 to the MNI305 2mm space, use

mri_vol2vol --mov mni305.2mm.nii.gz \ --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \ --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \ --inv --o output.mni305.2mm.nii.gz

This will resample MNI152_T1_2mm.nii.gz (or anything in that space) to the mni305 2mm space.

For your application, add --interp nearest, or use

mri_label2vol --seg BA_mask.mni152.nii \ --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \ --invertmtx --o outfile.nii

doug

Balaji Goparaju wrote:

...

Hello Freesurfers,

I have Brodmann Area binary masks in the ICBM MNI 152 space, that I acquired using WFU_PickAtlas toolbox in SPM. These masks are .nii files, and have a RAS orientation.

I am trying to resample these masks into the fsaverage MNI 305 space, specifically with the dimensions matching the "mni305.cor.subfov2.mgz" file found in the $FREESURFER_HOME/average file. This file is in the LIA orientation.

However, the mni152.register.dat file seems to be transforming volumes from the MNI 305 space to the MNI 152 Space in LAS orientation (MNI152_T1_2mm.nii in FSL).

Should I transform my Brodmann Area masks from the RAS orientation to a LAS orientation? If so, how can I achieve this? The RAS orientation is correct, so I know using mri_convert --out_dimension is out of the question.

I have tried to use *mri_label2vol --seg {BA_mask} --temp {$FREESURFER_HOME/average/mni305.cor.subfov2.mgz} --o {output_file} --reg mni152.register.dat --invertmtx*

Also, I have tried to use the inverted matrix from mni152.register.dat and use it with *mri_vol2vol -mov {BA_mask} --reg {inverted_mni152.register.dat} --o {output_file} --tal --talres 2* However, the output files had interchanged posterior (P) and anterior (A), and superior (S) and interior (I) orientations.

What is the best way to achieve the resampling? Any guidance is really appreciated!

Regards,

Balaji Goparaju

---

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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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.

Thank you for the help!

On Tue, Jun 14, 2011 at 9:10 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:

** You should be able to use the reg and mni305.2mm.nii.gz in 4.5 doug

On 6/14/11 12:25 PM, Balaji Goparaju wrote:

Thanks for the response! I seem to be getting better results.

I was wondering if there was any way the same resampling can be achieved using Freesurfer 4.5 since a lot of analysis (including analysis with other tasks) has already been done in it, or if it is okay to use JUST the reg.2mm.mni152.dat file from Freesurfer 5.1 and keep the rest of the analysis the same as before?

Thank you once again for this help!

Regards,

Balaji Goparaju

On Tue, Jun 14, 2011 at 11:46 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:

...

To go from mni152 to the MNI305 2mm space, use

mri_vol2vol --mov mni305.2mm.nii.gz \ --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \ --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \ --inv --o output.mni305.2mm.nii.gz

This will resample MNI152_T1_2mm.nii.gz (or anything in that space) to the mni305 2mm space.

For your application, add --interp nearest, or use

mri_label2vol --seg BA_mask.mni152.nii \ --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \ --invertmtx --o outfile.nii

doug

Balaji Goparaju wrote:

...

Hello Freesurfers,

I have Brodmann Area binary masks in the ICBM MNI 152 space, that I acquired using WFU_PickAtlas toolbox in SPM. These masks are .nii files, and have a RAS orientation.

I am trying to resample these masks into the fsaverage MNI 305 space, specifically with the dimensions matching the "mni305.cor.subfov2.mgz" file found in the $FREESURFER_HOME/average file. This file is in the LIA orientation.

However, the mni152.register.dat file seems to be transforming volumes from the MNI 305 space to the MNI 152 Space in LAS orientation (MNI152_T1_2mm.nii in FSL).

Should I transform my Brodmann Area masks from the RAS orientation to a LAS orientation? If so, how can I achieve this? The RAS orientation is correct, so I know using mri_convert --out_dimension is out of the question.

I have tried to use *mri_label2vol --seg {BA_mask} --temp {$FREESURFER_HOME/average/mni305.cor.subfov2.mgz} --o {output_file} --reg mni152.register.dat --invertmtx*

Also, I have tried to use the inverted matrix from mni152.register.dat and use it with *mri_vol2vol -mov {BA_mask} --reg {inverted_mni152.register.dat} --o {output_file} --tal --talres 2* However, the output files had interchanged posterior (P) and anterior (A), and superior (S) and interior (I) orientations.

What is the best way to achieve the resampling? Any guidance is really appreciated!

Regards,

Balaji Goparaju

---

---

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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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.

Hi John, We do have a set of QA scripts which were created to check the version of FS used, the order of the output files, the order of all the steps in FS, take several snapshots, and then create a summary log file and an html file to view the snapshots. The scripts have been neglected for some time, but recently I've been updating them and weeding out a couple bugs left over.

Here is the wiki page for the scripts: http://surfer.nmr.mgh.harvard.edu/fswiki/QATools

I'll send out an announcement when an updated and debugged version of the scripts has been posted. Should be relatively soon. -Louis

On Fri, 17 Jun 2011, West, John D. wrote:

Hello.

We are in the process of trying to develop a QC pipeline for our Freesurfer processed images. I was wondering if anyone has developed any type of automated QC they would be willing to share with us or have any suggestions on how to proceed.

Any help would be most appreciated.

Thanks. -John West Systems Admin/Imaging Analyst IU Center for Neuroimaging