Dear FreeSurfer Users,
I ran recon -all on my structural image and created ROI masks (using mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like to use these masks for further analysis with FSL. However, it seems that the ROI masks generated with mri_label2vol have different header information than that of the original structural image. As a result, I was unable to carry out further analysis with FSL (e.g., converting these ROI masks into functional space with hires2example_func.mat). I was wondering if there is a way to solve this issue.
Many thanks in advance. Frank
what was your mri_label2vol command and terminal output? doug
On 01/06/2014 02:35 AM, Frank Hsieh wrote:
Dear FreeSurfer Users,
I ran recon -all on my structural image and created ROI masks (using mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like to use these masks for further analysis with FSL. However, it seems that the ROI masks generated with mri_label2vol have different header information than that of the original structural image. As a result, I was unable to carry out further analysis with FSL (e.g., converting these ROI masks into functional space with hires2example_func.mat). I was wondering if there is a way to solve this issue.
Many thanks in advance. Frank
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, sorry to jump in, but maybe this solves your problem. What I've been doing is:
1.- Convert the .mgz ROI in Freesurfer to .nii format in FSL: mri_convert --in_type mgz --out_type nii --out_orientation RAS roi.mgz roi.nii
2.- Open the new roi.nii in mricron: mricron nu.nii -o roi.nii . Select it in the menu and just save it as *_mricron.nii again. (I converted nu.mgz with the same procedure as above to check that the roi was in place). This was the only way to make it visible in fslview and work with the roi in fsl afterwards.
Hope this workaround works for you! Gari
On Thu, Jan 9, 2014 at 12:53 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
what was your mri_label2vol command and terminal output? doug
On 01/06/2014 02:35 AM, Frank Hsieh wrote:
Dear FreeSurfer Users,
I ran recon -all on my structural image and created ROI masks (using mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like to use these masks for further analysis with FSL. However, it seems that the ROI masks generated with mri_label2vol have different header information than that of the original structural image. As a result, I was unable to carry out further analysis with FSL (e.g., converting these ROI masks into functional space with hires2example_func.mat). I was wondering if there is a way to solve this issue.
Many thanks in advance. Frank
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
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 Gari, Thanks so much for the tips! @ Doug: I basically followed the instructions on this sitehttp://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/to obtain my ROIs. Any thoughts?
Many thanks! Frank
On Thu, Jan 9, 2014 at 1:22 AM, Garikoitz Lerma-Usabiaga < garikoitz@gmail.com> wrote:
Hi, sorry to jump in, but maybe this solves your problem. What I've been doing is:
1.- Convert the .mgz ROI in Freesurfer to .nii format in FSL: mri_convert --in_type mgz --out_type nii --out_orientation RAS roi.mgz roi.nii
2.- Open the new roi.nii in mricron: mricron nu.nii -o roi.nii . Select it in the menu and just save it as *_mricron.nii again. (I converted nu.mgz with the same procedure as above to check that the roi was in place). This was the only way to make it visible in fslview and work with the roi in fsl afterwards.
Hope this workaround works for you! Gari
On Thu, Jan 9, 2014 at 12:53 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
what was your mri_label2vol command and terminal output? doug
On 01/06/2014 02:35 AM, Frank Hsieh wrote:
Dear FreeSurfer Users,
I ran recon -all on my structural image and created ROI masks (using mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like to use these masks for further analysis with FSL. However, it seems that the ROI masks generated with mri_label2vol have different header information than that of the original structural image. As a result, I was unable to carry out further analysis with FSL (e.g., converting these ROI masks into functional space with hires2example_func.mat). I was wondering if there is a way to solve this issue.
Many thanks in advance. Frank
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
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
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.
Frank, can you send the commands you used and the terminal output? doug
On 01/09/2014 04:35 AM, Frank Hsieh wrote:
Hi Gari, Thanks so much for the tips! @ Doug: I basically followed the instructions on this site http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ to obtain my ROIs. Any thoughts?
Many thanks! Frank
On Thu, Jan 9, 2014 at 1:22 AM, Garikoitz Lerma-Usabiaga <garikoitz@gmail.com mailto:garikoitz@gmail.com> wrote:
Hi, sorry to jump in, but maybe this solves your problem. What I've been doing is: 1.- Convert the .mgz ROI in Freesurfer to .nii format in FSL: mri_convert --in_type mgz --out_type nii --out_orientation RAS roi.mgz roi.nii 2.- Open the new roi.nii in mricron: mricron nu.nii -o roi.nii. Select it in the menu and just save it as *_mricron.nii again. (I converted nu.mgz with the same procedure as above to check that the roi was in place). This was the only way to make it visible in fslview and work with the roi in fsl afterwards. Hope this workaround works for you! Gari On Thu, Jan 9, 2014 at 12:53 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: what was your mri_label2vol command and terminal output? doug On 01/06/2014 02:35 AM, Frank Hsieh wrote: > Dear FreeSurfer Users, > > I ran recon -all on my structural image and created ROI masks (using > mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like > to use these masks for further analysis with FSL. However, it seems > that the ROI masks generated with mri_label2vol have different header > information than that of the original structural image. As a result, I > was unable to carry out further analysis with FSL (e.g., converting > these ROI masks into functional space with hires2example_func.mat). I > was wondering if there is a way to solve this issue. > > Many thanks in advance. > Frank > > > _______________________________________________ > 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 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 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.-- Frank
Hi Doug, many thanks for your help! This is the command i used: mri_label2vol --label lh.parstriangularis.label --temp $DIR/mri/orig.mgz --subject sub${isub} --hemi lh --o $OUTDIR/labels/sub${isub}_parstriangularis.nii.gz --proj frac 0 1 .1 --fillthresh .3 --reg $OUTDIR/labels/sub${isub}_register.dat
Here are the terminal outputs:
****************************************************************************************************************** PVF (null) Thesholding hit volume. mri_label2vol done Number of labels: 1 /Users/EXPTS/sub01/labels/rh.rostralmiddlefrontal.label Annot File: (null) Template Volume: /Applications/freesurfer/subjects/sub01/mri/orig.mgz Outut Volume: /Users/EXPTS/sub01/labels/sub01_rh_DLPFC.nii.gz Registration File: /Users/EXPTS/sub01/labels/sub01_register.dat Fill Threshold: 0.3 Label Vox Vol: 1 ProjType: frac ProjTypeId: 2 ProjStart: 0 ProjStop: 1 ProjDelta: 0.1 Subject: sub01 Hemi: lh UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /Applications/freesurfer/subjects $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; -0.000 -0.000 -1.000 128.000; -0.000 1.000 -0.000 128.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0.3 Loading registration from /Users/EXPTSsub01/labels/sub01_register.dat RegMat: -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; 0.000 0.000 -1.000 128.000; 0.000 1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading surface /Applications/freesurfer/subjects/sub01/surf/lh.white nvertices = 145372 Reading thickness /Applications/freesurfer/subjects/sub01/surf/lh.thickness nlabels = 1 Allocating Hit Volume (16777216) voxels Loading /Users/EXPTS/sub01/labels/rh.rostralmiddlefrontal.label ************************************************************************************************************************
On Jan 9, 2014, at 9:24 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Frank, can you send the commands you used and the terminal output? doug
On 01/09/2014 04:35 AM, Frank Hsieh wrote:
Hi Gari, Thanks so much for the tips! @ Doug: I basically followed the instructions on this site http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ to obtain my ROIs. Any thoughts?
Many thanks! Frank
On Thu, Jan 9, 2014 at 1:22 AM, Garikoitz Lerma-Usabiaga <garikoitz@gmail.com mailto:garikoitz@gmail.com> wrote:
Hi, sorry to jump in, but maybe this solves your problem. What I've been doing is:
1.- Convert the .mgz ROI in Freesurfer to .nii format in FSL: mri_convert --in_type mgz --out_type nii --out_orientation RAS roi.mgz roi.nii
2.- Open the new roi.nii in mricron: mricron nu.nii -o roi.nii. Select it in the menu and just save it as *_mricron.nii again. (I converted nu.mgz with the same procedure as above to check that the roi was in place). This was the only way to make it visible in fslview and work with the roi in fsl afterwards.
Hope this workaround works for you! Gari
On Thu, Jan 9, 2014 at 12:53 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what was your mri_label2vol command and terminal output? doug On 01/06/2014 02:35 AM, Frank Hsieh wrote: > Dear FreeSurfer Users, > > I ran recon -all on my structural image and created ROI masks (using > mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like > to use these masks for further analysis with FSL. However, it seems > that the ROI masks generated with mri_label2vol have different header > information than that of the original structural image. As a result, I > was unable to carry out further analysis with FSL (e.g., converting > these ROI masks into functional space with hires2example_func.mat). I > was wondering if there is a way to solve this issue. > > Many thanks in advance. > Frank > > > _______________________________________________ > 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 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
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.
-- Frank
-- 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@nmr.mgh.harvard.edu