[Freesurfer] Create brain outline from pial surface
Hi folks, I would like to create a brain outline based on the generated pial surface. This outline will completely cover the whole cortex (ignoring gyrus and sulcus info) and is treated as a brain outer surface on which some values in the brain could be projected. I tried mris_expand, but it doesn't work for this goal. Any suggestions would be appreciated. Best, Liang -- Liang Wang, PhD Institute of Psychology Chinese Academy of Sciences Beijing 100101, China ___ 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.
Re: [Freesurfer] Create brain outline from pial surface
Thanks Bruce. I applied mri_binarize to brainmask.mgz with specified threshold and got many holes in the mask. In addition, brainmask.mgz includes the cerebellum. I would like to only create the brain (cerebral cortex) outline based on the pial surface. Thanks. Best, Liang -- Liang Wang, PhD Institute of Psychology Chinese Academy of Sciences Beijing 100101, China ___ 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] Coordinate transformation between raw space and freesurfer confirm space
Hi, I need to convert a vast amount of coordinates (voxel unit: i, j, k) in raw space to freesurfer space (256*256*256 FOV). Could someone give some suggestions how to solve it? Thanks, Liang ___ 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.
Re: [Freesurfer] Coordinate transformation between raw space and freesurfer confirm space
Thanks, Bruce. I had solved this question. Liang 2012/9/11 Bruce Fischl > Hi Liang > > can you clarify what you mean by "freesurfer space"? What are you trying > to do with the coords? We have several coordinate systems, all of which are > documented on our wiki. > cheers > Brce > > > > On Sun, 9 Sep 2012, liang wang wrote: > > Hi, >> I need to convert a vast amount of coordinates (voxel unit: i, j, k) in >> raw space to freesurfer space (256*256*256 FOV). Could >> someone give some suggestions how to solve it? >> >> Thanks, >> Liang >> >> >> >> >> >> > > 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<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. > -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540 ___ 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] Anatomical variation between individual surface and average template
Dear FS folkers, I am working on a functional probabilistic atlas. I find that some functional regions (particular along a big sulcus) show quite high probability value over a large sample, whereas the probability for some regions are quite lower. I think this disparity could be accounted for by the anatomical variation on each surface node that appears while surface-based registering individual surface to the average template that was provided by Freesurfer. For instance, the anatomical variation could be pretty small within a big sulcus (like central sulcus). I assume that Freesurfer output a file which characterizes this type of anatomical variation. Could someone point me which file it is and how to use it to create a group-level measure in order to clear display somewhere has large variation. Thanks. Best, Liang -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540 ___ 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.
Re: [Freesurfer] Anatomical variation between individual surface and average template
Dear Bruce, Thanks for pointing me those information. That .tif file includes the mean and variance for the population sample that was used in Freesurfer. I would like to get similar measures for our own subjects. I think I could use the surface file (like surf/?h.sulc) in each subject folder to compute the mean and variance, right? Is this file already in spherical template space? Thanks again. Best, Liang 2012/9/14 Bruce Fischl > Hi Liang > > yes, that information is encoded in the .tif file that is the target of > the registration. You can use mrisp_paint to copy a frame out of > $FREESURFER_HOME/average/?h.**average.curvature.filled.**buckner40.tif > > the tif file is 3 sets of triplets in different frames. The first is the > mean of the measure, the second is the variance and the third is the > degrees of freedom. The 3 triplets are for the curvature of the inflated > surface, the sulc and mean curvature of the white surface. > > cheers > Bruce > > > On Thu, 13 Sep 2012, liang wang wrote: > > Dear FS folkers, >> I am working on a functional probabilistic atlas. I find that some >> functional >> regions (particular along a big sulcus) show quite high probability value >> over a >> large sample, whereas the probability for some regions are quite lower. I >> think >> this disparity could be accounted for by the anatomical variation on each >> surface >> node that appears while surface-based registering individual surface to >> the average >> template that was provided by Freesurfer. For instance, the anatomical >> variation >> could be pretty small within a big sulcus (like central sulcus). >> >> I assume that Freesurfer output a file which characterizes this type of >> anatomical >> variation. Could someone point me which file it is and how to use it to >> create a >> group-level measure in order to clear display somewhere has large >> variation. >> Thanks. >> >> Best, >> Liang >> >> -- >> Liang Wang, PhD >> Neuroscience of Attention and Perception Laboratory >> Princeton Neuroscience Institute >> Princeton University >> Princeton, NJ, 08540 >> >> >> >> >> > > 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<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. > -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540 ___ 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.
Re: [Freesurfer] Anatomical variation between individual surface and average template
Thanks Bruce. one more question: This is my command (5 subjects) mris_make_template lh sphere.reg subj1 subj2 subj3 subj4 subj5 ./Temp5subj.tif where I select sphere.reg as sphere surface. I assume 1) that the generated template Temp5subj.tif is in the Freesurfer buckner40 spherical space and 2) the mean and variance of the measure included in the new template are also in the buckner40 spherical space. Is that correct? In addition, could you simply explain what's the difference between lh.curv and lh.sulc. Both files look similar and include negative and positive valude, except that lh.sulc seems to be smoothed. Thanks. Best, Liang 2012/9/14 Bruce Fischl > yes, you can use mris_make_template to generate these results (it's what > we used to create the tif files in the first place) > > On Fri, 14 Sep 2012, liang wang wrote: > > Dear Bruce, >> Thanks for pointing me those information. That .tif file includes the >> mean and >> variance for the population sample that was used in Freesurfer. I would >> like to get >> similar measures for our own subjects. I think I could use the surface >> file (like >> surf/?h.sulc) in each subject folder to compute the mean and variance, >> right? Is >> this file already in spherical template space? Thanks again. >> >> Best, >> Liang >> >> 2012/9/14 Bruce Fischl >> Hi Liang >> >> yes, that information is encoded in the .tif file that is the >> target of >> the registration. You can use mrisp_paint to copy a frame out of >> $FREESURFER_HOME/average/?h.**average.curvature.filled.** >> buckner40.tif >> >> the tif file is 3 sets of triplets in different frames. The first is >> the mean of the measure, the second is the variance and the third is >> the degrees of freedom. The 3 triplets are for the curvature of the >> inflated surface, the sulc and mean curvature of the white surface. >> >> cheers >> Bruce >> >> On Thu, 13 Sep 2012, liang wang wrote: >> >> Dear FS folkers, >> I am working on a functional probabilistic atlas. I find >> that some functional >> regions (particular along a big sulcus) show quite high >> probability value over a >> large sample, whereas the probability for some regions are >> quite lower. I think >> this disparity could be accounted for by the anatomical >> variation on each surface >> node that appears while surface-based >> registering individual surface to the average >> template that was provided by Freesurfer. For instance, the >> anatomical variation >> could be pretty small within a big sulcus (like central >> sulcus). >> >> I assume that Freesurfer output a file which characterizes >> this type of anatomical >> variation. Could someone point me which file it is and how >> to use it to create a >> group-level measure in order to clear display somewhere has >> large variation. >> Thanks. >> >> Best, >> Liang >> >> -- >> Liang Wang, PhD >> Neuroscience of Attention and Perception Laboratory >> Princeton Neuroscience Institute >> Princeton University >> Princeton, NJ, 08540 >> >> >> >> >> >> >> 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<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. >> >> >> >> >> -- >> Liang Wang, PhD >> Neuroscience of Attention and Perception Laboratory >> Princeton Neuroscience Institute >> Princeton University >> Princeton, NJ, 08540 >> >> >> >> -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540 ___ 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] --reg in mri_vol2surf
Hi Experts, At subject level, I want to convert a functional volume (in a subject's native space) to this subject's native surface. The functional volume has been registered to this subject T1 images in native space. I know "mri_vol2surf' would do the job but unsure how to generate the registration matrix for --reg option. I appreciate any suggestions. Thanks -Liang ___ 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.
Re: [Freesurfer] --reg in mri_vol2surf
Hi Bruce, Thanks a lot for the suggestions! Here are some followup questions. 1) The functional volume was PET data and anatomical data have been processed with Freesurfer. I run the bbregister as: bbregister --mov PET.nii --s subject_name --reg register.dat --t1 --init-header It does not register the PET to anatomical images well. Since PET contrast does not like the typical t1/t2, I am not sure how to set the "--contrast" argument (already tried to both t1 and t2). Also, as PET and anatomical are both in native space, not sure how to set the "--init-" 2) Actually, the PET image has been aligned with orig.mgz well (in the native space) using a in-house method. The registration matrix likes below: 0.992629 0.109294 0.052358 10.4812 -0.102034 0.986829 -0.125525 16.5118 -0.065387 0.119257 0.990708 -23.4735 0.00 0.00 0.001. I wonder if there is a way that can convert this matrix to a readable format for "mri_vol2surf". 3) I tried to run mri_vol2surf (using a --regheader option as pet.nii and orig.mgz already aligning well) as: mri_vol2surf --mov PET.nii --hemi lh --regheader subject_name --o lh.pet.mgh. But the results does not look right. Any suggestions for these questions would be very appreciated! -Liang On Fri, Dec 5, 2014 at 5:40 PM, Bruce Fischl wrote: > Hi Liang > > try bbregister. > > cheers > Bruce > > On Fri, 5 Dec 2014, Liang Wang wrote: > > Hi Experts, >> >> At subject level, I want to convert a functional volume (in a subject's >> native space) to this subject's native surface. The functional volume has >> been registered to this subject T1 images in native space. I know >> "mri_vol2surf' would do the job but unsure how to generate the >> registration >> matrix for --reg option. I appreciate any suggestions. >> >> Thanks >> -Liang >> >> > ___ > 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.
Re: [Freesurfer] --reg in mri_vol2surf
Thanks Doug! Will try the --init-fsl or --init-spm for bbregister. -Liang On Wed, Dec 10, 2014 at 10:50 AM, Douglas N Greve wrote: > > Converting that matrix will not be easy. If you want to try, look at our > wiki page on coordinate systems and see how your coordinate systems > match up. It won't be easy. Your bbregister command is not going to work > for sure, you cannot use --init-header (which should only be used for > two MRIs acquired in the same session). Try --init-fsl or --init-spm. > Most PET tracers have an effective T2 weighting > > > > On 12/08/2014 04:52 PM, Liang Wang wrote: > > Hi Bruce, > > Thanks a lot for the suggestions! Here are some followup questions. > > 1) The functional volume was PET data and anatomical data have been > > processed with Freesurfer. I run the bbregister as: > > bbregister --mov PET.nii --s subject_name --reg register.dat --t1 > > --init-header > > It does not register the PET to anatomical images well. Since PET > > contrast does not like the typical t1/t2, I am not sure how to set the > > "--contrast" argument (already tried to both t1 and t2). Also, as PET > > and anatomical are both in native space, not sure how to set the > "--init-" > > 2) Actually, the PET image has been aligned with orig.mgz well (in the > > native space) using a in-house method. The registration matrix likes > > below: > > 0.992629 0.109294 0.052358 10.4812 > > -0.102034 0.986829 -0.125525 16.5118 > > -0.065387 0.119257 0.990708 -23.4735 > > 0.00 0.00 0.001. > > I wonder if there is a way that can convert this matrix to a readable > > format for "mri_vol2surf". > > 3) I tried to run mri_vol2surf (using a --regheader option as pet.nii > > and orig.mgz already aligning well) as: > > mri_vol2surf --mov PET.nii --hemi lh --regheader subject_name --o > > lh.pet.mgh. But the results does not look right. > > Any suggestions for these questions would be very appreciated! > > > > -Liang > > > > On Fri, Dec 5, 2014 at 5:40 PM, Bruce Fischl > > mailto:fis...@nmr.mgh.harvard.edu>> wrote: > > > > Hi Liang > > > > try bbregister. > > > > cheers > > Bruce > > > > On Fri, 5 Dec 2014, Liang Wang wrote: > > > > Hi Experts, > > > > At subject level, I want to convert a functional volume (in a > > subject's > > native space) to this subject's native surface. The functional > > volume has > > been registered to this subject T1 images in native space. I know > > "mri_vol2surf' would do the job but unsure how to generate > > the registration > > matrix for --reg option. I appreciate any suggestions. > > > > Thanks > > -Liang > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu 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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ 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] mris_calc or other calculators
Hi experts, I have cortical thickness on fsaverage surfaces (?h.thickness_on_fsaverage.mgh) from a group of individuals. I'd like to create a volume (.mgh) that represents group mean or sd or other descriptive statistics. I know mris_calc can do similar job but wonder if there is more straightforward way for this? Or I have to convert this (mgh) to other format and then use image calculator (e.g., fslmath etc) to do this? Thanks -Liang ___ 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.
Re: [Freesurfer] mris_calc or other calculators
Cool! Thanks Doug! -Liang On Wed, Dec 10, 2014 at 3:05 PM, Douglas N Greve wrote: > > You can use mri_concat, something like > > mri_concat file1.mgh file2.mgh --mean --o mean.mgh > > > > On 12/10/2014 04:00 PM, Liang Wang wrote: > > Hi experts, > > > > I have cortical thickness on fsaverage surfaces > > (?h.thickness_on_fsaverage.mgh) from a group of individuals. I'd like > > to create a volume (.mgh) that represents group mean or sd or other > > descriptive statistics. I know mris_calc can do similar job but wonder > > if there is more straightforward way for this? Or I have to convert > > this (mgh) to other format and then use image calculator (e.g., > > fslmath etc) to do this? > > > > Thanks > > -Liang > > > > > > > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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.
[Freesurfer] Extracting ROIs from aparc.a2009s+aseg.mgz
Hi FS experts, Does anyone know how to extract these ROIs (including all gyral and sulci) from the image . I just want to create a mask image based on this image by using 1, 2, .. to code different brain areas. Thanks for your solutions. Also, I can not display the image using the following command: tkmedit subjid orig -aux brain -aparc.a2009s+aseg.mgz, but can correctly display . Any advise would be appreciated. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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.
Re: [Freesurfer] Extracting ROIs from aparc.a2009s+aseg.mgz
Hi Allison, Thanks. I have used the command line below to separately create many label files, each of which include vertex number and XYZ coordinates. mri_annotation2label --subject BNC006 --hemi lh --labelbase aparc.a2009 Sorry for not declaring my intention previously. What I actually want to do is utilizing the gray ROIs recorded in aparc.a2009s+aseg.mgz to generate the average time courses of each ROI from BOLD fMRI scanned from the same subject. Can you give some advice how to accurately make it. Also, I am worried the registeration issues across different modality images. Best, Liang 2010/3/11 Allison Stevens > Liang, > mri_annotation2label will separate all the ROIs in the > ?h.aparc.a2009s.annot - is this what you need? I'm not sure what you mean by > "mask image based on this image using 1, 2". You can merge or split labels > as well. > > To display aparc.a2009s+aseg.mgz in tkmedit, you can do: > tkmedit subjid orig.mgz -segmentation aparc.a2005s+aseg.mgz > > Allison > -- > > On Wed, 10 Mar 2010, liang wang wrote: > > Hi FS experts, >> >> Does anyone know how to extract these ROIs (including all gyral and sulci) >> from the image . I just want to create a mask image >> based on this image by using 1, 2, .. to code different brain areas. >> Thanks >> for your solutions. >> >> Also, I can not display the image using the following command: tkmedit >> subjid orig -aux brain -aparc.a2009s+aseg.mgz, but can correctly display >> . Any advise would be appreciated. >> >> Liang >> >> >> > > 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. > > -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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.
Re: [Freesurfer] Extracting ROIs from aparc.a2009s+aseg.mgz
Hi Allison, Thanks for the website you provide me. Through reading, I understand how to averaged extract contrast effect size in each ROI generated by FreeSurfer (e.g. aparc.a2009s+aseg.mgz). You know, the contrast image is a 3D file for each subject. However, BOLD data usually is a 4D image (i.e. 3D + time course). I try to use the following commands to carry out what I need (Let me say *BNC006 *is a subject ID, *example_func.nii.gz* a motion correction template and *filtered_func.nii.gz* a 4D BOLD data with realigment to example.nii.gz). Note that The below id is just to test whether there is a correct output. $ bbregister --mov example_func.nii.gz --bold --s BNC006 --init-fsl --reg register.dat $ mri_vol2vol --mov filtered_func.nii.gz --reg register.dat --fstarg --interp nearnest --o filtered_func.anat.mgh $ mri_segstats --seg $SUBJECTS_DIR/BNC006/mri/aparc.a2009s+aseg.mgz --ctab $FREESURFER/FreeSurferColorLUT.txt --id \ 11101 --id 11105 --i fitered_fun.anat.mgh --sum filter.stats The fist two lines run fine, but the last one seems stop after displaying loading filter_fun.anat.mgh. Your any suggests will be appreciated. Best, Liang 2010/3/12 Allison Stevens > Liang, > We have a very good tutorial which takes you through what you would like to > do. It's located here: > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual > > There is also some information on registration here: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration > > Having the aparc divided up isn't necessary to do them though. > Allison > > -- > > On Thu, 11 Mar 2010, liang wang wrote: > > Hi Allison, >> >> Thanks. I have used the command line below to separately create many label >> files, each of which include vertex number and XYZ coordinates. >> mri_annotation2label --subject BNC006 --hemi lh --labelbase aparc.a2009 >> >> Sorry for not declaring my intention previously. What I actually want to >> do >> is utilizing the gray ROIs recorded in aparc.a2009s+aseg.mgz to generate >> the >> average time courses of each ROI from BOLD fMRI scanned from the same >> subject. Can you give some advice how to accurately make it. Also, I am >> worried the registeration issues across different modality images. >> >> Best, >> Liang >> >> 2010/3/11 Allison Stevens >> >> Liang, >>> mri_annotation2label will separate all the ROIs in the >>> ?h.aparc.a2009s.annot - is this what you need? I'm not sure what you mean >>> by >>> "mask image based on this image using 1, 2". You can merge or split >>> labels >>> as well. >>> >>> To display aparc.a2009s+aseg.mgz in tkmedit, you can do: >>> tkmedit subjid orig.mgz -segmentation aparc.a2005s+aseg.mgz >>> >>> Allison >>> -- >>> >>> On Wed, 10 Mar 2010, liang wang wrote: >>> >>> Hi FS experts, >>> >>>> >>>> Does anyone know how to extract these ROIs (including all gyral and >>>> sulci) >>>> from the image . I just want to create a mask >>>> image >>>> based on this image by using 1, 2, .. to code different brain areas. >>>> Thanks >>>> for your solutions. >>>> >>>> Also, I can not display the image using the following command: tkmedit >>>> subjid orig -aux brain -aparc.a2009s+aseg.mgz, but can correctly display >>>> . Any advise would be appreciated. >>>> >>>> Liang >>>> >>>> >>>> >>>> >>> 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. >>> >>> >>> >> >> >> -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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] How to transform brain.mgz back to native space
Hi FS experts, I find that FS does make a great skullstrip and extract a perfect brain (ie. brain.mgz). I am thinking to register this brain to MNI152 standard space using FSL. Does anyone know how to transfer the brain (256.^3, 1mm ) to subject-specific native space (224*256*176, 1mm). Thanks in advance. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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.
Re: [Freesurfer] How to transform brain.mgz back to native space
Hi Allison and Bruce, Thanks for your kind explanations and the website mentioned http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat. I am curious why I can not directly find this website from the main interface http://surfer.nmr.mgh.harvard.edu/fswiki. Is there a website listing all the great links. Thanks. Liang 2010/3/15 Allison Stevens > Liang, > You can find instructions on how to do this here: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat > > Sometimes using mri_convert will cause the orientation to be off so you may > want to follow those instructions instead. > Allison > > -- > > On Sat, 13 Mar 2010, Bruce Fischl wrote: > > Hi Liang, >> >> you should just be able to use the -rl (reslice like) option in >> mri_convert and give the orig/001.mgz as the target. >> >> cheers >> Bruce >> >> On Fri, 12 Mar 2010, liang >> wang wrote: >> >> Hi FS experts, >>> >>> I find that FS does make a great skullstrip and extract a perfect brain >>> (ie. >>> brain.mgz). I am thinking to register this brain to MNI152 standard space >>> using FSL. Does anyone know how to transfer the brain (256.^3, 1mm ) to >>> subject-specific native space (224*256*176, 1mm). Thanks in advance. >>> >>> Liang >>> >>> >>> ___ >> 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. > > -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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] Extracting time series from aparc.a2009s+aseg.mgz
Hi FSusers, Is there a way to extract averaged BOLD signal from the identified cortical regions in aparc.a2009s+aseg.mgz. Thanks Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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] Which way is better for mapping automatic segmentations
Hi FSusers, I am engaging to map automatic segmentation image (eg. aparc.a2009s+aseg.mgz) to raw functional space. According to the instructions from the FreeSurfer website, I found that there were two ways below to do it. However, the results from both methods are different and attached. Let me say BNC006 is a subject under $SUBJECTS_DIR (here /drive3/TEST). The functional data has been processed using FSL and found in bold.feat directory. *# one way* (red images in the attached picture) $ bbregister --mov example_func.nii.gz --bold --s BNC006 --init-fsl --reg register.dat $ mri_label2vol --seg BNC006/mri/aparc.a2009s+aseg.mgz --temp example_func.nii.gz --reg register.dat --fillthresh 0.5 --o BNC006 .aseg-in-fun.nii.gz *# anther way* (blue images in the attached picture) $ reg-feat2anat --feat /drive3/TEST/BOLD/bold.feat --subject BNC006 $ aseg2feat --feat /drive3/TEST/BOLD/bold.feat --aseg aparc.a2009s+aseg cd /drive3/TEST/BOLD/bold.feat/reg/freesurfer *BNC006 .aseg-in-fun.nii.gz* and *aparc.a2009s+aseg.nii.gz* are outputs from the first and second one, respectively. Does anyone give me some suggestion about which method is suitable to my situation. Best, Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com <>___ 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] Displaying significant difference with a threshold of cluster size
Hi, Using mri_glmfit, I found significant between-group difference in cortical thickness in some regions. However, there are a lot regions with very small vertices surviving the given threshold. What I need to do is displaying large clusters (e.g. having 20 vertices at least) assumed as "true" difference. I don't know how to make it by a selected threshold of cluster size . Any suggestions would be appreciated. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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.
Re: [Freesurfer] Displaying significant difference with a threshold of cluster size
Hello Doug, Thanks for your kind response. I have tried to use mri_glmfit-sim to correct the results. However, no significant differences were observed. To compare with other studies, I would like to report the results (p < 0.001, uncorrected) and mention that they will disappear if corrected by cluster-based threshold method. Is it a acceptable way? Liang 2010/7/11 Douglas N Greve > You should correct for multiple comparisons using cluster-wise correction. > See the tutorials on group analysis on our wiki. > > doug > > liang wang wrote: > >> Hi, >> >> Using mri_glmfit, I found significant between-group difference in cortical >> thickness in some regions. However, there are a lot regions with very small >> vertices surviving the given threshold. What I need to do is displaying >> large clusters (e.g. having 20 vertices at least) assumed as "true" >> difference. I don't know how to make it by a selected threshold of cluster >> size . Any suggestions would be appreciated. >> >> Liang >> >> -- >> Liang Wang, PhD >> Postdoctoral Fellow >> Woodward Lab >> Department of Psychiatry >> University of British Columbia >> BC Mental Health & Addiction Services >> 938 West 28th Avenue >> Vancouver BC V5Z 4H4 >> Telephone: 1-604-875-2000 (ext. 4735) >> Fax: 1-604-875-3871 >> Email: wangl...@gmail.com <mailto:wangl...@gmail.com> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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] Creating table of segmentation volumes
Hi, I was starting to create a table of segmentation volumes corresponding to several given label (--segno 255 i.e., CC_Anterior). However, I found the volume values for a same strucutre were different between the two files *aseg.stats and wmparc.stats*. For example, for CC_Anterior, one subject was 745 mm^3 in the aseg.stats, but 729 mm^3 in the wmparc.stats. I am not sure why they are different and which file should be selected to represent the volumes. I am appreciated for any suggestions. Best, Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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] A region loss in the ?h.aparc.stats
Hi, My freesurfer version is v4.5.0. Using tksurfer, I can find the corpus callosum shown in the ?h.aparc.annot (e.g., .. -annot aparc.annot). Moreover in the FreeSurferColorLUT.txt, this region exists (e.g. #No. 1004 ctx-lh-copuscallosum). However, I am surprised when finding its loss in the ?h.aparc.stats file. For all subjects, I did not find any morphometric measures of this region. Also, when using tksurfer to present ?h.aparc.annot, I can not find the insula in the displayed surface, though this region is existing in the ?h.aparc.stats and the FreeSurferColorLUT.txt (e.g. #No. 1035 ctx-lh-insula). I am creating a figure to show all these ROIs. Hence I am curious why there is not the insula shown. I am appreciated if anyone could give me a hand for solving this seemly conflicting information. Thanks so much. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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.
Re: [Freesurfer] A region loss in the ?h.aparc.stats
Hi > >> Also, when using tksurfer to present ?h.aparc.annot, I can not find the >> insula in the displayed surface, though this region is existing in the >> ?h.aparc.stats and the FreeSurferColorLUT.txt (e.g. #No. 1035 >> ctx-lh-insula). I am creating a figure to show all these ROIs. Hence I am >> curious why there is not the insula shown. >> > What is where the insula should be? > I think that the insula should be displayed in the ?h.aparc.annot, because ?h.aparc.stats reports several surface measurements of this regions. But I can't find it. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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.
Re: [Freesurfer] A region loss in the ?h.aparc.stats
Hi Doug, Maybe I can't give clear information about my problem in the previous post. Please allow me report it again. My question is that I can't find the insula in the averaged ?h.aparc.annot obtained from the command make_average_surface. I check ?h.aparc.annot of each subject and find existence of the insula inside each subject's file. I don't know what's the wrong during the average process. I am looking forward to your suggestions. Thanks. Liang 2010/7/13 liang wang > Hi > > >> >>> Also, when using tksurfer to present ?h.aparc.annot, I can not find the >>> insula in the displayed surface, though this region is existing in the >>> ?h.aparc.stats and the FreeSurferColorLUT.txt (e.g. #No. 1035 >>> ctx-lh-insula). I am creating a figure to show all these ROIs. Hence I am >>> curious why there is not the insula shown. >>> >> What is where the insula should be? >> > I think that the insula should be displayed in the ?h.aparc.annot, because > ?h.aparc.stats reports several surface measurements of this regions. But I > can't find it. > > Liang > > -- > Liang Wang, PhD > Postdoctoral Fellow > Woodward Lab > Department of Psychiatry > University of British Columbia > BC Mental Health & Addiction Services > 938 West 28th Avenue > Vancouver BC V5Z 4H4 > Telephone: 1-604-875-2000 (ext. 4735) > Fax: 1-604-875-3871 > Email: wangl...@gmail.com > -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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] Extracting fMRI time course and computing correlations among them
Hi, Does anyone know one of studies which uses the parcellations (aparc or aparc.a2009s) Freesurfer provides to extract fMRI time course from each subject's fMRI data. Reading the instructions in Freesurfer Wiki, I know how to do that. However, I am not sure whether I should use the parcellations from the average output (obtained from make_average_subject), or the parcellations based on each subject. I would next compute functional connectivity between these regions. I am appreciated for any suggestions. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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] Creating aparc.a2009s+aseg.mgz for the averaged data
Hi, When I use make_average_subject to generate an average data, I can't find aparc.a2009s+aseg.mgz within the new average/mri. To get common parcellation to all subjects, I need to create this file. I understand that " mri_aparc2aseg --s average --a2009s " enable to perform what I want. However, when running this command, a error message shows up "ERROR: cannot find /drive3/Stammer/Thickness/average/mri/ribbon.mgz". As displayed by this message, I did not find the ribbon.mgz file. I don't konw how to figure out this problem. Any suggestions? By the way, my make_average_surface file is updated by Nick's new one. And it does not include ribbon.mgz before updating. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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.
Re: [Freesurfer] Extracting fMRI time course and computing correlations among them
Dear Doug, Thanks for your comments. However, I am worried about the different number of voxels within each parcellation between subjects, if extracting fmri time course from individual parcellation result. Also, I am using the following combined commands to carry out the steps. Do you think it's correct? reg-feat2anat --feat SUBID/bold.feat --subject SUBID aseg2feat --feat SUBID/bold.feat --aseg aparcs+aseg mri_segstats --seg SUBID/bold.feat/reg/freesurfer/aparc.a2009s+aseg.nii.gz --in filtered_fun_data.nii.gz -avgwf file.dat Thanks, Liang 2010/7/18 Doug Greve > > definitely use the individuals. Use mri_vol2surf to convert the motion > corrected (and otherwise unsmoothed) fmri time courses to the > surface. Then use mri_segstats with the --avgwf and --annot options > to compute the mean time course over the parcellations. > > doug > > > > > On Sat, 17 Jul 2010, liang wang wrote: > > Hi, >> >> Does anyone know one of studies which uses the parcellations (aparc or >> aparc.a2009s) Freesurfer provides to extract fMRI time course from each >> subject's fMRI data. Reading the instructions in Freesurfer Wiki, I know >> how >> to do that. However, I am not sure whether I should use the parcellations >> from the average output (obtained from make_average_subject), or the >> parcellations based on each subject. I would next compute functional >> connectivity between these regions. I am appreciated for any suggestions. >> >> Liang >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: 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. > > -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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.
Re: [Freesurfer] Extracting fMRI time course and computing correlations among them
Dear Doug, Thanks. According to your suggestions, I would extract fmri time course from an individual paracellation with subcortical regions (e.g. caudate, thalamus...). Would you like to help me to make sure whether the following commands are correct. Here the filtered_fun_data.nii.gz did not be smoothed. Thanks a lot. reg-feat2anat --feat SUBID/bold.feat --subject SUBID aseg2feat --feat SUBID/bold.feat --aseg aparcs+aseg mri_segstats --seg SUBID/bold.feat/reg/ freesurfer/aparc.a2009s+aseg.nii.gz --in filtered_fun_data.nii.gz -avgwf file.dat Liang 2010/7/19 Douglas N Greve > mapping the time courses to the average subject does not solve this > problem, it just hides it. I'm not sure why this would be of a concern > anyway. There might be a tiny difference in the expected variance for each > subject, but, unless the region is very small, the differences won't amount > for much. > > doug > > liang wang wrote: > >> Dear Doug, >> >> Thanks for your comments. However, I am worried about the different number >> of voxels within each parcellation between subjects, if extracting fmri time >> course from individual parcellation result. >> >> Also, I am using the following combined commands to carry out the steps. >> Do you think it's correct? >> reg-feat2anat --feat SUBID/bold.feat --subject SUBID >> aseg2feat --feat SUBID/bold.feat --aseg aparcs+aseg >> mri_segstats --seg SUBID/bold.feat/reg/freesurfer/aparc.a2009s+aseg.nii.gz >> --in filtered_fun_data.nii.gz -avgwf file.dat >> >> Thanks, >> Liang >> >> 2010/7/18 Doug Greve > gr...@nmr.mgh.harvard.edu>> >> >> >> >>definitely use the individuals. Use mri_vol2surf to convert the motion >>corrected (and otherwise unsmoothed) fmri time courses to the >> surface. Then use mri_segstats with the --avgwf and --annot options >>to compute the mean time course over the parcellations. >> >>doug >> >> >> >> >>On Sat, 17 Jul 2010, liang wang wrote: >> >>Hi, >> >>Does anyone know one of studies which uses the parcellations >>(aparc or >>aparc.a2009s) Freesurfer provides to extract fMRI time course >>from each >>subject's fMRI data. Reading the instructions in Freesurfer >>Wiki, I know how >>to do that. However, I am not sure whether I should use the >>parcellations >>from the average output (obtained from make_average_subject), >>or the >>parcellations based on each subject. I would next compute >>functional >>connectivity between these regions. I am appreciated for any >>suggestions. >> >>Liang >> >> >> >>-- Douglas N. Greve, Ph.D. >>MGH-NMR Center >>gr...@nmr.mgh.harvard.edu <mailto:gr...@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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >><http://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. >> >> >> >> >> -- >> Liang Wang, PhD >> Postdoctoral Fellow >> Woodward Lab >> Department of Psychiatry >> University of British Columbia >> BC Mental Health & Addiction Services >> 938 West 28th Avenue >> Vancouver BC V5Z 4H4 >> Telephone: 1-604-875-2000 (ext. 4735) >> Fax: 1-604-875-3871 >> Email: wangl...@gmail.com <mailto:wangl...@gmail.com> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone N
Re: [Freesurfer] Creating aparc.a2009s+aseg.mgz for the averaged data
Dear Doug, Thanks for your prompted answer, but I have another question about this. When I read the paper Kuperberg et al., Arch Gen Psychiatry 2003;60:878-888, I understand that in this paper, the authors computed the averaged surface. They then extracted ROIs from the average data and back-projected the ROIs to individual conformed space (Figure 2), followed by calculating mean cortical thickness of each ROI individually. My questions are: 1) Can I be allowed to project the average paracellation (including subcortical and cortical surface) to fMRI data space using reg-feat2anat for extracting mean BOLD signal of each paracellation. Sorry for continuously bothering you about this confusing question to me. 2) Can you give me a further explanation about the means hidden under "Don't extract volumes, etc. If you want to use one of the surface parcellations, do a surface-based analysis." All the best, Liang 2010/7/18 Doug Greve > > You can create a ribbon volume with the command below: > > mris_volmask \ >--label_left_white 2 --label_left_ribbon 3 \ >--label_right_white 41 --label_right_ribbon 42 \ >--save_ribbon --save_distance youraveragesubject > > Note this when you make the aparc+aseg in this way, it should only be > used when visualizing data on the mni305 brain. Don't extract volumes, > etc. If you want to use one of the surface parcellations, do a > surface-based analysis. > > doug > > > On Sat, 17 Jul 2010, liang wang wrote: > > Hi, >> >> When I use make_average_subject to generate an average data, I can't find >> aparc.a2009s+aseg.mgz within the new average/mri. To get common >> parcellation >> to all subjects, I need to create this file. I understand that " >> mri_aparc2aseg --s average --a2009s >> " enable to perform what I want. However, when running this command, a >> error >> message shows up "ERROR: cannot find >> /drive3/Stammer/Thickness/average/mri/ribbon.mgz". As displayed by this >> message, I did not find the ribbon.mgz file. I don't konw how to figure >> out >> this problem. Any suggestions? >> By the way, my make_average_surface file is updated by Nick's new one. And >> it does not include ribbon.mgz before updating. >> >> Liang >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: 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. > > -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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] Creating a label
Hi, I can create a label file from either ?h.aparc.annot (using mri_annotation2label) or aparc+aseg.mgz (using mri_cor2label). However, I find the two same label are shown different using tksurfer. Specifically, the label created by mri_annotation2label display compact and clear, whereas one obtained by mri_cor2label seemingly includes more tiny, disperse vertices. Does anyone know what's happening? Thanks. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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] Transforming aseg.mgz to DTI space
Hi, I wanted to transform mri/aseg.mgz (obtained by the command: make_average_subject) to a standard DTI space. I used the following command to get a register.data applied to the DTI data to obtain to a new DTI data in the Freesurfer conformed space. bbregister --mov mean_FA.nii.gz --dti --s average --init-fsl --reg register.dat and then using tkregister2 to adjust the mean_FA to align well with ?h.avg.white. The new register.dat was saved to replace the old one. I think that if I can inversely apply the register.dat to aseg.mgz, it would work. However, I don't know how to reversely apply this transformation file. I tried to use --apply_inverse_transform in mri_convert, but it doesn't work. Any suggestions would be appreciated. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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] Errors for talairach transformation
Hi FSusers, The terminal displays errors when I run "recon-all -autorecon1 -subjid ..." to get a skull-stripped brain image. The processing exits with the following errors regarding talairach transformation. Here is the talairach.xfm: MNI Transform File % tkregister2 Transform_Type = Linear; Linear_Transform = 39.07553864 15.93667889 -36.86604309 -1474.05761719 1861.34423828 844.27008057 -1897.87268066 -75416.71093750 -606.90667725 -274.30368042 622.14581299 24711.26757812 ; Any suggestions would be appreciated. Best, Liang # #...@# Talairach Failure Detection Wed Nov 17 10:15:36 EST 2010 /mnt/cd/kastner/liang/resting_state/ph_062210/fs_skull/ph/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050) Linux node37.cluster 2.6.18-128.el5 #1 SMP Wed Jan 21 10:41:14 EST 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ph exited with ERRORS at Wed Nov 17 10:15:36 EST 2010 -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540 ___ 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.
Re: [Freesurfer] Errors for talairach transformation
Hi Bruce, I run the command on a NIFTI image converted by dicom files. The image can be skull stripped using bet in FSL, but some skulls were not removed clearly. Here is the information by mri_info. It seems to me normal, but several scan parameters loss. For the nifti image, I use to3d (AFNI code) to convert DICOM to nifti format and use 3drefit to fix up correctly the orientation. #--- type: nii dimensions: 256 x 256 x 160 voxel sizes: 0.5000, 0.5000, 1. type: SHORT (4) fov: 128.000 dof: 0 xstart: -64.0, xend: -64.0 ystart: -64.0, yend: -64.0 zstart: -80.0, zend: -80.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 1., y_r = -0., z_r = -0., c_r = -2.6988 : x_a = -0., y_a = -1., z_a = -0., c_a = -1.3494 : x_s = 0., y_s = 0., z_s = -1., c_s = 6.9217 Orientation : RPI Primary Slice Direction: axial voxel to ras transform: 0.5000 -0. -0. -66.6988 -0. -0.5000 -0.62.6506 0. 0. -1.86.9217 0. 0. 0. 1. voxel-to-ras determinant 0.25 ras to voxel transform: 2. -0. -0. 133.3976 0. -2. 0. 125.3012 0. 0. -1.86.9217 0. 0. 0. 1. 2010/11/17 Bruce Fischl > wow, that's a completely wacky talairach xform. Did you run this straight > on the dicom images? The talairach clearly failed for some reason. Try > running mri_info on the dicoms to see if there is something strange in them > > > On Wed, 17 Nov 2010, liang wang wrote: > > Hi FSusers, >> >> The terminal displays errors when I run "recon-all -autorecon1 -subjid >> ..." >> to get a skull-stripped brain image. The processing exits with the >> following >> errors regarding talairach transformation. Here is the talairach.xfm: >> >> MNI Transform File >> % tkregister2 >> >> Transform_Type = Linear; >> Linear_Transform = >> 39.07553864 15.93667889 -36.86604309 -1474.05761719 >> 1861.34423828 844.27008057 -1897.87268066 -75416.71093750 >> -606.90667725 -274.30368042 622.14581299 24711.26757812 ; >> >> >> Any suggestions would be appreciated. >> >> Best, >> Liang >> >> # >> #...@# Talairach Failure Detection Wed Nov 17 10:15:36 EST 2010 >> /mnt/cd/kastner/liang/resting_state/ph_062210/fs_skull/ph/mri >> >> talairach_afd -T 0.005 -xfm transforms/talairach.xfm >> >> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >> ***FAILED*** (p=0., pval=0. < threshold=0.0050) >> Linux node37.cluster 2.6.18-128.el5 #1 SMP Wed Jan 21 10:41:14 EST 2009 >> x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s ph exited with ERRORS at Wed Nov 17 10:15:36 EST 2010 >> >> >> >> > > 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. > > -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540 ___ 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.
Re: [Freesurfer] Errors for talairach transformation
Hi Bruce, I had tried to run recon-all on the dicoms. But the same errors show up. This image covering whole brain is obtained (Siemens 3T) actually from a monkey and looks good. Here is the header information from the dicom image. According to the suggestion in Freesurfer FAQ, I run "tkregister2 --mgz --s subj --fstal". Surprisingly, a strange image appears and looks a white line. Seemingly the brain image is rotated to a invisible orientation. Any suggestions? Best, Liang #--- Volume information for 001.mgz type: MGH dimensions: 256 x 256 x 160 voxel sizes: 0.5000, 0.5000, 1. type: SHORT (4) fov: 160.000 dof: 0 xstart: -64.0, xend: 64.0 ystart: -64.0, yend: 64.0 zstart: -80.0, zend: 80.0 TR: 2500.00 msec, TE: 4.38 msec, TI: 1100.00 msec, flip angle: 8.00 degrees nframes: 1 PhEncDir: ROW ras xform present xform info: x_r = -1., y_r = -0., z_r = -0., c_r = 2.6988 : x_a = -0., y_a = -0., z_a = -1., c_a = 6.9217 : x_s = 0., y_s = -1., z_s = 0., c_s = -1.3494 talairach xfm : Orientation : LIP Primary Slice Direction: coronal voxel to ras transform: -0.5000 -0. -0.66.6988 -0. -0. -1.86.9217 0. -0.5000 0.62.6506 0. 0. 0. 1. voxel-to-ras determinant 0.25 ras to voxel transform: -2. 0. 0. 133.3976 -0. -0. -2. 125.3012 0. -1. 0.86.9217 0. 0. 0. 1. 2010/11/17 Bruce Fischl > can you try running recon-all directly on the dicoms? Also, it's probably > pretty noisy at .5mm in-plane - how does it look? Is it whole brain? > > > On Wed, 17 Nov 2010, liang wang wrote: > > Hi Bruce, >> >> I run the command on a NIFTI image converted by dicom files. The image can >> be skull stripped using bet in FSL, but some skulls were not removed >> clearly. Here is the information by mri_info. It seems to me normal, but >> several scan parameters loss. For the nifti image, I use to3d (AFNI code) >> to >> convert DICOM to nifti format and use 3drefit to fix up correctly the >> orientation. >> >> #--- >> type: nii >> dimensions: 256 x 256 x 160 >> voxel sizes: 0.5000, 0.5000, 1. >> type: SHORT (4) >> fov: 128.000 >> dof: 0 >> xstart: -64.0, xend: -64.0 >> ystart: -64.0, yend: -64.0 >> zstart: -80.0, zend: -80.0 >> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 >> degrees >> nframes: 1 >> PhEncDir: UNKNOWN >> ras xform present >> xform info: x_r = 1., y_r = -0., z_r = -0., c_r = >> -2.6988 >> : x_a = -0., y_a = -1., z_a = -0., c_a = >> -1.3494 >> : x_s = 0., y_s = 0., z_s = -1., c_s = >> 6.9217 >> Orientation : RPI >> Primary Slice Direction: axial >> >> voxel to ras transform: >> 0.5000 -0. -0. -66.6988 >> -0. -0.5000 -0.62.6506 >> 0. 0. -1.86.9217 >> 0. 0. 0. 1. >> >> voxel-to-ras determinant 0.25 >> >> ras to voxel transform: >> 2. -0. -0. 133.3976 >> 0. -2. 0. 125.3012 >> 0. 0. -1.86.9217 >> 0. 0. 0. 1. >> >> >> 2010/11/17 Bruce Fischl >> >> wow, that's a completely wacky talairach xform. Did you run this straight >>> on the dicom images? The talairach clearly failed for some reason. Try >>> running mri_info on the dicoms to see if there is something strange in >>> them >>> >>> >>> On Wed, 17 Nov 2010, liang wang wrote: >>> >>> Hi FSusers, >>> >>>> >>>> The terminal displays errors when I run "recon-all -autorecon1 -subjid >>>> ..." >>>> to get a skull-stripped brain image. The processing exits with the >>>> following >>>> errors regarding talairach transformation. Here is the talairach.xfm: >>>> >>>> MNI Transform File >>>> % tkregister2 >>>> >>>> Transform_Type = Linear; >>>> Linear_Transform = >>
