Dear Dr. Fischl, Thank you for offering to look at our data.
I have used the FTP server to upload a zip archive, based on the website instructions (http://freesurfer.net/fswiki/FtpFileExchange) The file is in: transfer/incoming/1353.zip (using anonymous and my email address for the user/password) Please let us know if you have any thoughts on how we can improve our temporal lobe pial reconstruction. Sincerely, Las 2014-07-18 18:00 GMT+02:00 <freesurfer-requ...@nmr.mgh.harvard.edu>: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: mni152reg error (jaco...@nmr.mgh.harvard.edu) > 2. template replacement (Ilwoo Lyu) > 3. unit of each index (thickness, volume, sulc, curv) after > mri_glmfit-sim (wang kangcheng) > 4. Re: unit of each index (thickness, volume, sulc, curv) after > mri_glmfit-sim (Douglas Greve) > 5. Re: mni152reg error (Douglas Greve) > 6. Re: unit of each index (thickness, volume, sulc, curv) after > mri_glmfit-sim (wang kangcheng) > 7. Re: unit of each index (thickness, volume, sulc, curv) after > mri_glmfit-sim (Douglas Greve) > 8. Spatial smoothing in Matlab (Reza Rajimehr) > 9. Re: unit of each index (thickness, volume, sulc, curv) after > mri_glmfit-sim (wang kangcheng) > 10. Re: Anterior Temporal Lobe / Pial Reconstruc?tion Troubles - > part 1 (Las Blawimo) > 11. Re: selxavg3-sess error in ==> fast_selxavg3 at 434 > (pfannmo...@uni-greifswald.de) > 12. Errors in Mapping of Brodmann Areas (pfannmo...@uni-greifswald.de) > 13. Re: mni152reg error (jaco...@nmr.mgh.harvard.edu) > 14. Re: Errors in Mapping of Brodmann Areas (Bruce Fischl) > 15. Re: Errors in Mapping of Brodmann Areas > (pfannmo...@uni-greifswald.de) > 16. Re: Anterior Temporal Lobe / Pial Reconstruc?tion Troubles - > part 1 (Bruce Fischl) > 17. Thickness measurements on longitudinal data set (Bastian Cheng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Jul 2014 13:14:43 -0400 (EDT) > From: "jaco...@nmr.mgh.harvard.edu" <jaco...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mni152reg error > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <44065.172.20.147.36.1405617283.squir...@mail.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hello again Doug, > > Thank you for sending the updated version of mri152reg. It ran without > error and generated the reg.mni152.2mm.dat registration matrix. > > Unfortunately though, when I tried to apply the transformation to the same > subject's t_000.bfloat, the registration is not correct (command below). > > mri_vol2vol --inv --targ /.../t_000.bfloat --mov > $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o > CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg > /.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat > > On a positive note, I was able to load the output image and > MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed to be > shifted too far anterior. > > With my next attempt, I used mri_convert to make the t_000.bfloat into a > .mgz and than ran mri_vol2vol, but the same misalignment occurred (see > attached photo). > > Using tkmedit, I have confirmed that this file aligns properly on this > subject's native structural image, so I am not quite sure why the > registration matrix may be off. Given that the reg.mni152.2mm.dat file > reflects the transformation of the native struc to MNI, I wonder if I need > to account for the reg file between the func data and the native struc? > > Can you please let me know what I may be doing incorrectly? > > As always, your help is very appreciated. > > Jacob > > > > > > > Yea, i fixed this problem. I've attached a new version with the fix. doug > > > > On 07/17/2014 10:35 AM, jaco...@nmr.mgh.harvard.edu wrote: > >> Hello Freesurfer Experts, > >> I am trying to view stats generated with FsFast in fslview/MNIspace, > and > >> in doing so I have run mni152reg to generate the registration matrix. > That said, mni152reg did not complete correctly and below I have pasted > the terminal output: > >> Thu Jul 17 09:58:10 EDT 2014 > >> setenv SUBJECTS_DIR > >> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons > >> cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons > /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s > >> CD_cerv_pat4_sess1_recon > >> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 > UTC > >> 2014 x86_64 x86_64 x86_64 GNU/Linux > >> fslregister --mov > >> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz > --s CD_cerv_pat4_sess1_recon --reg > >> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat > --dof 12 > >> mkdir: cannot create directory > >> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833': > Permission denied > >> Log file is > >> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log > Thu Jul 17 09:58:11 EDT 2014 > >> --mov > >> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz > --s CD_cerv_pat4_sess1_recon --reg > >> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat > --dof 12 > >> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ > >> purkinje > >> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 > UTC > >> 2014 x86_64 x86_64 x86_64 GNU/Linux > >> nIters 1 > >> -------------------------------------- > >> /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons > >> mri_convert > >> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz > > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > mri_convert > >> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz > > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > niiWrite(): error opening file > >> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from > >> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz... > TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00 > >> i_ras = (-1, 0, 0) > >> j_ras = (-0, -0, -1) > >> k_ras = (0, 1, 0) > >> writing to > >> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii... > ERROR: failure writing > >> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > I tried to run the fslregister command from within the subject's > directory > >> (in hopes to possible correct what may be a permissions issue), but > this > >> produces the same final error, "ERROR: failure writing > >> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii." > Lastly, probably to no surprise, the > >> /.../mri/transforms/reg.mni152.2mm.dat file was never generated. Any > ideas how I may be able to correct these errors? > >> Thank you for the help! > >> Jacob > >> _______________________________________________ > >> 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 > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: t_000.bfloat2MNI152.jpeg > Type: image/jpeg > Size: 89464 bytes > Desc: not available > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140717/a8f20950/attachment-0001.jpeg > > ------------------------------ > > Message: 2 > Date: Thu, 17 Jul 2014 19:51:54 -0400 > From: Ilwoo Lyu <ilwoo...@email.unc.edu> > Subject: [Freesurfer] template replacement > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <CAKi6891Ve6HYHH70eOyjo54cdrDHoaUSAuUxQx+zm0= > 1srp...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear FS experts, > > I am trying to adapt a macaque template (dim: 250 by 300 by 300, voxel > size: 0.8202 mm). > I changed voxel spacing and dimensions to be the same as the MNI305 > template in freesurfer, > but it seems not to work correctly for the affine transformation in the > Talairach space. > > Here are my questions: > > 1) Should I change the voxel size and dimensions of the macaque template? > 2) Should I change the original coordinate system of the > macaque template into the Talairach space? If so, how can I do that (eg, > roughly aligned to (or registration) the MNI template)? > > Thank you! > Ilwoo > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140717/0cbdb664/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Fri, 18 Jul 2014 10:55:07 +0800 > From: "wang kangcheng" <kangchengwang0...@gmail.com> > Subject: [Freesurfer] unit of each index (thickness, volume, sulc, > curv) after mri_glmfit-sim > To: freesurfer <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <2014071810550526177...@gmail.com> > Content-Type: text/plain; charset="us-ascii" > > Dear freesurfer experts > After using the command of mri_glmfit-sim (mri_glmfit-sim > --glmdir aaa.thickness(or thickness, volume, sulc, curv ).lh.10 --cache 1.3 > pos --cwp 1 --2spaces). I check the data in the fie of > cache.th13.pos.y.ocn.dat and found that the data of volume was so small ( > e.g 1.39463 1.50616 2.53250).Data of thickness was same as volume (e.g > 1.83629 3.01648 2.16078). > Could you tell the unit of each index? And could the data be used as > further analysis, e.g correlation with IQ or other behaviors? > > Thank you > > Wang kangcheng > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140718/b32c90eb/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Thu, 17 Jul 2014 22:59:12 -0400 > From: Douglas Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] unit of each index (thickness, volume, sulc, > curv) after mri_glmfit-sim > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <53c88d80.6010...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > > where are you getting those numbers? Thickness will be between 0 and 5, > so those numbers look ok. > doug > > > > On 7/17/14 10:55 PM, wang kangcheng wrote: > > Dear freesurfer experts > > After using the command of mri_glmfit-sim (mri_glmfit-sim --glmdir > > aaa.thickness(or thickness, volume, sulc, curv ).lh.10 --cache 1.3 pos > > --cwp 1 --2spaces). I check the data in the fie > > ofcache.th13.pos.y.ocn.dat and found that the data of volume was so > > small (e.g 1.39463 1.50616 2.53250).Data of thickness was same as > > volume (e.g 1.83629 3.01648 2.16078). > > Could you tell the unit of each index? And could the data be used as > > further analysis, e.g correlation with IQ or other behaviors? > > > > Thank you > > > > Wang kangcheng > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140717/ac10c8ef/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Thu, 17 Jul 2014 23:05:54 -0400 > From: Douglas Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mni152reg error > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <53c88f12.1000...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > > I'm not sure what you are trying to do, but that command line looks like > things are not set up properly. What is t_000.bfloat? (And why are you > using bfloats?) > doug > > > On 7/17/14 1:14 PM, jaco...@nmr.mgh.harvard.edu wrote: > > Hello again Doug, > > > > Thank you for sending the updated version of mri152reg. It ran without > > error and generated the reg.mni152.2mm.dat registration matrix. > > > > Unfortunately though, when I tried to apply the transformation to the > same > > subject's t_000.bfloat, the registration is not correct (command below). > > > > mri_vol2vol --inv --targ /.../t_000.bfloat --mov > > $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o > > CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg > > /.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat > > > > On a positive note, I was able to load the output image and > > MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed to be > > shifted too far anterior. > > > > With my next attempt, I used mri_convert to make the t_000.bfloat into a > > .mgz and than ran mri_vol2vol, but the same misalignment occurred (see > > attached photo). > > > > Using tkmedit, I have confirmed that this file aligns properly on this > > subject's native structural image, so I am not quite sure why the > > registration matrix may be off. Given that the reg.mni152.2mm.dat file > > reflects the transformation of the native struc to MNI, I wonder if I > need > > to account for the reg file between the func data and the native struc? > > > > Can you please let me know what I may be doing incorrectly? > > > > As always, your help is very appreciated. > > > > Jacob > > > > > > > >> Yea, i fixed this problem. I've attached a new version with the fix. > doug > >> > >> On 07/17/2014 10:35 AM, jaco...@nmr.mgh.harvard.edu wrote: > >>> Hello Freesurfer Experts, > >>> I am trying to view stats generated with FsFast in fslview/MNIspace, > > and > >>> in doing so I have run mni152reg to generate the registration matrix. > > That said, mni152reg did not complete correctly and below I have pasted > > the terminal output: > >>> Thu Jul 17 09:58:10 EDT 2014 > >>> setenv SUBJECTS_DIR > >>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons > >>> cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons > > /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s > >>> CD_cerv_pat4_sess1_recon > >>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 > > UTC > >>> 2014 x86_64 x86_64 x86_64 GNU/Linux > >>> fslregister --mov > >>> > /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz > > --s CD_cerv_pat4_sess1_recon --reg > >>> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat > > --dof 12 > >>> mkdir: cannot create directory > >>> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833': > > Permission denied > >>> Log file is > >>> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log > > Thu Jul 17 09:58:11 EDT 2014 > >>> --mov > >>> > /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz > > --s CD_cerv_pat4_sess1_recon --reg > >>> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat > > --dof 12 > >>> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ > >>> purkinje > >>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 > > UTC > >>> 2014 x86_64 x86_64 x86_64 GNU/Linux > >>> nIters 1 > >>> -------------------------------------- > >>> /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons > >>> mri_convert > >>> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz > > > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > > mri_convert > >>> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz > > > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > > niiWrite(): error opening file > >>> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from > >>> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz... > > TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00 > >>> i_ras = (-1, 0, 0) > >>> j_ras = (-0, -0, -1) > >>> k_ras = (0, 1, 0) > >>> writing to > >>> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii... > > ERROR: failure writing > >>> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > > I tried to run the fslregister command from within the subject's > > directory > >>> (in hopes to possible correct what may be a permissions issue), but > > this > >>> produces the same final error, "ERROR: failure writing > >>> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii." > > Lastly, probably to no surprise, the > >>> /.../mri/transforms/reg.mni152.2mm.dat file was never generated. Any > > ideas how I may be able to correct these errors? > >>> Thank you for the help! > >>> Jacob > >>> _______________________________________________ > >>> 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 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140717/cf5bf3ef/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Fri, 18 Jul 2014 12:18:29 +0800 > From: "wang kangcheng" <kangchengwang0...@gmail.com> > Subject: Re: [Freesurfer] unit of each index (thickness, volume, sulc, > curv) after mri_glmfit-sim > To: freesurfer <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <2014071812182560063...@gmail.com> > Content-Type: text/plain; charset="us-ascii" > > Thank you doug > Data of thickness: 1.83629 3.01648 2.16078 corresponds to > lateraloccipital, frontalpole and superiorparietal. > > Why the number of volume (e.g 1.39463 1.50616 2.53250) was also so small ? > was the unit cm^3? > > > Wang Kangcheng > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140718/e1cd3a70/attachment-0001.html > > ------------------------------ > > Message: 7 > Date: Fri, 18 Jul 2014 00:29:50 -0400 > From: Douglas Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] unit of each index (thickness, volume, sulc, > curv) after mri_glmfit-sim > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <53c8a2be.40...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > > How are you computing the volume? Or is this from a volume map? It is > probably computing the average volume of each vertex in which case you > can multiple the value by the number of vertices to get the total volume > for the cluster > > > > > On 7/18/14 12:18 AM, wang kangcheng wrote: > > Thank you doug > > Data of thickness: 1.83629 3.01648 > > 2.16078correspondstolateraloccipital, frontalpole and superiorparietal. > > > > Why the number of volume (e.g 1.39463 1.50616 2.53250) was also so > > small ? was the unit cm^3? > > ------------------------------------------------------------------------ > > > > Wang Kangcheng > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140718/be812bdb/attachment-0001.html > > ------------------------------ > > Message: 8 > Date: Fri, 18 Jul 2014 01:12:04 -0400 (EDT) > From: "Reza Rajimehr" <r...@nmr.mgh.harvard.edu> > Subject: [Freesurfer] Spatial smoothing in Matlab > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <64989.18.93.14.208.1405660324.squir...@mail.nmr.mgh.harvard.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Hi, > > For a simulation purpose, I want to load a surface into Matlab, assign a > random value (taken from a normal distribution) to each vertex, do spatial > smoothing on the surface with a given FWHM (e.g. 5mm), then do some > computations with the smoothed values. > > I am wondering if there is a Matlab code that I can use for surface > smoothing, similar to what FS-FAST preprocessing does in Freesurfer > version 5 and above. > > Thanks, > Reza > > ***************** > Reza Rajimehr, MD > Postdoctoral Research Fellow > > McGovern Institute for Brain Research > Massachusetts Institute of Technology (MIT) > > NMR Martinos Center > Massachusetts General Hospital (MGH) > Harvard University > ***************** > > > ------------------------------ > > Message: 9 > Date: Fri, 18 Jul 2014 13:37:57 +0800 > From: "wang kangcheng" <kangchengwang0...@gmail.com> > Subject: Re: [Freesurfer] unit of each index (thickness, volume, sulc, > curv) after mri_glmfit-sim > To: freesurfer <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <2014071813373409391...@gmail.com> > Content-Type: text/plain; charset="us-ascii" > > Thanks doug > I first merge the data using command of mris_preproc and then do the > GLM analysis using command of mri_glmfit. After that, using the following > command to look the result: > > mri_surfcluster --in leg.volume.lh.10/g2v2/sig.mgh --csd > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th13/mc-z.csd > --mask leg.volume.lh.10/mask.mgh --cwsig > leg.volume.lh.10/g2v2/cache.th13.pos.sig.cluster.mgh --vwsig > leg.volume.lh.10/g2v2/cache.th13.pos.sig.voxel.mgh --sum > leg.volume.lh.10/g2v2/cache.th13.pos.sig.cluster.summary --ocn > leg.volume.lh.10/g2v2/cache.th13.pos.sig.ocn.mgh --oannot > leg.volume.lh.10/g2v2/cache.th13.pos.sig.ocn.annot --annot aparc --csdpdf > leg.volume.lh.10/g2v2/cache.th13.pos.pdf.dat --cwpvalthresh 1 --o > leg.volume.lh.10/g2v2/cache.th13.pos.sig.masked.mgh --no-fixmni > --bonferroni 2 --surf white > > Did you mean that I multiple the value by the number of vertices (NVtxs, > which in the file of cache.th13.pos.sig.cluster.summary ) to get the total > volume for the cluster? > > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs > Annot > 1 4.623 7401 1647.03 -8.8 -49.3 5.4 0.00719 0.00559 0.00878 4199 > isthmuscingulate > 2 3.984 46872 1185.43 -7.7 -71.9 50.4 0.06375 0.05929 0.06820 2487 > precuneus > 3 3.960 57039 3597.23 -10.6 64.4 -5.0 0.00020 0.00000 0.00040 5545 > frontalpole > > > > Wang Kangcheng > Faculty of Psychology, Southwest University, China > Email: kangchengwang0...@gmail.com / wangkangcheng....@163.com > Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140718/86a91f25/attachment-0001.html > > ------------------------------ > > Message: 10 > Date: Fri, 18 Jul 2014 09:37:46 +0200 > From: Las Blawimo <lasblaw...@gmail.com> > Subject: Re: [Freesurfer] Anterior Temporal Lobe / Pial > Reconstruc?tion Troubles - part 1 > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <CAKBuV= > td5z9vvab4rt1vkuyhe24-geg1nuqsnkag45xvz5r...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear dr. Fischl, > > I was wondering if you've had any chance to look at our images (image 3 and > 4 are attached to a second e-mail with the subject: Anterior Temporal Lobe > / Pial Reconstruction Troubles - part 2)? > > Sincerely, > Las > > > 2014-07-11 16:06 GMT+02:00 Las Blawimo <lasblaw...@gmail.com>: > > > Dear Dr. Fischl, > > > > Thanks for your quick reply. > > > > Attached you will find some images (image 1&2) showing the issues we're > > having (I'll send a second e-mail including image 3&4). > > > > The images are as follows: > > > > 1.) sagittal_1353_norm2+3T_vs_default -> the v5.3 suggested norm2 flags > > (from the release notes) and the -3T flag vs. the default v5.3 pipeline. > > Blue is the norm2/3T flag pipeline, yellow is the default. > > > > 2.) sagittal_1353_wusl_vs_default->v5.3 using the -washu_mprage flag, > > obvious improvement in temporal lobe pial surface. Blue is -washu_mprage > > flag, yellow is the default v5.3 pipeline > > > > 3.) axial_1353_norm2+3T_white -> The white surface, which appears OK > > using v5.3 with the suggested norm2 parameters and the -3T flag > > > > 4.) axial_1353_wusl_white_error -> the white surface, with an obvious > > error in the lh_postcentral area, using the -washu_mprage flag. > > > > Let me know if you have any suggestions on other parameters I should try > > to improve the temporal lobe pial surface, without compromising the white > > matter surface reconstruction. > > > > Sincerely, > > > > Las > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140718/ecd0c084/attachment-0001.html > > ------------------------------ > > Message: 11 > Date: Fri, 18 Jul 2014 09:38:39 +0200 > From: pfannmo...@uni-greifswald.de > Subject: Re: [Freesurfer] selxavg3-sess error in ==> fast_selxavg3 at > 434 > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <20140718093839.8e51a7353203ac529ee61...@uni-greifswald.de> > Content-Type: text/plain; charset=US-ASCII > > Thank you for your Help. I figured out that it was a problem with the data > which caused this error. > > > > > > On Wed, 04 Jun 2014 12:00:08 -0400 > Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > > > > This is a strange error that I cannot figure out from the terminal > > output. What version of FS are you using? Here's something you can try: > > > > Run selxavg3-sess with --monly sxa3.m This will return right away having > > created sxa3.m > > > > Start matlab and run sxa3. It will stop at the error below. Then type > > > > flac0.inorm > > > > gmean > > > > Each of these will print something out to the terminal. Send the results > > to the list > > > > doug > > > > > > On 06/02/2014 06:27 AM, pfannmo...@uni-greifswald.de wrote: > > > Dear Experts, > > > > > > during an fsfast analysis an error occured after selxavg3-sess was > executed. The corresponding commands were: > > > > > > mkanalysis-sess -fsd bold -surface self lh -fwhm 0 -event-related > -paradigm sensory.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip > 8 -polyfit 2 -analysis analysis.lh -delay 0 -per-run -force -mcextreg > > > mkcontrast-sess -analysis analysis.lh -contrast stim-v-base -a 1 > > > > > > selxavg3-sess -s ./sessdir -analysis analysis.lh -no-preproc -force > > > > > > > > > > > > The output of selxavg3-sess was: > > > > > > > > > sxa3pwd = > > > > > > /.../evaluation > > > > > > sxa3cmd = > > > > > > /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./sessdir -analysis > analysis.lh -no-preproc -force > > > > > >>> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m > > > #@# sessdir ############################### > > > /.../evaluation/sessdir > > > ------------------------- > > > $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ > > > /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m > > > /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m > > > /usr/local/freesurfer/matlab/MRIread.m > > > ------------------------- > > > outtop = /.../evaluation > > > Extension format = nii.gz > > > 1 stim-v-base.mat > > > Excluding 8 points > > > nruns = 1 > > > autostimdur = > > > > > > > > > outanadir = /.../evaluation/sessdir/bold/analysis.lh > > > Excluding 8 points > > > Found 145573/155188 (93.8) voxels in mask > > > Creating Design Matrix > > > ... creation time = 0.008 sec > > > DoMCFit = 1 > > > ntptot = 108, nX = 15, DOF = 93 > > > Saving X matrix to /.../evaluation/sessdir/bold/analysis.lh/Xtmp.mat > > > XCond = 64.7067 (normalized) > > > Computing compensation for resdual AR1 bias > > > 1 -0.5 -0.468819 (t=0.005249) > > > 2 -0.25 -0.252194 (t=0.007053) > > > 3 0 -0.0449419 (t=0.008126) > > > 4 0.25 0.149516 (t=0.00935) > > > 5 0.5 0.319324 (t=0.010795) > > > AR1 Correction M: 0.0749452 1.26122 > > > Computing contrast matrices > > > OLS Beta Pass > > > run 1 t= 0.0 > > > Global Mean > > > Global In-Mask Mean = (0.664951) > > > ??? Error using ==> mrdivide > > > Matrix dimensions must agree. > > > > > > Error in ==> fast_selxavg3 at 434 > > > RescaleFactor = flac0.inorm/gmean; > > > > > >>> ------------------------------------------ > > > ERROR: fast_selxavg3() failed\n > > > > > > > > > Do you have an idea what went wrong? > > > > > > Sincerely yours pfannmoe > > > _______________________________________________ > > > 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. > > > > > -- > Joerg Pfannmoeller <pfannmo...@uni-greifswald.de> > > > ------------------------------ > > Message: 12 > Date: Fri, 18 Jul 2014 09:58:52 +0200 > From: pfannmo...@uni-greifswald.de > Subject: [Freesurfer] Errors in Mapping of Brodmann Areas > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <20140718095852.02c2fb37113fc851d9188...@uni-greifswald.de> > Content-Type: text/plain; charset="us-ascii" > > Dear Experts, > > I am working with freesurfer 5.3 on Mac OSX. I applied recon-all to a data > set. This has been done with the same data on a Linux system with > Freesurfer 5.3 without any problems. Everything works fine on the Mac > except of the labelling of Brodmann Areas. On the Mac the regions are not > created as a single areal with a border at the outline. Instead they > consist of an outside border and several small regions inside the label. > > I already tried to create the Brodmann Areas by myself using the command: > > mri_label2label --srclabel /.../subjects/fsaverage/label/lh.BA3b.label > --srcsubject fsaverage --trglabel lh.BA3b.test.label --trgsubject subjid > --regmethod surface --hemi lh > > > This does not change the result. I attached a screen shot of the label in > fsaverage and one of my subjects. Any help is highly appreciated. > > Regards pfannmoe > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: screenshot.png > Type: image/png > Size: 100255 bytes > Desc: not available > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140718/8c56a002/attachment-0001.png > > ------------------------------ > > Message: 13 > Date: Fri, 18 Jul 2014 08:34:09 -0400 (EDT) > From: "jaco...@nmr.mgh.harvard.edu" <jaco...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mni152reg error > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Cc: abl...@nmr.mgh.harvard.edu > Message-ID: > <45924.172.20.147.36.1405686849.squir...@mail.nmr.mgh.harvard.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Hello Doug, > > Ideally, I am trying to take subject tstat maps from FsFast (stable3 > environment) and register these native structural space maps to the > MNI152_2mm standard brain. > > The t_000.bfloat file is what was generated relative to my contrast that > was set up in FsFast stable3. There are a series of these files ranging > from t_000.bfloat to t_029.bfloat and there are also these same named > files with a .hdr extension. t_000.bfloat is the file I designate when I > select an overlay within tkmedit. > > Your help sorting out this registration is very appreciated. > > Thank you, > Jacob > > > > > > > > I'm not sure what you are trying to do, but that command line looks like > > things are not set up properly. What is t_000.bfloat? (And why are you > > using bfloats?) > > doug > > > > > > On 7/17/14 1:14 PM, jaco...@nmr.mgh.harvard.edu wrote: > >> Hello again Doug, > >> > >> Thank you for sending the updated version of mri152reg. It ran without > >> error and generated the reg.mni152.2mm.dat registration matrix. > >> > >> Unfortunately though, when I tried to apply the transformation to the > >> same > >> subject's t_000.bfloat, the registration is not correct (command below). > >> > >> mri_vol2vol --inv --targ /.../t_000.bfloat --mov > >> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o > >> CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg > >> /.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat > >> > >> On a positive note, I was able to load the output image and > >> MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed to > >> be > >> shifted too far anterior. > >> > >> With my next attempt, I used mri_convert to make the t_000.bfloat into a > >> .mgz and than ran mri_vol2vol, but the same misalignment occurred (see > >> attached photo). > >> > >> Using tkmedit, I have confirmed that this file aligns properly on this > >> subject's native structural image, so I am not quite sure why the > >> registration matrix may be off. Given that the reg.mni152.2mm.dat file > >> reflects the transformation of the native struc to MNI, I wonder if I > >> need > >> to account for the reg file between the func data and the native struc? > >> > >> Can you please let me know what I may be doing incorrectly? > >> > >> As always, your help is very appreciated. > >> > >> Jacob > >> > >> > >> > >>> Yea, i fixed this problem. I've attached a new version with the fix. > >>> doug > >>> > >>> On 07/17/2014 10:35 AM, jaco...@nmr.mgh.harvard.edu wrote: > >>>> Hello Freesurfer Experts, > >>>> I am trying to view stats generated with FsFast in fslview/MNIspace, > >> and > >>>> in doing so I have run mni152reg to generate the registration matrix. > >> That said, mni152reg did not complete correctly and below I have pasted > >> the terminal output: > >>>> Thu Jul 17 09:58:10 EDT 2014 > >>>> setenv SUBJECTS_DIR > >>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons > >>>> cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons > >> /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s > >>>> CD_cerv_pat4_sess1_recon > >>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 > >> UTC > >>>> 2014 x86_64 x86_64 x86_64 GNU/Linux > >>>> fslregister --mov > >>>> > /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz > >> --s CD_cerv_pat4_sess1_recon --reg > >>>> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat > >> --dof 12 > >>>> mkdir: cannot create directory > >>>> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833': > >> Permission denied > >>>> Log file is > >>>> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log > >> Thu Jul 17 09:58:11 EDT 2014 > >>>> --mov > >>>> > /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz > >> --s CD_cerv_pat4_sess1_recon --reg > >>>> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat > >> --dof 12 > >>>> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ > >>>> purkinje > >>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 > >> UTC > >>>> 2014 x86_64 x86_64 x86_64 GNU/Linux > >>>> nIters 1 > >>>> -------------------------------------- > >>>> /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons > >>>> mri_convert > >>>> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz > >> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > >> mri_convert > >>>> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz > >> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > >> niiWrite(): error opening file > >>>> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > >> reading from > >>>> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz... > >> TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00 > >>>> i_ras = (-1, 0, 0) > >>>> j_ras = (-0, -0, -1) > >>>> k_ras = (0, 1, 0) > >>>> writing to > >>>> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii... > >> ERROR: failure writing > >>>> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > >> I tried to run the fslregister command from within the subject's > >> directory > >>>> (in hopes to possible correct what may be a permissions issue), but > >> this > >>>> produces the same final error, "ERROR: failure writing > >>>> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii." > >> Lastly, probably to no surprise, the > >>>> /.../mri/transforms/reg.mni152.2mm.dat file was never generated. Any > >> ideas how I may be able to correct these errors? > >>>> Thank you for the help! > >>>> Jacob > >>>> _______________________________________________ > >>>> 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 > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 14 > Date: Fri, 18 Jul 2014 09:18:15 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Errors in Mapping of Brodmann Areas > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Cc: Zeke Kaufman <zkauf...@nmr.mgh.harvard.edu> > Message-ID: <alpine.lrh.2.03.1407180917340.32...@nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi pfannmoe > > this is a bug in mri_label2label that we fixed a while ago. Zeke: can > post a new version and let people on the list know where it is? > > thanks > Bruce > > On Fri, 18 Jul 2014, > pfannmo...@uni-greifswald.de wrote: > > > Dear Experts, > > > > I am working with freesurfer 5.3 on Mac OSX. I applied recon-all to a > data set. This has been done with the same data on a Linux system with > Freesurfer 5.3 without any problems. Everything works fine on the Mac > except of the labelling of Brodmann Areas. On the Mac the regions are not > created as a single areal with a border at the outline. Instead they > consist of an outside border and several small regions inside the label. > > > > I already tried to create the Brodmann Areas by myself using the command: > > > > mri_label2label --srclabel /.../subjects/fsaverage/label/lh.BA3b.label > --srcsubject fsaverage --trglabel lh.BA3b.test.label --trgsubject subjid > --regmethod surface --hemi lh > > > > > > This does not change the result. I attached a screen shot of the label > in fsaverage and one of my subjects. Any help is highly appreciated. > > > > Regards pfannmoe > > > > > > > > > ------------------------------ > > Message: 15 > Date: Fri, 18 Jul 2014 15:37:39 +0200 > From: pfannmo...@uni-greifswald.de > Subject: Re: [Freesurfer] Errors in Mapping of Brodmann Areas > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <20140718153739.4cf68ead20e0e95074a7a...@uni-greifswald.de> > Content-Type: text/plain; charset=US-ASCII > > It would be very helpful for me. > > > On Fri, 18 Jul 2014 09:18:15 -0400 (EDT) > Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > > > Hi pfannmoe > > > > this is a bug in mri_label2label that we fixed a while ago. Zeke: can > > post a new version and let people on the list know where it is? > > > > thanks > > Bruce > > > > On Fri, 18 Jul 2014, > > pfannmo...@uni-greifswald.de wrote: > > > > > Dear Experts, > > > > > > I am working with freesurfer 5.3 on Mac OSX. I applied recon-all to a > data set. This has been done with the same data on a Linux system with > Freesurfer 5.3 without any problems. Everything works fine on the Mac > except of the labelling of Brodmann Areas. On the Mac the regions are not > created as a single areal with a border at the outline. Instead they > consist of an outside border and several small regions inside the label. > > > > > > I already tried to create the Brodmann Areas by myself using the > command: > > > > > > mri_label2label --srclabel /.../subjects/fsaverage/label/lh.BA3b.label > --srcsubject fsaverage --trglabel lh.BA3b.test.label --trgsubject subjid > --regmethod surface --hemi lh > > > > > > > > > This does not change the result. I attached a screen shot of the label > in fsaverage and one of my subjects. Any help is highly appreciated. > > > > > > Regards pfannmoe > > > > > > > > > > > _______________________________________________ > > 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. > > > > > -- > Joerg Pfannmoeller <pfannmo...@uni-greifswald.de> > > > ------------------------------ > > Message: 16 > Date: Fri, 18 Jul 2014 09:58:22 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Anterior Temporal Lobe / Pial > Reconstruc?tion Troubles - part 1 > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <alpine.lrh.2.03.1407180958020.32...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Las > > it's tough to tell from just those images. Can you upload the entire > subject directory? > > cheers > Bruce > > > On Fri, 18 Jul 2014, Las Blawimo wrote: > > > Dear dr. Fischl, > > ? > > I was wondering if you've had any chance to look at our images (image 3 > and > > 4 are attached to a second e-mail with the subject: Anterior Temporal > Lobe / > > Pial Reconstruction Troubles - part 2)? > > ? > > Sincerely, > > Las > > > > > > 2014-07-11 16:06 GMT+02:00 Las Blawimo <lasblaw...@gmail.com>: > > > > Dear Dr. Fischl, > > > > Thanks for your quick reply. > > > > Attached you will find some images (image 1&2) showing the > > issues we're having (I'll send a second e-mail including image > > 3&4). > > > > The images are as follows: > > > > 1.) sagittal_1353_norm2+3T_vs_default -> the v5.3 suggested > > norm2 flags (from the release notes) and the -3T flag vs. the > > default v5.3 pipeline. Blue is the norm2/3T flag pipeline, > > yellow is the default. > > > > 2.) sagittal_1353_wusl_vs_default->v5.3 using the -washu_mprage > > flag, obvious improvement in temporal lobe pial surface. Blue is > > -washu_mprage flag, yellow is the default v5.3 pipeline > > > > 3.) axial_1353_norm2+3T_white -> The white surface, which > > appears OK using v5.3 with the suggested norm2 parameters and > > the -3T flag > > > > 4.) axial_1353_wusl_white_error -> the white surface, with an > > obvious error in the lh_postcentral area, using the > > -washu_mprage flag. > > > > Let me know if you have any suggestions on other parameters I > > should try to improve the temporal lobe pial surface, without > > compromising the white matter surface reconstruction. > > > > Sincerely, > > > > Las > > > > > > > > > > ------------------------------ > > Message: 17 > Date: Fri, 18 Jul 2014 16:45:52 +0200 > From: Bastian Cheng <bastianch...@gmail.com> > Subject: [Freesurfer] Thickness measurements on longitudinal data set > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <CA+oKOp= > 7tc1_-96p_0h5_oqeybtwvmwk-9mfdvp8t_sw0uh...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Dear Freesurfer-Experts, > > I am currently trying to measure Cortical Thickness of a > Volume-defined ROI in a patient measured at 4 timepoints. > > Basically, I am interested in a ROI resulting from fMRI activation > measured on Timepoint 1. > I would then like to get thickness values in the same ROI for all > Timepoints 1-4. > > I have read the instructions here: > https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness > this works. > > now, my idea is: > > ROI from TP1 >> register to base image of longit. recon. ("base") > ROI from base >> TP1.long (from long recon) > ROI from base >> TP2.long (from long recon) > ROI from base >> TP3 long (from long recon) > ROI from base >> TP4.long (from long recon) > > OR should I simpy map my ROI to fsaverage and project it back all > individual timepoints? > ROI from TP1 >> register to fsaverage > ROI from fsaverage >> TP1 (not from long recon) > ROI from fsaverage >> TP2 (not from long recon) > etc. > > I understand that registration using the long. recon is more robust... > > Best regards, > Bastian > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 125, Issue 30 > ******************************************* >
_______________________________________________ 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.
