[Freesurfer] PROBLEM DOWLOAD LINUX VERSION
External Email - Use Caution Dear Freesurfer expert, I'm not able to download the Linux version of Freesurfer by your website. For some reason it doesn't open the page. Could you please send me an another link or the version? Thanks in advance Davide ___ 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] lazy symbol binding errors
External Email - Use Caution Dear experts, I was running mri2mesh command and I got this error: mris_convert /Users/davidemomi/Desktop/DAVE/sim_fem/fs_subj60/surf/rh.white /Users/davidemomi/Desktop/DAVE/sim_fem/m2m_subj60/tmp/wm.rh.stl dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib So I've tried to source Freesurfer and run sudo -E fs_update But I got another error rsync -zbrlv --progress --suffix=.1531384527_bak rsync:// surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/* /Applications/freesurfer rsync: failed to connect to surfer.nmr.mgh.harvard.edu: Operation timed out (60) rsync error: error in socket IO (code 10) at /BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52/rsync/clientserver.c(106) [receiver=2.6.9] Could you please help me with both errors? Thanks in advance Davide Title: mri2mesh report == ==> mri2mesh started Mon Jul 9 12:40:02 CEST 2018 ... == command line options: --all subj60 T1w.nii.gz == ==> --brain/--brainf: Preparing GM and WM surfaces ... == == ==> running FreeSurfer recon-all on T1fs! ... == fslreorient2std T1w.nii.gz /Users/davidemomi/Desktop/DAVE/sim_fem/m2m_subj60/T1fs.nii.gz flirt -in /usr/local/fsl/data/standard/MNI152_T1_1mm.nii.gz -ref /Users/davidemomi/Desktop/DAVE/sim_fem/m2m_subj60/T1fs.nii.gz -out /Users/davidemomi/Desktop/DAVE/sim_fem/m2m_subj60/tmp/MNIfs_reg fslroi /Users/davidemomi/Desktop/DAVE/sim_fem/m2m_subj60/T1fs.nii.gz /Users/davidemomi/Desktop/DAVE/sim_fem/m2m_subj60/T1fs_roi 0 256 0 256 0 166 recon-all -i /Users/davidemomi/Desktop/DAVE/sim_fem/m2m_subj60/T1fs_roi.nii.gz -s /Users/davidemomi/Desktop/DAVE/sim_fem/fs_subj60 recon-all -s /Users/davidemomi/Desktop/DAVE/sim_fem/fs_subj60 -all -3T -cubic == ==> Convert WM and GM hemispheres to STL ... == mris_convert /Users/davidemomi/Desktop/DAVE/sim_fem/fs_subj60/surf/rh.white /Users/davidemomi/Desktop/DAVE/sim_fem/m2m_subj60/tmp/wm.rh.stl dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib error code 134 exiting mri2mesh ___ 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] lazy symbol binding errors
External Email - Use Caution Dear Robert, Thanks for both your help and your prompt response I've followed the instruction and everything seems fine Thanks again Davide Momi --- PhD Candidate Unit of Behavioral Economics and Neuroeconomics Department of Neuroscience, Imaging and Clinical Sciences University "G. d'Annunzio" of Chieti Via dei Vestini 31, 66013 Chieti, Italy Mobile ++39 - 348-2650293 2018-07-12 16:27 GMT+02:00 Dicamillo, Robert : > Hello David, > > Please try downloading the following archive, unzip it, and follow the > instructions in the README to update the files that have the lazy symbol > issue. > > https://drive.google.com/open?id=1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR > > -rob > > On Jul 12, 2018, at 4:48 AM, Davide Momi wrote: > > External Email - Use Caution > > Dear experts, > > I was running mri2mesh command and I got this error: > > mris_convert /Users/davidemomi/Desktop/DAVE/sim_fem/fs_subj60/surf/rh.white > /Users/davidemomi/Desktop/DAVE/sim_fem/m2m_subj60/tmp/wm.rh.stl > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address > Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > dyld: Symbol not found: ___emutls_get_address > Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > > So I've tried to source Freesurfer and run > > sudo -E fs_update > > But I got another error > > rsync -zbrlv --progress --suffix=.1531384527_bak rsync://surfer.nmr.mgh. > harvard.edu/pub/dist/freesurfer/patches/freesurfer- > Darwin-OSX-stable-pub-v6.0.0-2beb96c/* /Applications/freesurfer > rsync: failed to connect to surfer.nmr.mgh.harvard.edu: Operation timed > out (60) > rsync error: error in socket IO (code 10) at /BuildRoot/Library/Caches/com. > apple.xbs/Sources/rsync/rsync-52/rsync/clientserver.c(106) > [receiver=2.6.9] > > > Could you please help me with both errors? > > Thanks in advance > > Davide > ___ > 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 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] Extract Cortical Thickness Values from ROI.nii
External Email - Use Caution Dear all, I've just completed the recon -all command and I would like to extract Cortical thickness values in subject space at vertex level (without any sort of normalization). Could you please give me an insight on how to do it? Thanks in advance Dav e ___ 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] Error with mris_anatomical_stats
External Email - Use Caution Dear FreeSurfer, I have a problem when I use mris_anatomical_stats. It gives me an error saying that it couldn't read the input volume which is the wm.mgz file. would you please help me how I should fix this problem? this is the command which I used: mris_anatomical_stats -a label/lh.aparc.annot -b 60_AV rh computing statistics for each annotation in label/lh.aparc.annot. reading volume /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz... mghRead(/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz, -1): could not open file mris_anatomical_stats: could not read input volume /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz Thanks in advance Davide ___ 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] Error with mris_anatomical_stats
External Email - Use Caution Dear Bruce, thanks for your response. my SUBJECTS_DIR is set to: /Users/davidemomi/Downloads/Broad_60_AV, which is actually where the output of recon-all is located. the file wm.mgz exists and is in the $SUBJECTS_DIR/mri directory Thanks again Il giorno ven 24 ago 2018 alle ore 16:49 Bruce Fischl < fis...@nmr.mgh.harvard.edu> ha scritto: > Hi Davide > > does that file exist? What is your SUBJECTS_DIR set to? > > cheers > Bruce > On Fri, 24 Aug 2018, > Davide Momi wrote: > > > > > External Email - Use Caution > > > > Dear FreeSurfer, > > > > I have a problem when I use mris_anatomical_stats. It gives me an error > saying that it couldn't read > > the input volume which is the wm.mgz file. > > would you please help me how I should fix this problem? > > this is the command which I used: > > > > mris_anatomical_stats -a label/lh.aparc.annot -b 60_AV rh > > > > computing statistics for each annotation in label/lh.aparc.annot. > > > > reading volume > /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz... > > > > mghRead(/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz, -1): > could not open file > > > > mris_anatomical_stats: could not read input volume > > /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz > > > > > > Thanks in advance > > > > > > Davide > > > >___ > 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] Error with mris_anatomical_stats
External Email - Use Caution Yes, I meant the second one and rh.aparc.annot (not lh) given that as you said I specified rh. As for the ls -l on wm.mgz this is the output: -rw---@ 1 davidemomi staff 432151 Jun 13 2017 wm.mgz Thanks Il giorno ven 24 ago 2018 alle ore 17:35 Bruce Fischl < fis...@nmr.mgh.harvard.edu> ha scritto: > Hi Davide > > do you mean $SUBJECTS_DIR/mri or $SUBJECTS_DIR/60_AV/mri? It should be the > latter, not the former. Also, can you send us the output of ls -l on the > wm.mgz? And finally, you probably want to use rh.aparc.annot not > lh.aparc.annot since you specified rh on the command line > > cheers > Bruce > > > On Fri, 24 Aug 2018, Davide Momi wrote: > > > > > External Email - Use Caution > > > > Dear Bruce, > > > > thanks for your response. > > > > my SUBJECTS_DIR is set to: /Users/davidemomi/Downloads/Broad_60_AV, > which is actually where the > > output of recon-all is located. > > > > the file wm.mgz exists and is in the $SUBJECTS_DIR/mri directory > > > > Thanks again > > > > > > > > > > Il giorno ven 24 ago 2018 alle ore 16:49 Bruce Fischl < > fis...@nmr.mgh.harvard.edu> ha scritto: > > Hi Davide > > > > does that file exist? What is your SUBJECTS_DIR set to? > > > > cheers > > Bruce > > On Fri, 24 Aug 2018, > > Davide Momi wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FreeSurfer, > > > > > > I have a problem when I use mris_anatomical_stats. It gives me > an error saying that it > > couldn't read > > > the input volume which is the wm.mgz file. > > > would you please help me how I should fix this problem? > > > this is the command which I used: > > > > > > mris_anatomical_stats -a label/lh.aparc.annot -b 60_AV rh > > > > > > computing statistics for each annotation in label/lh.aparc.annot. > > > > > > reading volume > /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz... > > > > > > > mghRead(/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz, -1): > could not open > > file > > > > > > mris_anatomical_stats: could not read input volume > > > /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz > > > > > > > > > Thanks in advance > > > > > > > > > Davide > > > > > >___ > > 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 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] Error with mris_anatomical_stats
External Email - Use Caution Bruce, this is the output: mri_info wm.mgz Volume information for wm.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.00, 1.00, 1.00 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 8.21 msec, TE: 3.22 msec, TI: 450.00 msec, flip angle: 12.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.00 ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = -6.3280 : x_a = 0., y_a = 0., z_a = 1., c_a = 28.2400 : x_s = 0., y_s = -1., z_s = 0., c_s = 19.2471 talairach xfm : /Users/davidemomi/Downloads/Broad_60_AV/60_AV/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 121.6720 0. 0. 1. -99.7600 0. -1. 0. 147.2471 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 121.6720 -0. -0. -1. 147.2471 -0. 1. -0.99.7600 -0. -0. -0. 1. thanks Il giorno ven 24 ago 2018 alle ore 18:02 Bruce Fischl < fis...@nmr.mgh.harvard.edu> ha scritto: > can you run mri_info on it? And please include the full screen output > including the command line that you run as well as what it produces. > > thanks > Bruce > On Fri, > 24 Aug 2018, Davide Momi wrote: > > > > > External Email - Use Caution > > > > Yes, I meant the second one and rh.aparc.annot (not lh) given that as > you said I specified rh. > > > > As for the ls -l on wm.mgz this is the output: > > > > -rw---@ 1 davidemomi staff 432151 Jun 13 2017 wm.mgz > > > > Thanks > > > > > > > > Il giorno ven 24 ago 2018 alle ore 17:35 Bruce Fischl < > fis...@nmr.mgh.harvard.edu> ha scritto: > > Hi Davide > > > > do you mean $SUBJECTS_DIR/mri or $SUBJECTS_DIR/60_AV/mri? It > should be the > > latter, not the former. Also, can you send us the output of ls -l > on the > > wm.mgz? And finally, you probably want to use rh.aparc.annot not > > lh.aparc.annot since you specified rh on the command line > > > > cheers > > Bruce > > > > > > On Fri, 24 Aug 2018, Davide Momi wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear Bruce, > > > > > > thanks for your response. > > > > > > my SUBJECTS_DIR is set to: > /Users/davidemomi/Downloads/Broad_60_AV, which is actually > > where the > > > output of recon-all is located. > > > > > > the file wm.mgz exists and is in the $SUBJECTS_DIR/mri directory > > > > > > Thanks again > > > > > > > > > > > > > > > Il giorno ven 24 ago 2018 alle ore 16:49 Bruce Fischl < > fis...@nmr.mgh.harvard.edu> ha > > scritto: > > > Hi Davide > > > > > > does that file exist? What is your SUBJECTS_DIR set to? > > > > > > cheers > > > Bruce > > > On Fri, 24 Aug 2018, > > > Davide Momi wrote: > > > > > > > > > > > External Email - Use Caution > > > > > > > > Dear FreeSurfer, > > > > > > > > I have a problem when I use mris_anatomical_stats. It > gives me an error saying > > that it > > > couldn't read > > > > the input volume which is the wm.mgz file. > > > > would you please help me how I should fix this problem? > > > > this is the command which I used: > > > > > > > > mris_anatomical_stats -a label/lh.aparc.annot -b 60_AV rh > > > > > > > > computing statistics for each annotation in > label/lh.aparc.annot. > > > > > > > > reading volume > /Users/davidemomi/Downloads/Br
[Freesurfer] Edit surface in Freeview
External Email - Use Caution Dear Freesurfer expert, I am working with bem model and I have created the outer and the inner skull. Unfortunately, for few subjects the two surfaces intersect each other (see attached). I've tried to edit it manually but I had hard time in figuring it out. Could you please help me with this? thanks Dave ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Edit surface in Freeview
External Email - Use Caution Thanks Doug, I followed your tips and try to run mris_remove_intersection. However the result looks like the same than before. Maybe I am doing something wrong. Could you please provide me more details? Do you have any other suggestions? Thanks again for your help Dave Il giorno sab 11 gen 2020 alle ore 15:56 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > YOu can try running mris_remove_intersection (or something like that) > > On 1/11/2020 12:48 PM, Davide Momi wrote: > > External Email - Use Caution > Dear Freesurfer expert, > > I am working with bem model and I have created the outer and the inner > skull. Unfortunately, for few subjects the two surfaces intersect each > other (see attached). I've tried to edit it manually but I had hard time in > figuring it out. Could you please help me with this? > > thanks > > Dave > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Using Buckner Cerebellar Parcellation
External Email - Use Caution Dear expert, I am trying to coregister the Buckner cerebellar parcellation ( http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011) in all my sample. However the results that I got using mri_vol2vol are not so good (see attached). Indeed in most cases the parcellation is bigger than the anatomical cerebellum of my subjects. Do you have any tips? Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Using Buckner Cerebellar Parcellation
External Email - Use Caution Dear Thomas, yes I am trying to warp the Buckner Parcellation to anatomical of all my subjects Please find below the command that I used: mri_vol2vol --mov ../Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz \ --s 114823 \ --targ 114823/mri/brainmask.mgz \ --o Buckner2011_atlas_freesurfer_internal_space.nii.gz \ --interp nearest Unfortunately the output is much bigger than the anatomical as I showed you in my previous email Would you have any suggestions? Thanks Il giorno sab 8 feb 2020 alle ore 21:43 Thomas Yeo ha scritto: > External Email - Use Caution > > Hi Davide, > > Can you elaborate more? You are trying to warp the Buckner parcellation > from MNI parcellation to where? > > What's the exact command that you used? > > --Thomas > > On Sun, Feb 9, 2020 at 2:03 AM Davide Momi > wrote: > >> External Email - Use Caution >> >> Dear expert, >> >> I am trying to coregister the Buckner cerebellar parcellation ( >> http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011) in >> all my sample. However the results that I got using mri_vol2vol are not so >> good (see attached). Indeed in most cases the parcellation is bigger than >> the anatomical cerebellum of my subjects. Do you have any tips? >> >> Thanks >> ___ >> 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
Re: [Freesurfer] Using Buckner Cerebellar Parcellation
External Email - Use Caution Thanks Thomas, it worked perfectly Best Il giorno dom 9 feb 2020 alle ore 09:20 Thomas Yeo ha scritto: > External Email - Use Caution > > Hi Davide, > > Here's a previous email I sent to the list about warping Choi's > striatum atlas to individual subject's striatum (which I have modified > for the cerebellum). Let us know if this works. > > 1) Assuming you are quite happy with the freesurfer cerebellum > parcellation in your subjects, then I am assuming freesurfer nonlinear > registration (talairach.m3z) is working quite well. Talairach.m3z > warps your subject to an internal freesurfer space (kinda like MNI305, > but not quite). Let's say the freesurfer recon-all output is at > /SUBJECT_FS/ > > 2) Run the MNI152 1mm template (the one from FSL) through recon-all. > Recon-all will give you a Talairach.m3z that allows you to map the > MNI152 1mm template to the internal freesurfer space. Let's say the > freesurfer recon-all output is at /MNI152_FS/ > > 3) Then do the following: > > a) Use mri_vol2vol to upsample the Buckner cerebellum atlas which is > 2mm resolution to the 1mm MNI152 template: > > >> mri_vol2vol --mov Buckner_atlas.nii.gz --targ MNI152/mri/norm.mgz > --regheader --o Buckner_atlas1mm.nii.gz --no-save-reg --interp nearest > > Notice that I use norm.mgz of the MNI template rather than the > original MNI template. norm.mgz is the 256 x 256 x 256 conformed > version of the MNI template that recon-all puts through. > > b) warp the Buckner_atlas1mm.nii.gz to freesurfer nonlinear volumetric > space: > > >> setenv SUBJECTS_DIR > >> mri_vol2vol_used --mov Buckner_atlas1mm.nii.gz --s MNI152_FS --targ > $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o > Buckner_atlas_freesurfer_internal_space.nii.gz --interp nearest > > c) warp the Buckner_atlas_freesurfer_internal_space.nii.gz to your subject: > > >> setenv SUBJECTS_DIR > >> mri_vol2vol --mov $SUBJECTS_DIR/SUBJECT_FS/mri/norm.mgz --s SUBJECT_FS > --targ Buckner_atlas_freesurfer_internal_space.nii.gz --m3ztalairach.m3z > --o Buckner_atlas_subject.nii.gz --interp nearest --inv-morph > > This is not optimal because of the double interpolation. You might > want to use the MNI template instead of the Buckner_atlas to test the > above, so you can check the goodness of the warp. The final warped MNI > template should hopefully look identical to your subject. If that > works, then use the Buckner_atlas. Note that mri_vol2vol does not work > properly for talairach.m3z below version 5, so you should use version > 5x mri_vol2vol. > > Regards, > Thomas > > On Sun, Feb 9, 2020 at 9:39 PM Davide Momi > wrote: > >> External Email - Use Caution >> >> Dear Thomas, >> >> yes I am trying to warp the Buckner Parcellation to anatomical of all my >> subjects >> Please find below the command that I used: >> >> mri_vol2vol --mov >> ../Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz \ >> >>--s 114823 \ >> >> --targ 114823/mri/brainmask.mgz \ >> >> --o >> Buckner2011_atlas_freesurfer_internal_space.nii.gz \ >> >> --interp nearest >> >> >> Unfortunately the output is much bigger than the anatomical as I showed >> you in my previous email >> >> >> Would you have any suggestions? >> >> >> Thanks >> >> >> >> >> >> Il giorno sab 8 feb 2020 alle ore 21:43 Thomas Yeo >> ha scritto: >> >>> External Email - Use Caution >>> >>> Hi Davide, >>> >>> Can you elaborate more? You are trying to warp the Buckner parcellation >>> from MNI parcellation to where? >>> >>> What's the exact command that you used? >>> >>> --Thomas >>> >>> On Sun, Feb 9, 2020 at 2:03 AM Davide Momi >>> wrote: >>> >>>> External Email - Use Caution >>>> >>>> Dear expert, >>>> >>>> I am trying to coregister the Buckner cerebellar parcellation ( >>>> http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011) >>>> in all my sample. However the results that I got using mri_vol2vol are not >>>> so good (see attached). Indeed in most cases the parcellation is bigger >>>> than the anatomical cerebellum of my subjects. Do you have any tips? >>>> >>>> Than
