Re: [Freesurfer] Using a2009s.annot as seed masks for tractography
Hi Lee, Thanks for your reply. I have repeated this step in /Applications/freesurfer/subjects/HC001/mri using the following command: mri_label2vol --seg left_thalamus.nii.gz --temp b0_brain.nii.gz --reg registration2b0.dat --o left_thalamus_dwi_seed.nii.gz And got this output: Number of labels: 0 Annot File: (null) Template Volume: b0_brain.nii.gz Outut Volume: left_thalamus_dwi_seed.nii.gz Registration File: registration2b0.dat Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /Applications/freesurfer/subjects $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -0.400 0.000 0.000 64.000; -0.000 -0.000 -0.400 48.000; -0.000 0.400 -0.000 27.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 15.625 nHits Thresh: 0 Loading registration from registration2b0.dat RegMat: 0.996 0.088 -0.024 3.909; 0.025 -0.007 1.000 0.627; 0.088 -0.996 -0.009 -10.557; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -0.398 -0.035 0.010 62.436; -0.035 0.398 0.004 52.223; 0.010 -0.003 0.400 27.251; 0.000 0.000 0.000 1.000; ASeg2Vol: Building LUT ASeg2Vol: Sorting ASeg2Vol: Mapping ASeg2Vol: Reverse Map nmisses = 137063 (0 filled) ASeg2Vol: done I think everything is fine now? Many thanks for your great help André Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]quot; im Auftrag von quot;Lee Tirrell [ltirr...@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 23. April 2015 20:15 An: Freesurfer support list Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for tractography Hi André, Could you send the command that you ran to produce this ouput? Also (just to check), do you have permissions to read the b0_brain.nii.gz file, and is it here: /Applications/freesurfer/subjects/HC001/b0_brain.nii.gz Thanks, Lee On Thu, 23 Apr 2015, André Schmidt wrote: Dear Lee, Thanks a lot for your help. Unfortunately, now I've go the following error: Number of labels: 0 Annot File: (null) Template Volume: b0_brain.nii.gz Outut Volume: left_thalamus_dwi_seed Registration File: registration2b0.dat Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /Applications/freesurfer/subjects $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ niiRead(): error opening file /Applications/freesurfer/subjects/HC001/b0_brain.nii.gz ERROR: reading b0_brain.nii.gz header I attach my b0_brain.nii.gz file. Do you know what's wrong? Thanks again André Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]quot; im Auftrag von quot;Lee Tirrell [ltirr...@nmr.mgh.harvard.edu] Gesendet: Freitag, 27. März 2015 19:07 An: Freesurfer support list Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for tractography On Thu, 26 Mar 2015, André Schmidt wrote: Hi Andre, Try using the --seg flag with vol2label, as in: mri_label2vol --seg left_putamen2.nii.gz --temp b0_brain.nii.gz --reg registration2b0.dat --o left_putamen_dwi_seed left_putamen2.nii.gz is a segmentation, where each voxel in the volume is assigned a number (in your case 1 for left putamen and 0 everywhere else). Freesurfer label files have a different format. Run mri_label2vol --help for more information. Hope this helps, and let us know if there are more problems. Best, Lee Hi Anastasia, Sorry for not being clearer. According to your email, I have labelled all my regions of interest using this command: mri_binarize --match ID --i aparc.a2009s+aseg.mgz --o labelID.nii.gz Let's take the left putamen as an example: cmdline mri_binarize --match 12 --i aparc+aseg.mgz --o left_putamen2.nii.gz sysname Darwin hostname Andres-MacBook-Pro.local machine x86_64 user andre input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output left_putamen2.nii.gz Binarizing based on matching values nMatch 1 012 binval1 binvalnot 0 Found 6228 values in range Counting number of voxels Found 6228 voxels in final mask mri_binarize done Please find attached the output file (left_putamen2.nii.gz). After this, I used the following command to create the register.dat file: bbregister --s HC001 --mov HC001/mri/bo_brain.nii.gz --reg HC001/mri/registration2b0.dat --dti --init-fsl Please find attached the registration2b0.dat file. Then I wanted to convert the label file into diffusion space with mri_label2vol with this
[Freesurfer] labelling
Dear freesurfer experts, I intend to create ROIs from the aparc+seg.mgz file and would like to ask whether the following assignments are correct (sorry for the long list): 10: left_thalamus 11: left_caudate 12: left_putamen 13: left_pallidum 17: left_hippocampus 18: left_amygdala 26: left_accumbens 49: right_thalamus 50: right_caudate 51: right_putamen 52: right_pallidum 53: right_hippocampus 54: right_amygdala 58: right_accumbens 1001: left_bankssts 1002: left_caudalanteriorcingulate 1003: left_caudalmiddlefrontal 1005: left_cuneus 1006: left_entorhinal 1007: left_fusiform 1008: left_inferiorparietal 1009: left_inferiortemporal 1010: left_isthumscingulate 1011: left_lateraloccipital 1012: left_lateralorbitofrontal 1013: left_lingual 1014: left_medialorbitofrontal 1015: left_middletemporal 1016: left_parahippocampal 1017: left_paracentral 1018: left_parsopercularis 1019: left_parsorbitalis 1020: left_parstriangularis 1021: left_pericalcarine 1022: left_postcentral 1023: left_posteriorcingulate 1024: left_precentral 1025: left_precuneus 1026: left_rostralanteriorcingulate 1027: left_rostralmiddlefrontal 1028: left_superiorfrontal 1029: left_superiorparietal 1030: left_superiortemporal 1031: left_supramarginal 1032: left_frontalpole 1033: left_temporalpole 1034: left_transversetemporal 1035: left_insula 2001: right_banksst 2002: right_caudalanteriorcingulate 2003: right_caudalmiddlefrontal 2005: right_cuneus 2006: right_entorhinal 2007: right_fusiform 2008: right_inferiorparietal 2009: right_inferiortemporal 2010: right_isthumscingulate 2011: right_lateraloccipital 2012: right_lateralorbitofrontal 2013: right_lingual 2014: right_medialorbitofrontal 2015: right_middletemporal 2016: right_parahippocampal 2017: right_paracentral 2018: right_parsopercularis 2019: right_parsorbitalis 2020: right_parstriangularis 2021: right_pericalcarine 2022: right_postcentral 2023: right_posteriorcingulate 2024: right_precentral 2025: right_precuneus 2026: right_rostralanteriorcingulate 2027: right_rostralmiddlefrontal 2028: right_superiorfrontal 2029: right_superiorparietal 2030: right_superiortemporal 2031: right_supramarginal 2032: right_frontalpole 2033: right_temporalpole 2034: right_transversetemporal 2035: right_insula Many thanks for the check. Best wishes André ___ 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] crossing medial surfaces
Dear Bruce, thanks for the reply. I often have the case that the aseg.mgz is already correct, however the surfaces cross because the aparc+aseg.mgz incorrectly classified the hemispheres. If running autorecon2-cp uses the aseg.mgz, which is already correct, would that make any changes to the aparc+aseg.mgz? Cheers, Clara - Ursprüngliche Mail - Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Freitag, 24. April 2015 03:12:55 Betreff: Re: [Freesurfer] crossing medial surfaces I don't think you want noaseg. Why not try autorecon2-cp so it starts after the aseg but uses it? cheers Bruce On Thu, 23 Apr 2015, Clara Kuehn wrote: Hi Paul, thanks for your reply. I think the problem is that after editing the aseg.mgz and rerunning -autorecon2-noaseg it doesn't update the aparc+aseg.mgz, so the surfaces still cross. Cheers, Clara - Ursprüngliche Mail - Von: silve...@gmx.com An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 23. April 2015 03:24:51 Betreff: Re: [Freesurfer] crossing medial surfaces Hi Clara, The method for dealing with the crossing medial surfaces that works for me is decribed in the email below. Though, I'm not sure if there are any issues or concerns with this approach particularly in regard to thickness or the segmentations. Paul Sent: Tuesday, October 22, 2013 at 9:49 AM From: silve...@gmx.com silve...@gmx.com To: Bruce Fischl fis...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] medial wall crossing the surface: repost Thanks Bruce for your response, I'll fix aseg where it is incorrect, but what about the instances where the aseg is correct and the pial surfaces cross? Other than needing to update aseg.stats, are there any other concerns with the 'hemisphere' approach I described below? Thanks again, Paul - Original Message - From: Bruce Fischl Sent: 10/22/13 09:46 AM To: silve...@gmx.com Subject: Re: [Freesurfer] medial wall crossing the surface: repost Try fixing the aseg and rerunning Cheers Bruce On Oct 21, 2013, at 6:23 PM, silve...@gmx.com silve...@gmx.com wrote: Not always, but yes, in some instances the aseg crosses. - Original Message - From: Bruce Fischl Sent: 10/18/13 01:22 PM To: silve...@gmx.com Subject: Re: [Freesurfer] medial wall crossing the surface Does the aseg cross as well? On Oct 17, 2013, at 10:07 PM, silve...@gmx.com silve...@gmx.com wrote: Dear All, I too am seeing the medial pial surfaces crossing hemispheres in some subjects. The approach that appears to be working for me involves making copies of brainmask.mgz and aseg.mgz For the left hemisphere crossing into the right, edit brainmask.mgz and aseg.mgz to delete voxels at the crossing belonging to the right hemisphere. I then run recon-all -autorecon-pial -hemi lh -subjid subject followed by returning the brainmask.mgz and aseg.mgz back to their original copy. This is similarly repeated for the right hemisphere crossing into the left. Are there any issues or concerns with this approach particularly in regard to thickness or the segmentations? Thanks, Paul ___ 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 ___ 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
Re: [Freesurfer] labelling
Hi Andre they look right, but check the FreeSurferColorLUT.txt file - that is the definitive location cheers Bruce On Fri, 24 Apr 2015, André Schmidt wrote: Dear freesurfer experts, I intend to create ROIs from the aparc+seg.mgz file and would like to ask whether the following assignments are correct (sorry for the long list): 10: left_thalamus 11: left_caudate 12: left_putamen 13: left_pallidum 17: left_hippocampus 18: left_amygdala 26: left_accumbens 49: right_thalamus 50: right_caudate 51: right_putamen 52: right_pallidum 53: right_hippocampus 54: right_amygdala 58: right_accumbens 1001: left_bankssts 1002: left_caudalanteriorcingulate 1003: left_caudalmiddlefrontal 1005: left_cuneus 1006: left_entorhinal 1007: left_fusiform 1008: left_inferiorparietal 1009: left_inferiortemporal 1010: left_isthumscingulate 1011: left_lateraloccipital 1012: left_lateralorbitofrontal 1013: left_lingual 1014: left_medialorbitofrontal 1015: left_middletemporal 1016: left_parahippocampal 1017: left_paracentral 1018: left_parsopercularis 1019: left_parsorbitalis 1020: left_parstriangularis 1021: left_pericalcarine 1022: left_postcentral 1023: left_posteriorcingulate 1024: left_precentral 1025: left_precuneus 1026: left_rostralanteriorcingulate 1027: left_rostralmiddlefrontal 1028: left_superiorfrontal 1029: left_superiorparietal 1030: left_superiortemporal 1031: left_supramarginal 1032: left_frontalpole 1033: left_temporalpole 1034: left_transversetemporal 1035: left_insula 2001: right_banksst 2002: right_caudalanteriorcingulate 2003: right_caudalmiddlefrontal 2005: right_cuneus 2006: right_entorhinal 2007: right_fusiform 2008: right_inferiorparietal 2009: right_inferiortemporal 2010: right_isthumscingulate 2011: right_lateraloccipital 2012: right_lateralorbitofrontal 2013: right_lingual 2014: right_medialorbitofrontal 2015: right_middletemporal 2016: right_parahippocampal 2017: right_paracentral 2018: right_parsopercularis 2019: right_parsorbitalis 2020: right_parstriangularis 2021: right_pericalcarine 2022: right_postcentral 2023: right_posteriorcingulate 2024: right_precentral 2025: right_precuneus 2026: right_rostralanteriorcingulate 2027: right_rostralmiddlefrontal 2028: right_superiorfrontal 2029: right_superiorparietal 2030: right_superiortemporal 2031: right_supramarginal 2032: right_frontalpole 2033: right_temporalpole 2034: right_transversetemporal 2035: right_insula Many thanks for the check. Best wishes André ___ 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] crossing medial surfaces
no, I don't think it would. If you upload a case with crossing surfaces I'll take a look cheers Bruce On Fri, 24 Apr 2015, Clara Kuehn wrote: Dear Bruce, thanks for the reply. I often have the case that the aseg.mgz is already correct, however the surfaces cross because the aparc+aseg.mgz incorrectly classified the hemispheres. If running autorecon2-cp uses the aseg.mgz, which is already correct, would that make any changes to the aparc+aseg.mgz? Cheers, Clara - Ursprüngliche Mail - Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Freitag, 24. April 2015 03:12:55 Betreff: Re: [Freesurfer] crossing medial surfaces I don't think you want noaseg. Why not try autorecon2-cp so it starts after the aseg but uses it? cheers Bruce On Thu, 23 Apr 2015, Clara Kuehn wrote: Hi Paul, thanks for your reply. I think the problem is that after editing the aseg.mgz and rerunning -autorecon2-noaseg it doesn't update the aparc+aseg.mgz, so the surfaces still cross. Cheers, Clara - Ursprüngliche Mail - Von: silve...@gmx.com An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 23. April 2015 03:24:51 Betreff: Re: [Freesurfer] crossing medial surfaces Hi Clara, The method for dealing with the crossing medial surfaces that works for me is decribed in the email below. Though, I'm not sure if there are any issues or concerns with this approach particularly in regard to thickness or the segmentations. Paul Sent: Tuesday, October 22, 2013 at 9:49 AM From: silve...@gmx.com silve...@gmx.com To: Bruce Fischl fis...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] medial wall crossing the surface: repost Thanks Bruce for your response, I'll fix aseg where it is incorrect, but what about the instances where the aseg is correct and the pial surfaces cross? Other than needing to update aseg.stats, are there any other concerns with the 'hemisphere' approach I described below? Thanks again, Paul - Original Message - From: Bruce Fischl Sent: 10/22/13 09:46 AM To: silve...@gmx.com Subject: Re: [Freesurfer] medial wall crossing the surface: repost Try fixing the aseg and rerunning Cheers Bruce On Oct 21, 2013, at 6:23 PM, silve...@gmx.com silve...@gmx.com wrote: Not always, but yes, in some instances the aseg crosses. - Original Message - From: Bruce Fischl Sent: 10/18/13 01:22 PM To: silve...@gmx.com Subject: Re: [Freesurfer] medial wall crossing the surface Does the aseg cross as well? On Oct 17, 2013, at 10:07 PM, silve...@gmx.com silve...@gmx.com wrote: Dear All, I too am seeing the medial pial surfaces crossing hemispheres in some subjects. The approach that appears to be working for me involves making copies of brainmask.mgz and aseg.mgz For the left hemisphere crossing into the right, edit brainmask.mgz and aseg.mgz to delete voxels at the crossing belonging to the right hemisphere. I then run recon-all -autorecon-pial -hemi lh -subjid subject followed by returning the brainmask.mgz and aseg.mgz back to their original copy. This is similarly repeated for the right hemisphere crossing into the left. Are there any issues or concerns with this approach particularly in regard to thickness or the segmentations? Thanks, Paul ___ 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 ___ 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
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hi Cecilio this means that the automatic checking determined that the Talairach transform to be very unlikely and probably a failure. What was your input data? If you bring it up in tkmedit or freeview do the directions on the screen correspond to true anatomical ones (e.g. is A really anterior)? cheers Bruce On Fri, 24 Apr 2015, Cecilio C Baro Perez wrote: Hi! My name is Cecilio! I'm using the freesurfer 5.3 and I'm having some issues that I hope you could help me with. When I perform: recon-all -s patienttesta -all I get this error: recon-all -s patienttesta exited with ERRORS ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm After reading on the internet I even try this command: recon-all -s patienttesta -all -use-mritotal But it stills give me the same error Could you please tell me what the problem could be? Thank you in advance! Best regards, Cecilio. ___ 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] Viewing gfeat results on inflated brain
If you're just doing a one-sample group mean, then use --osgm instead of --X and --C doug On 4/23/15 7:47 PM, ghazal.ki...@alumni.ubc.ca wrote: Hi, We are working on the analysis step of a project, in which we are interested in the brain activation pattern in response to five different body part movement. We have done a group analysis using FSL (N=10), to see the average activation pattern for each body part. However, we are having problem viewing the average group activation pattern on the FreeSurfer inflated brain. We have tried to use the steps at the last section of the following link (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer); however, we are not sure about the design and contrast matrix in Step 4. We were wondering if you have any suggestions about how to view the group data on the inflated brain? We greatly appreciate your response. Thanks, Ghazal Kiani ___ 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] Fwd: Problem with Freesurfer 5.3
Hi! My name is Cecilio! I'm using the freesurfer 5.3 and I'm having some issues that I hope you could help me with. When I perform: recon-all -s patienttesta -all I get this error: recon-all -s patienttesta exited with ERRORS ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm After reading on the internet I even try this command: recon-all -s patienttesta -all -use-mritotal But it stills give me the same error Could you please tell me what the problem could be? Thank you in advance! Best regards, Cecilio. ___ 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] Visualising surfaces at different fractional depths
Thank you - right as you sent your reply I was writing an apology because I'd just seen that flag. It's Friday evening here in the UK and it might be time to stop sending emails for a little while! So sorry! And thank you! Kx On 24 April 2015 at 18:33, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie you can pick the interpolation method with --interp string where string is one of: nearest trilinear sinc cubic cheers Bruce On Fri, 24 Apr 2015, Kirstie Whitaker wrote: I'm sorry, I did wonder if my email wasn't clear as soon as I clicked send. I'm using mri_vol2surf and I've read the --help output and this page: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf The help is very clear about which surface the volume is being sampled to etc, but I can't see a section that describes exactly how the values are interpolated (if they're interploated) onto the surface. The assumption that I was trying to clarify in my (too short) email was that the voxel through which the vertex passes is the value that is mapped to that vertex. Possible alternatives would be some sort of weighted sum of the neighboring voxels, perhaps, but I had assumed that if there were interpolations happening it would be mentioned in the help file? Does this make sense? I do apologise if I've missed an obvious reference that explains all this! Best wishes Kx On 24 April 2015 at 17:38, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie I think you get to decide how you want the sampling done in mri_vol2surf. cheers Bruce On Fri, 24 Apr 2015, Kirstie Whitaker wrote: Thank you Bruce - that's excellent and works perfectly. Can I ask - when I sample from the new surface from a volume is it the voxel value in which the vertex lands that is assigned to the vertex or is there any interpolation across multiple voxels before assigning the vertex a value? Thanks again for the help! Kx On 20 April 2015 at 14:46, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie you can do this with mris_expand. For example: mris_expand -thickness lh.white 0.5 lh.graymid will generate a surface halfway between white and pial. Using that surface to sample is probably a better method than using profrac, although I expect the differences will be small unless you have very highres data. cheers Bruce On Mon, 20 Apr 2015, Kirstie Whitaker wrote: Hi experts, I've used the command mri_vol2surf with the --projfrac 0.5 flag to sample a volume halfway between the pial and white matter surfaces. I was wondering if there was a way to visualise where this surface lay on the volume? Ideally I'd like to show a figure with the pial, white and this halfway surface overlayed on the volume. Any ideas? Thank you Kirstie -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.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
Re: [Freesurfer] Visualising surfaces at different fractional depths
no worries. I hope it works for you Bruce On Fri, 24 Apr 2015, Kirstie Whitaker wrote: Thank you - right as you sent your reply I was writing an apology because I'd just seen that flag. It's Friday evening here in the UK and it might be time to stop sending emails for a little while! So sorry! And thank you! Kx On 24 April 2015 at 18:33, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie you can pick the interpolation method with --interp string where string is one of: nearest trilinear sinc cubic cheers Bruce On Fri, 24 Apr 2015, Kirstie Whitaker wrote: I'm sorry, I did wonder if my email wasn't clear as soon as I clicked send. I'm using mri_vol2surf and I've read the --help output and this page: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf The help is very clear about which surface the volume is being sampled to etc, but I can't see a section that describes exactly how the values are interpolated (if they're interploated) onto the surface. The assumption that I was trying to clarify in my (too short) email was that the voxel through which the vertex passes is the value that is mapped to that vertex. Possible alternatives would be some sort of weighted sum of the neighboring voxels, perhaps, but I had assumed that if there were interpolations happening it would be mentioned in the help file? Does this make sense? I do apologise if I've missed an obvious reference that explains all this! Best wishes Kx On 24 April 2015 at 17:38, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie I think you get to decide how you want the sampling done in mri_vol2surf. cheers Bruce On Fri, 24 Apr 2015, Kirstie Whitaker wrote: Thank you Bruce - that's excellent and works perfectly. Can I ask - when I sample from the new surface from a volume is it the voxel value in which the vertex lands that is assigned to the vertex or is there any interpolation across multiple voxels before assigning the vertex a value? Thanks again for the help! Kx On 20 April 2015 at 14:46, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie you can do this with mris_expand. For example: mris_expand -thickness lh.white 0.5 lh.graymid will generate a surface halfway between white and pial. Using that surface to sample is probably a better method than using profrac, although I expect the differences will be small unless you have very highres data. cheers Bruce On Mon, 20 Apr 2015, Kirstie Whitaker wrote: Hi experts, I've used the command mri_vol2surf with the --projfrac 0.5 flag to sample a volume halfway between the pial and white matter surfaces. I was wondering if there was a way to visualise where this surface lay on the volume? Ideally I'd like to show a figure with the pial, white and this halfway surface overlayed on the volume. Any ideas? Thank you Kirstie -- Kirstie
Re: [Freesurfer] advice/question regarding your LME toolbox for freesurfer
Dear Jorge, Just wondering if you had any thoughts on the below? Particularly point 1 - that is, how to assess whether linear or quadratic time effects fit the data better? Thanks, Sarah From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sarah Whittle [swhit...@unimelb.edu.au] Sent: Tuesday, 21 April 2015 7:15 AM To: jorge luis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] advice/question regarding your LME toolbox for freesurfer Thanks Jorge! In our case, at step 4, an F-test does show significant evidence for a quadratic term, but not across the whole brain. We have a strong hypothesis that there should be a time effect (linear or quadratic) across most of the brain, and it makes sense that some regions will show linear and others will show quadratic effects. We thought that a top-down approach makes sense, whereby we drop the quadratic term from the model to investigate significant linear time effects. This results in overlap in regions showing a significant quadratic effect (first model) and a significant linear effect (second model). 1. Do you have any thoughts on this approach, and on how to decide whether there are linear or quadratic effects across different regions of the brain? 2. We also want to look at group differences. We find no significant group x quadratic time effects, but we do find significant group x linear time effects (in our second model). The significant regions overlap with those regions where we found significant quadratic effects for the whole group (first model). While this scenario makes sense to me statistically, we have had some researchers tell us that this scenario is not possible/doesn't make sense. Do you have any advice for looking at group differences in our situation? Thank you for your time/help. Sarah From: jorge luis [jbernal0...@yahoo.es] Sent: Tuesday, 21 April 2015 2:37 AM To: Sarah Whittle Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: advice/question regarding your LME toolbox for freesurfer Hi Sara For those analysis I went through the following steps: First considered a full model for both the mean and the covariance and selected the best model for the covariance: 1- Fitted a full model (model1) including intercept, time and time squared as both fixed effects and random effects. 2- Separately fitted a model (model2) including intercept, time and time squared as fixed effects but only including intercept and time as random effects. 3- In order to compare the previous models I then applied the likelihood ratio test vertex-wise and corrected for multiple comparisons using FDR. The result was that over 80% of the vertices showed no significant results for the previous test after correcting for multiple comparisons. So the model with three random effects wasn't significantly better than the model with two random effects and thus I considered model2 a better fit for the data. Once the best model for the covariance was selected I proceeded to select the best model for the mean: 4- I tested the null hypothesis of no quadratic term in the model for the mean using an F-test on model2. After correction for multiple comparisons there was no significant evidence for a quadratic term so I dropped it from the model for the mean. So the final model was one including intercept and time as both fixed and random effects. No quadratic term included either in the model for the mean or the model for the covariance. Hope that helps -Jorge De: Sarah Whittle swhit...@unimelb.edu.au Para: jber...@nmr.mgh.harvard.edu jber...@nmr.mgh.harvard.edu; jbernal0...@yahoo.es jbernal0...@yahoo.es Enviado: Lunes 20 de abril de 2015 2:15 Asunto: advice/question regarding your LME toolbox for freesurfer Dear Dr. Bernal-Rusiel, I was hoping that you could please give me some advice about model selection using the LME tools that you have developed for freesurfer. My colleague has posted to the mailing list about this but hasn't got a response. I am wondering specifically about the best approach for identifying quadratic versus linear age effects for mass-univariate analysis of longitudinal data, in addition to group differences in linear versus quadratic age effects. I have read the following in your 2013 paper: After correcting for multiple comparisons, over 80% of the cortex vertices included both the intercept and time, and not time squared, as the optimal set of random effects. Hence, these two random effects were included in the final model for all remaining analyses and time squared (the quadratic term) was not included as a random effect. We then tested the null hypothesis of no group differences in the quadratic term (i.e., the coefficient of the “time squared” fixed effect) and no vertex exhibited a statistically significant association after multiple
Re: [Freesurfer] Visualising surfaces at different fractional depths
Thank you Bruce - that's excellent and works perfectly. Can I ask - when I sample from the new surface from a volume is it the voxel value in which the vertex lands that is assigned to the vertex or is there any interpolation across multiple voxels before assigning the vertex a value? Thanks again for the help! Kx On 20 April 2015 at 14:46, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie you can do this with mris_expand. For example: mris_expand -thickness lh.white 0.5 lh.graymid will generate a surface halfway between white and pial. Using that surface to sample is probably a better method than using profrac, although I expect the differences will be small unless you have very highres data. cheers Bruce On Mon, 20 Apr 2015, Kirstie Whitaker wrote: Hi experts, I've used the command mri_vol2surf with the --projfrac 0.5 flag to sample a volume halfway between the pial and white matter surfaces. I was wondering if there was a way to visualise where this surface lay on the volume? Ideally I'd like to show a figure with the pial, white and this halfway surface overlayed on the volume. Any ideas? Thank you Kirstie -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.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. -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.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] Visualising surfaces at different fractional depths
Hi Kirstie I think you get to decide how you want the sampling done in mri_vol2surf. cheers Bruce On Fri, 24 Apr 2015, Kirstie Whitaker wrote: Thank you Bruce - that's excellent and works perfectly. Can I ask - when I sample from the new surface from a volume is it the voxel value in which the vertex lands that is assigned to the vertex or is there any interpolation across multiple voxels before assigning the vertex a value? Thanks again for the help! Kx On 20 April 2015 at 14:46, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie you can do this with mris_expand. For example: mris_expand -thickness lh.white 0.5 lh.graymid will generate a surface halfway between white and pial. Using that surface to sample is probably a better method than using profrac, although I expect the differences will be small unless you have very highres data. cheers Bruce On Mon, 20 Apr 2015, Kirstie Whitaker wrote: Hi experts, I've used the command mri_vol2surf with the --projfrac 0.5 flag to sample a volume halfway between the pial and white matter surfaces. I was wondering if there was a way to visualise where this surface lay on the volume? Ideally I'd like to show a figure with the pial, white and this halfway surface overlayed on the volume. Any ideas? Thank you Kirstie -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.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. -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.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] Visualising surfaces at different fractional depths
I'm sorry, I did wonder if my email wasn't clear as soon as I clicked send. I'm using mri_vol2surf and I've read the --help output and this page: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf The help is very clear about which surface the volume is being sampled to etc, but I can't see a section that describes exactly how the values are interpolated (if they're interploated) onto the surface. The assumption that I was trying to clarify in my (too short) email was that the voxel through which the vertex passes is the value that is mapped to that vertex. Possible alternatives would be some sort of weighted sum of the neighboring voxels, perhaps, but I had assumed that if there were interpolations happening it would be mentioned in the help file? Does this make sense? I do apologise if I've missed an obvious reference that explains all this! Best wishes Kx On 24 April 2015 at 17:38, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie I think you get to decide how you want the sampling done in mri_vol2surf. cheers Bruce On Fri, 24 Apr 2015, Kirstie Whitaker wrote: Thank you Bruce - that's excellent and works perfectly. Can I ask - when I sample from the new surface from a volume is it the voxel value in which the vertex lands that is assigned to the vertex or is there any interpolation across multiple voxels before assigning the vertex a value? Thanks again for the help! Kx On 20 April 2015 at 14:46, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie you can do this with mris_expand. For example: mris_expand -thickness lh.white 0.5 lh.graymid will generate a surface halfway between white and pial. Using that surface to sample is probably a better method than using profrac, although I expect the differences will be small unless you have very highres data. cheers Bruce On Mon, 20 Apr 2015, Kirstie Whitaker wrote: Hi experts, I've used the command mri_vol2surf with the --projfrac 0.5 flag to sample a volume halfway between the pial and white matter surfaces. I was wondering if there was a way to visualise where this surface lay on the volume? Ideally I'd like to show a figure with the pial, white and this halfway surface overlayed on the volume. Any ideas? Thank you Kirstie -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.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. -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.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. -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.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
Re: [Freesurfer] Visualising surfaces at different fractional depths
Hi Kirstie you can pick the interpolation method with --interp string where string is one of: nearest trilinear sinc cubic cheers Bruce On Fri, 24 Apr 2015, Kirstie Whitaker wrote: I'm sorry, I did wonder if my email wasn't clear as soon as I clicked send. I'm using mri_vol2surf and I've read the --help output and this page: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf The help is very clear about which surface the volume is being sampled to etc, but I can't see a section that describes exactly how the values are interpolated (if they're interploated) onto the surface. The assumption that I was trying to clarify in my (too short) email was that the voxel through which the vertex passes is the value that is mapped to that vertex. Possible alternatives would be some sort of weighted sum of the neighboring voxels, perhaps, but I had assumed that if there were interpolations happening it would be mentioned in the help file? Does this make sense? I do apologise if I've missed an obvious reference that explains all this! Best wishes Kx On 24 April 2015 at 17:38, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie I think you get to decide how you want the sampling done in mri_vol2surf. cheers Bruce On Fri, 24 Apr 2015, Kirstie Whitaker wrote: Thank you Bruce - that's excellent and works perfectly. Can I ask - when I sample from the new surface from a volume is it the voxel value in which the vertex lands that is assigned to the vertex or is there any interpolation across multiple voxels before assigning the vertex a value? Thanks again for the help! Kx On 20 April 2015 at 14:46, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie you can do this with mris_expand. For example: mris_expand -thickness lh.white 0.5 lh.graymid will generate a surface halfway between white and pial. Using that surface to sample is probably a better method than using profrac, although I expect the differences will be small unless you have very highres data. cheers Bruce On Mon, 20 Apr 2015, Kirstie Whitaker wrote: Hi experts, I've used the command mri_vol2surf with the --projfrac 0.5 flag to sample a volume halfway between the pial and white matter surfaces. I was wondering if there was a way to visualise where this surface lay on the volume? Ideally I'd like to show a figure with the pial, white and this halfway surface overlayed on the volume. Any ideas? Thank you Kirstie -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.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. -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy
[Freesurfer] TRACULA: distance between tract sections in pathstats.byvoxel.txt
Hi Anastasia and Tracula experts I did analyses with Tracula using the very nice feature that allows to perform the statistics along the tracts. I reported the result as function of location along the tracts expressed as voxel index, meaning that the first section was voxel index 1, the 2nd tract section was voxel index 2 etc along the entire path. However, I just got a reviewer comment asking for the actual distance between each voxel index. I guess this depends on the voxel size, but maybe also on the curvature of the tract? Is there a simple way to have the average distance between 2 sections along one tract? Thank you Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ 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] Reconall not properly parcellating brain
Yes, attached is a screenshot of talairach.xfm. It does look brighter in the same region that was excluded in the white/pial matter. Could this be the problem, and what do you suggest I do? Thanks!! ___ 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.
