Re: [Freesurfer] how to interpret a change in area of 0.004 mm² per year?
Hi Bruce (and Jorge), Yes, it's the wm surface. I have also done the analyses with the pial surface and the results are similar to wm surface. To your second question: White matter volume increased over this time period (lme analysis; controls: logP = 8.49, patients: logP = 6.34). Since the cortical analyses were done using lme, which can handle missing data, some of the subjects have only one time point. So I created a difference map for those subjects for whom we have data on both time points, to see if area on the first time point is consistently larger than on the second time point. Almost all subjects showed larger values on tp1 than tp2 and the maps of average area change (across subjects) confirm that. In addition, I ran an lme analysis with the same subjects and found results very similar to those for the entire sample. Would you agree that this apparent reduction in cortical area seems plausible? There is a reduction over time in raw data, and pial surface area show the same trend as wm surface, and the lme analysis with only subjects that have data on both time points shows very similar results as the lme with all subjects. On the other hand, I suppose we wouldn't expect increased wm volume together with reduced area? As for the effect size maps, I have worked on finding a way to represent change in area over time that is intuitive for a reader not familiar with FreeSurfer: I figured one solution could be to log transform the dependent variable (wm or pial area). This way the significance tests are done with log transformed data and for purposes of illustration I do exp(beta)*100-100 on the beta for time, which ensures that if there is e.g. a 1% reduction, the figure shows -1, and 1 for a 1% increase. I find this is a good way of demonstrating the effects (attached figure: lh_wmarea_logtransf_expBeta2_s30_inflated_lateral.tif ). What do you think? I could of course also transform the dependent variable into percentages. That is, baseline == 100 and tp2 expressed in percent of baseline. However, I find this to be a less attractive solution because we basically lose the baseline values, and this makes the model less useful for all other purposes. For instance, we can't investigate group differences at the various time points within the model. Perhaps more importantly, it's unclear what assumptions we are making. The lme assumes a normal distribution and it's unclear to me what the distribution of such ratios are. Thank you! LMR yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway Bruce Fischl http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=from:%22Bruce+Fischl%22 Sat, 06 Sep 2014 07:00:14 -0700 http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=date:20140906 Hi Lars which surface are you using? If it's the white surface you might try looking at white matter volume to see if it is decreasing cheers Bruce On Sat, 6 Sep 2014, Lars M. Rimol wrote: Hi, I have performed a longitudinal analysis using the lme module in FreeSurfer, with this model: intercept(random effect) + centered age + group + group x centered age + sex I tested the effect of time with this contrast vector [ 0 1 0 0 0 ]. Dependent variable is area. Here, mapping the second beta means mapping the effect size for (change over) time. In the beta map, I find values from 0 to 0.004. I would interpret that to mean that local area shrinks by at most 0.004 mm² per year in the reference group. But I'm not 100% sure about the biological (or geometrical) meaning of that. Can I interpret this literally as the mean yearly shrinkage of the three triangles surrounding a given vertex, the average of whose area comprises the area score of the vertex, being 4/1000 mm? Of course, these maps are smoothed with 30mm, so the real spatial resolution is nowhere near this Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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. yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway On Mon, Oct 27, 2014 at 9:59 AM, Lars M. Rimol lari...@gmail.com wrote: Hi Bruce (and Jorge), Yes, it's the wm surface. I have also done the analyses with the pial surface and the results are similar to wm surface (attached p-maps:
[Freesurfer] adding insula voxels
Hi Bruce and FS group, Thanks again for the speedy replies and help with everything. Quick question about editing voxels (specifically those in the lh/rh insula). Should I simply add specific voxels to the aparc+aseg for this step? It was a little unclear on the wiki. Also, is there a specific command to re-run the stats/etc. after these edits are performed? Thanks a lot, Adam ___ 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 when completing cortical thickness analysis
I am conducting cortical thickness analyses between hundreds of individuals for a study we are conducting. I was getting this error Unrecognized sub-option flag 'annot_outline'. and so I tried to do the group analysis tutorial and input the command from the end of it (please see command below) but still got the same error. Freeview would open but it would not show any images. Could you help me to resolve this issue please? Also, what does it mean when it spits out invalid drawable? freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d Thank you so much for your help! Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot* ___ 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] Pial surface with point-to-point correspondance between subjects
Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] how to interpret a change in area of 0.004 mm² per year?
Hi Lars yes, it seems plausible, particularly since it is so universal. cheers Bruce On Wed, 29 Oct 2014, Lars M. Rimol wrote: Hi Bruce (and Jorge), Yes, it's the wm surface. I have also done the analyses with the pial surface and the results are similar to wm surface. To your second question: White matter volume increased over this time period (lme analysis; controls: logP = 8.49, patients: logP = 6.34). Since the cortical analyses were done using lme, which can handle missing data, some of the subjects have only one time point. So I created a difference map for those subjects for whom we have data on both time points, to see if area on the first time point is consistently larger than on the second time point. Almost all subjects showed larger values on tp1 than tp2 and the maps of average area change (across subjects) confirm that. In addition, I ran an lme analysis with the same subjects and found results very similar to those for the entire sample. Would you agree that this apparent reduction in cortical area seems plausible? There is a reduction over time in raw data, and pial surface area show the same trend as wm surface, and the lme analysis with only subjects that have data on both time points shows very similar results as the lme with all subjects. On the other hand, I suppose we wouldn't expect increased wm volume together with reduced area? As for the effect size maps, I have worked on finding a way to represent change in area over time that is intuitive for a reader not familiar with FreeSurfer: I figured one solution could be to log transform the dependent variable (wm or pial area). This way the significance tests are done with log transformed data and for purposes of illustration I do exp(beta)*100-100 on the beta for time, which ensures that if there is e.g. a 1% reduction, the figure shows -1, and 1 for a 1% increase. I find this is a good way of demonstrating the effects (attached figure: lh_wmarea_logtransf_expBeta2_s30_inflated_lateral.tif ). What do you think? I could of course also transform the dependent variable into percentages. That is, baseline == 100 and tp2 expressed in percent of baseline. However, I find this to be a less attractive solution because we basically lose the baseline values, and this makes the model less useful for all other purposes. For instance, we can't investigate group differences at the various time points within the model. Perhaps more importantly, it's unclear what assumptions we are making. The lme assumes a normal distribution and it's unclear to me what the distribution of such ratios are. Thank you! LMR yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway Bruce Fischl Sat, 06 Sep 2014 07:00:14 -0700 Hi Lars which surface are you using? If it's the white surface you might try looking at white matter volume to see if it is decreasing cheers Bruce On Sat, 6 Sep 2014, Lars M. Rimol wrote: Hi, I have performed a longitudinal analysis using the lme module in FreeSurfer, with this model: intercept(random effect) + centered age + group + group x centered age + sex I tested the effect of time with this contrast vector [ 0 1 0 0 0 ]. Dependent variable is area. Here, mapping the second beta means mapping the effect size for (change over) time. In the beta map, I find values from 0 to 0.004. I would interpret that to mean that local area shrinks by at most 0.004 mm² per year in the reference group. But I'm not 100% sure about the biological (or geometrical) meaning of that. Can I interpret this literally as the mean yearly shrinkage of the three triangles surrounding a given vertex, the average of whose area comprises the area score of the vertex, being 4/1000 mm? Of course, these maps are smoothed with 30mm, so the real spatial resolution is nowhere near this Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail. yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway On Mon, Oct 27, 2014 at 9:59 AM, Lars M. Rimol lari...@gmail.com wrote: Hi Bruce (and Jorge), Yes, it's the wm surface. I have also done the analyses with the pial surface and the results are similar to wm surface (attached p-maps: lh_0-1000_wmarea_s30_log10p_inflated_lateral.tif vs. lh_0-1000_wmarea_s30_log10p_inflated_lateral.tif).
Re: [Freesurfer] adding insula voxels
Hi Adam sorry, I've lost the context for this. Why are you adding voxels to the aparc+aseg in the insula? cheers Bruce On Wed, 29 Oct 2014, Adam Mezher wrote: Hi Bruce and FS group, Thanks again for the speedy replies and help with everything. Quick question about editing voxels (specifically those in the lh/rh insula). Should I simply add specific voxels to the aparc+aseg for this step? It was a little unclear on the wiki. Also, is there a specific command to re-run the stats/etc. after these edits are performed? Thanks a lot, Adam ___ 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] Pial surface with point-to-point correspondance between subjects
Hi Alexandre can you tell us what you want to do with the point-to-point correspondence? We don't usually map surfaces into a common space since we want to have uniform resolution/sampling in the individual coords. cheers Bruce On Wed, 29 Oct 2014, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ 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] Pial surface with point-to-point correspondance between subjects
Hello Bruce, I would like to build an atlas of subcortical structures and pial surface on my population of study. But given the anatomical complexity of the pial surface (and the number of points), I would like to use point-to-point correspondence so as to have a L^2 metric (I use another metric for subcortical structures). I don't know if I am clear enough but since I estimate the template and the variability between the template and the subjects, I would like to detect information such as atrophy thanks to the deformation parameters. Is there any solution? Alexandre 2014-10-29 13:49 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Alexandre can you tell us what you want to do with the point-to-point correspondence? We don't usually map surfaces into a common space since we want to have uniform resolution/sampling in the individual coords. cheers Bruce On Wed, 29 Oct 2014, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ 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] Pial surface with point-to-point correspondance between subjects
I'm not sure what you mean by working with the pial surfaces with respect to point-to-point correspondence. Can you give more info? doug On 10/29/2014 06:29 AM, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ 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.
Re: [Freesurfer] Pial surface with point-to-point correspondance between subjects
What I wanted to say is that there is the exact number of points of the pial surface for each subject and if I look to the i-th vertex of the pial surface of a given subject, it should be located on the same area for another subject. Alexandre 2014-10-29 15:25 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: I'm not sure what you mean by working with the pial surfaces with respect to point-to-point correspondence. Can you give more info? doug On 10/29/2014 06:29 AM, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] 7T reconstruction
Create a voxel shift map using epidewarp.fsl (only the shift map is needed, don't use this to dewarp the data). Save this in bold/b0dcmap.nii (or nii.gz). When you run preproc-sess and mkanalysis-sess add -b0dc (stands for B0 distortion correction). doug On 10/28/2014 01:14 PM, B V wrote: Hello, I am interested in using functional data collected from 7t using freesurfer and fsfast. We would like to use EPI field maps to warp this data to 3T anatomical space. Can anyone guide me as to how to do this. Best, B ___ 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.
Re: [Freesurfer] Pial surface with point-to-point correspondance between subjects
This is not something we support. On 10/29/2014 10:32 AM, Alexandre Routier wrote: What I wanted to say is that there is the exact number of points of the pial surface for each subject and if I look to the i-th vertex of the pial surface of a given subject, it should be located on the same area for another subject. Alexandre 2014-10-29 15:25 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: I'm not sure what you mean by working with the pial surfaces with respect to point-to-point correspondence. Can you give more info? doug On 10/29/2014 06:29 AM, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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
Re: [Freesurfer] how to interpret a change in area of 0.004 mm² per year?
Hi Lars, two thoughts that came up reading this thread: - each vertex has usually more than 3 triangles (your first mail), the number differs depending on where you are. With a uniform mesh you'd have nearly 60 degree angles so you'd have approx 6 triangles at a vertex. - wm volume can increase when area shrinks. If especially the slucii move further outside the whole surface gets more spherical, decreasing area, but increasing volume. Best, Martin On 10/29/2014 08:44 AM, Bruce Fischl wrote: Hi Lars yes, it seems plausible, particularly since it is so universal. cheers Bruce On Wed, 29 Oct 2014, Lars M. Rimol wrote: Hi Bruce (and Jorge), Yes, it's the wm surface. I have also done the analyses with the pial surface and the results are similar to wm surface. To your second question: White matter volume increased over this time period (lme analysis; controls: logP = 8.49, patients: logP = 6.34). Since the cortical analyses were done using lme, which can handle missing data, some of the subjects have only one time point. So I created a difference map for those subjects for whom we have data on both time points, to see if area on the first time point is consistently larger than on the second time point. Almost all subjects showed larger values on tp1 than tp2 and the maps of average area change (across subjects) confirm that. In addition, I ran an lme analysis with the same subjects and found results very similar to those for the entire sample. Would you agree that this apparent reduction in cortical area seems plausible? There is a reduction over time in raw data, and pial surface area show the same trend as wm surface, and the lme analysis with only subjects that have data on both time points shows very similar results as the lme with all subjects. On the other hand, I suppose we wouldn't expect increased wm volume together with reduced area? As for the effect size maps, I have worked on finding a way to represent change in area over time that is intuitive for a reader not familiar with FreeSurfer: I figured one solution could be to log transform the dependent variable (wm or pial area). This way the significance tests are done with log transformed data and for purposes of illustration I do exp(beta)*100-100 on the beta for time, which ensures that if there is e.g. a 1% reduction, the figure shows -1, and 1 for a 1% increase. I find this is a good way of demonstrating the effects (attached figure: lh_wmarea_logtransf_expBeta2_s30_inflated_lateral.tif ). What do you think? I could of course also transform the dependent variable into percentages. That is, baseline == 100 and tp2 expressed in percent of baseline. However, I find this to be a less attractive solution because we basically lose the baseline values, and this makes the model less useful for all other purposes. For instance, we can't investigate group differences at the various time points within the model. Perhaps more importantly, it's unclear what assumptions we are making. The lme assumes a normal distribution and it's unclear to me what the distribution of such ratios are. Thank you! LMR yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway Bruce Fischl Sat, 06 Sep 2014 07:00:14 -0700 Hi Lars which surface are you using? If it's the white surface you might try looking at white matter volume to see if it is decreasing cheers Bruce On Sat, 6 Sep 2014, Lars M. Rimol wrote: Hi, I have performed a longitudinal analysis using the lme module in FreeSurfer, with this model: intercept(random effect) + centered age + group + group x centered age + sex I tested the effect of time with this contrast vector [ 0 1 0 0 0 ]. Dependent variable is area. Here, mapping the second beta means mapping the effect size for (change over) time. In the beta map, I find values from 0 to 0.004. I would interpret that to mean that local area shrinks by at most 0.004 mm² per year in the reference group. But I'm not 100% sure about the biological (or geometrical) meaning of that. Can I interpret this literally as the mean yearly shrinkage of the three triangles surrounding a given vertex, the average of whose area comprises the area score of the vertex, being 4/1000 mm? Of course, these maps are smoothed with 30mm, so the real spatial resolution is nowhere near this Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror
Re: [Freesurfer] Pial surface with point-to-point correspondance between subjects
Oh, okay. I thought this kind of data could be obtained since it exists for longitudinal analysis. Thanks for your answer anyway! 2014-10-29 15:35 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: This is not something we support. On 10/29/2014 10:32 AM, Alexandre Routier wrote: What I wanted to say is that there is the exact number of points of the pial surface for each subject and if I look to the i-th vertex of the pial surface of a given subject, it should be located on the same area for another subject. Alexandre 2014-10-29 15:25 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: I'm not sure what you mean by working with the pial surfaces with respect to point-to-point correspondence. Can you give more info? doug On 10/29/2014 06:29 AM, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Pial surface with point-to-point correspondance between subjects
you can just compute the jacobian of the ?h.sphere.reg for deformation. I'm not sure I understand how you would use an L2 metric. There are tools in AFNI/SUMA for converting a freesurfer surface to a standard mesh that you could use cheers Bruce On Wed, 29 Oct 2014, Alexandre Routier wrote: Hello Bruce, I would like to build an atlas of subcortical structures and pial surface on my population of study. But given the anatomical complexity of the pial surface (and the number of points), I would like to use point-to-point correspondence so as to have a L^2 metric (I use another metric for subcortical structures). I don't know if I am clear enough but since I estimate the template and the variability between the template and the subjects, I would like to detect information such as atrophy thanks to the deformation parameters. Is there any solution? Alexandre 2014-10-29 13:49 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Alexandre can you tell us what you want to do with the point-to-point correspondence? We don't usually map surfaces into a common space since we want to have uniform resolution/sampling in the individual coords. cheers Bruce On Wed, 29 Oct 2014, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ 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] Pial surface with point-to-point correspondance between subjects
no, but I think SUMA does. Check it out. I'll cc Ziad so he can chime in. cheers Bruce On Wed, 29 Oct 2014, Douglas N Greve wrote: This is not something we support. On 10/29/2014 10:32 AM, Alexandre Routier wrote: What I wanted to say is that there is the exact number of points of the pial surface for each subject and if I look to the i-th vertex of the pial surface of a given subject, it should be located on the same area for another subject. Alexandre 2014-10-29 15:25 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: I'm not sure what you mean by working with the pial surfaces with respect to point-to-point correspondence. Can you give more info? doug On 10/29/2014 06:29 AM, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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] LGI fails for fsaverage
Our usual method for electrode localization remains in the patient's space: co-register post-op MR and CT with pre-op MR brainmask (our reference space) and snap electrodes to patient's outer pial surface. My idea was: register the patient's (crappy) brainmask volume to the Talairach fsaverage volume (not surface), which I can correct manually; use the Talairach.xfm transform to bring the electrodes into that same fsaverage volume, and then snap the electrodes to fsaverage's outer pial surface. But that last step I can't perform. I'm aware that the localization would be pretty inaccurate. I'll look into what you suggest Marie. In case all else fails, the last resort is to show the actual post-op MR and CT slices for electrodes of interest, but that just does not look as appealing as pial surfaces! -- Pierre Mégevand, MD, PhD PLOS Neuro Community http://neuro.plos.org editor - Follow us on Twitter http://twitter.com/PLOSNeuro Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter http://twitter.com/pierre_vanmedge - Read my blog here http://neuroscimed.wordpress.com On Wed, Oct 29, 2014 at 12:29 AM, Marie Schaer marie.sch...@unige.ch wrote: So what I don't get in your pipeline is how you'll register the post-op brain to fsaverage if you don't have any cortical surface in the post-op? If I were you, if you want precise registration that includes the sulci, I'd go with the white surface from the pre-op gadolinium scan. And if you just want a rough registration of the skull shape, then you can probably find a way to create the outer surface directly on the gadolinium scan: if your brain mask is good, then mris_fill should work (maybe you need to binarize the data first (in any case a few lines of code in matlab should do the trick). If the brain mask is not good due to gadolinium, then either playing with mri_watershed (and maybe try mri_fill to separate the hemispheres / pons and cerebellum) and then mris_fill for the tessellation. Or if it doesn't work with mri_watershed, playing a bit with threshold with another skull-stripping program (e.g. MRIcro), then importing the volume back in FreeSurfer and use mris_fill to get a good tessellation. Both solutions will need you to play a bit, but I guess you cannot really afford to simply throw these data and take another subject! Good luck, Marie On Oct 28, 2014, at 2:57 PM, Pierre Mégevand pierre.megev...@gmail.com wrote: You're right, we can't use the post-op surface because of the deformation caused by surgery and the electrode artifacts. Getting a surface right from the brainmask would be OK, if we can't get anything better, but the nice thing about using the fsaverage surface is that you can plot and compare electrode locations from multiple patients. Just in case we have nothing better, though, how would you do it? Thanks again! -- Pierre Mégevand, MD, PhD PLOS Neuro Community http://neuro.plos.org/ editor - Follow us on Twitter http://twitter.com/PLOSNeuro Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter http://twitter.com/pierre_vanmedge - Read my blog here http://neuroscimed.wordpress.com/ On Tue, Oct 28, 2014 at 5:23 PM, Marie Schaer marie.sch...@unige.ch wrote: Hi Pierre, Tricky question. So you can't really use the post-op cortical surface for this participant, right? Otherwise I would simply use the outer smoothed pial for this subject directly, which would be much more similar to the pre-op than the outer surface from the fsaverage (?). Otherwise, with the gadolinium MRI, maybe you can still get an adequate white surface, but I'm not sure that it would help you. The other option is to use the brain mask volume (which may work even with gadolinium if you are lucky, otherwise you can play with the watershed parameters), and tesselate a surface directly on this volume. But you'll get the two hemispheres at once (and probably the cerebellum as well), which may not be what you want? Best, Marie On Oct 28, 2014, at 2:10 PM, Pierre Mégevand pierre.megev...@gmail.com wrote: Thanks Marie. Here is what I'm trying to do. In fact, all I need from LGI are the first few steps, until ?h.pial-outer-smoothed has been generated. I'm not actually interested in the local GI for fsaverage. Our intra-cranial electrode localization method relies on post-implant CT and MRI scans to localize the electrodes, and a pre-implant MR scan to which we co-register the post-op exams and to whose smoothed outer pial surface we then snap the electrodes to, in order to account for the brain shift caused by the implantation procedure (Dykstra et al., 2012). Now, for one of our patients, the pre-op MRI was acquired with a lot of gadolinium, and we can't get Freesurfer to compute the pial surface. So I thought I would co-register the post-op exams to the fsaverage brain, and then snap the electrodes to fsaverage's outer
Re: [Freesurfer] LGI fails for fsaverage
have you tried using bbregister to register post-op MRI with the pre-op surfaces? On Wed, 29 Oct 2014, Pierre Mégevand wrote: Our usual method for electrode localization remains in the patient's space: co-register post-op MR and CT with pre-op MR brainmask (our reference space) and snap electrodes to patient's outer pial surface. My idea was: register the patient's (crappy) brainmask volume to the Talairach fsaverage volume (not surface), which I can correct manually; use the Talairach.xfm transform to bring the electrodes into that same fsaverage volume, and then snap the electrodes to fsaverage's outer pial surface. But that last step I can't perform. I'm aware that the localization would be pretty inaccurate. I'll look into what you suggest Marie. In case all else fails, the last resort is to show the actual post-op MR and CT slices for electrodes of interest, but that just does not look as appealing as pial surfaces! -- Pierre Mégevand, MD, PhD PLOS Neuro Community editor - Follow us on Twitter Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter - Read my blog here On Wed, Oct 29, 2014 at 12:29 AM, Marie Schaer marie.sch...@unige.ch wrote: So what I don't get in your pipeline is how you'll register the post-op brain to fsaverage if you don't have any cortical surface in the post-op? If I were you, if you want precise registration that includes the sulci, I'd go with the white surface from the pre-op gadolinium scan. And if you just want a rough registration of the skull shape, then you can probably find a way to create the outer surface directly on the gadolinium scan: if your brain mask is good, then mris_fill should work (maybe you need to binarize the data first (in any case a few lines of code in matlab should do the trick). If the brain mask is not good due to gadolinium, then either playing with mri_watershed (and maybe try mri_fill to separate the hemispheres / pons and cerebellum) and then mris_fill for the tessellation. Or if it doesn't work with mri_watershed, playing a bit with threshold with another skull-stripping program (e.g. MRIcro), then importing the volume back in FreeSurfer and use mris_fill to get a good tessellation. Both solutions will need you to play a bit, but I guess you cannot really afford to simply throw these data and take another subject! Good luck, Marie On Oct 28, 2014, at 2:57 PM, Pierre Mégevand pierre.megev...@gmail.com wrote: You're right, we can't use the post-op surface because of the deformation caused by surgery and the electrode artifacts. Getting a surface right from the brainmask would be OK, if we can't get anything better, but the nice thing about using the fsaverage surface is that you can plot and compare electrode locations from multiple patients. Just in case we have nothing better, though, how would you do it? Thanks again! -- Pierre Mégevand, MD, PhD PLOS Neuro Community editor - Follow us on Twitter Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter - Read my blog here On Tue, Oct 28, 2014 at 5:23 PM, Marie Schaer marie.sch...@unige.ch wrote: Hi Pierre, Tricky question. So you can't really use the post-op cortical surface for this participant, right? Otherwise I would simply use the outer smoothed pial for this subject directly, which would be much more similar to the pre-op than the outer surface from the fsaverage (?). Otherwise, with the gadolinium MRI, maybe you can still get an adequate white surface, but I'm not sure that it would help you. The other option is to use the brain mask volume (which may work even with gadolinium if you are lucky, otherwise you can play with the watershed parameters), and tesselate a surface directly on this volume. But you'll get the two hemispheres at once (and probably the cerebellum as well), which may not be what you want? Best, Marie On Oct 28, 2014, at 2:10 PM, Pierre Mégevand pierre.megev...@gmail.com wrote: Thanks Marie. Here is what I'm trying to do. In fact, all I need from LGI are the first few steps, until ?h.pial-outer-smoothed has been generated. I'm not actually interested in the local GI for fsaverage. Our intra-cranial electrode localization method relies on post-implant CT and MRI scans to localize the electrodes, and a pre-implant MR scan to which we co-register the post-op exams and to whose smoothed outer pial surface we then snap the electrodes to, in order to account for the brain shift caused by the implantation procedure (Dykstra et al., 2012). Now, for one of our patients, the pre-op MRI was acquired with a lot of gadolinium, and we can't get Freesurfer to compute the pial surface. So I thought I would co-register the post-op exams to the fsaverage brain, and then snap the electrodes to fsaverage's outer smoothed pial surface as an approximation. Any idea
Re: [Freesurfer] LGI analysis of single subject
Hi Marie - Thanks for your response. After sending my email I found the hemisphere average values, but the values at each vertex and in each ROI will be very helpful! I tried the command you provided in tkmedit and it looks perfect - thanks! But when I try what I think is the corresponding command in freeview: freeview -v SUBJ/mri/brainmask.mgz SUBJ/mri/T1.mgz -f SUBJ/surf/lh.pial-outer-smoothed the images don't align (see attached). Am I doing something wrong? ~ Maria ___ 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] Pial surface with point-to-point correspondance between subjects
Okay, thanks for the answer, I'll have a look on this software. Alexandre 2014-10-29 16:05 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: no, but I think SUMA does. Check it out. I'll cc Ziad so he can chime in. cheers Bruce On Wed, 29 Oct 2014, Douglas N Greve wrote: This is not something we support. On 10/29/2014 10:32 AM, Alexandre Routier wrote: What I wanted to say is that there is the exact number of points of the pial surface for each subject and if I look to the i-th vertex of the pial surface of a given subject, it should be located on the same area for another subject. Alexandre 2014-10-29 15:25 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: I'm not sure what you mean by working with the pial surfaces with respect to point-to-point correspondence. Can you give more info? doug On 10/29/2014 06:29 AM, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 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] LGI fails for fsaverage
Unfortunately, our pre-implant MR was acquired with double-dose gadolinium and we can't seem to extract the pial surface from it. have you tried using bbregister to register post-op MRI with the pre-op surfaces? On Wed, 29 Oct 2014, Pierre M?gevand wrote: Our usual method for electrode localization remains in the patient's space: co-register post-op MR and CT with pre-op MR brainmask (our reference space) and snap electrodes to patient's outer pial surface. My idea was: register the patient's (crappy) brainmask volume to the Talairach fsaverage volume (not surface), which I can correct manually; use the Talairach.xfm transform to bring the electrodes into that same fsaverage volume, and then snap the electrodes to fsaverage's outer pial surface. But that last step I can't perform. I'm aware that the localization would be pretty inaccurate. I'll look into what you suggest Marie. In case all else fails, the last resort is to show the actual post-op MR and CT slices for electrodes of interest, but that just does not look as appealing as pial surfaces! -- Pierre M?gevand, MD, PhD PLOS Neuro Community editor - Follow us on Twitter Postdoc @?Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter - Read my blog here On Wed, Oct 29, 2014 at 12:29 AM, Marie Schaer marie.sch...@unige.ch wrote: So what I don't get in your pipeline is how you'll register the post-op brain to fsaverage if you don't have any cortical surface in the post-op?? If I were you, if you want precise registration that includes the sulci, I'd go with the white surface from the pre-op gadolinium scan. And if you just want a rough registration of the skull shape, then you can probably find a way to create the outer surface directly on the gadolinium scan: if your brain mask is good, then mris_fill should work (maybe you need to binarize the data first (in any case a few lines of code in matlab should do the trick). If the brain mask is not good due to gadolinium, then either playing with mri_watershed (and maybe try mri_fill to separate the hemispheres / pons and cerebellum) and then mris_fill for the tessellation. Or if it doesn't work with mri_watershed,?playing a bit with threshold with another skull-stripping program (e.g. MRIcro), then importing the volume back in FreeSurfer and use mris_fill to get a good tessellation. Both solutions will need you to play a bit, but I guess you cannot really afford to simply throw these data and take another subject!? Good luck, Marie On Oct 28, 2014, at 2:57 PM, Pierre M?gevand pierre.megev...@gmail.com wrote: You're right, we can't use the post-op surface because of the deformation caused by surgery and the electrode artifacts. Getting a surface right from the brainmask would be OK, if we can't get anything better, but the nice thing about using the fsaverage surface is that you can plot and compare electrode locations from multiple patients. Just in case we have nothing better, though, how would you do it? Thanks again! -- Pierre M?gevand, MD, PhD PLOS Neuro Community editor - Follow us on Twitter Postdoc @?Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter - Read my blog here On Tue, Oct 28, 2014 at 5:23 PM, Marie Schaer marie.sch...@unige.ch wrote: Hi Pierre, Tricky question. So you can't really use the?post-op cortical surface for this participant, right? Otherwise I would simply use the outer smoothed pial for this subject directly, which would be much more similar to the pre-op than the outer surface from the fsaverage (?).?Otherwise, with the gadolinium MRI, maybe you can still get an adequate white surface, but I'm not sure that it would help you. The other option is to use the brain mask volume (which may work even with gadolinium if you are lucky, otherwise you can play with the watershed parameters), and tesselate a surface directly on this volume. But you'll get the two hemispheres at once (and probably the cerebellum as well), which may not be what you want? Best, Marie On Oct 28, 2014, at 2:10 PM, Pierre M?gevand pierre.megev...@gmail.com ?wrote: Thanks Marie. Here is what I'm trying to do. In fact, all I need from LGI are the first few steps, until ?h.pial-outer-smoothed has been generated. I'm not actually interested in the local GI for fsaverage. Our intra-cranial electrode localization method relies on post-implant CT and MRI scans to localize the electrodes, and a pre-implant MR scan to which we co-register the post-op exams and to whose smoothed outer pial surface we then snap the electrodes to, in order to account for the brain shift caused by the implantation procedure (Dykstra et al., 2012). Now, for one of our patients, the pre-op MRI was acquired with a lot of gadolinium, and we can't get Freesurfer to compute the
Re: [Freesurfer] LGI analysis of single subject
Hi Maria, I have to say that I rarely use freeview, I prefer tkmedit and tksurfer that I know better. So I didn't realize that the images were shifted, I guess it's some preference in how to read the surface. I just tried and have the same kind of shift when using freeview, so I don't think you are doing something wrong. Unless someone else know how to correct for the shift, I would advise you to use tkmedit... Best, Marie On Oct 29, 2014, at 10:27 AM, Maria Holland mho...@stanford.edumailto:mho...@stanford.edu wrote: Hi Marie - Thanks for your response. After sending my email I found the hemisphere average values, but the values at each vertex and in each ROI will be very helpful! I tried the command you provided in tkmedit and it looks perfect - thanks! But when I try what I think is the corresponding command in freeview: freeview -v SUBJ/mri/brainmask.mgz SUBJ/mri/T1.mgz -f SUBJ/surf/lh.pial-outer-smoothed the images don't align (see attached). Am I doing something wrong? ~ Maria Screen Shot 2014-10-29 at 10.23.56 AM.png___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] NIH funded postdoctoral position at Harvard Medical School/Brigham and Women's Hospital
Professor Jill Goldstein is recruiting a postdoctoral fellow with expertise in affective or cognitive neuroscience to join her lab, the CNL-SD ( http://cnl-sd.bwh.harvard.edu) *Job Description* This position requires the individual to have expertise in functional MRI. Experience with psychiatric disorders is preferable. Knowledge of paradigm development, data analytic software (e.g., SPM, FSL), and statistical underpinnings of fMRI are required. Responsibilities of this position include analyses of fMRI studies of the stress response, mood and anxiety, and hormonal responses; fetal programming of sex differences in mood and psychotic disorders; and implementation and analyses involved in a new neurostimulation study of mood and autonomic nervous system function. Thus, the position includes implementing methods for the analysis of fMRI data; developing project-specific methods when necessary (i.e., ROI analysis); utilization of advanced statistical methods to analyze fMRI, psychophysiological and serology data; preparation of manuscripts for publication; preparation of study findings and presentation at professional meetings; review and summarization of relevant literature for manuscript background and grant preparation; supervision of research assistant working on the study. There are many opportunities for education and growth in multiple domains in which we operate: neuroendocrinology, further neuroimaging training, neuroanatomy, neuro-immune interface. We collaborate with world-class scientists who are part of Brigham and Women’s Hospital, Massachusetts General Hospital, and others outside of the Harvard system. Applicant should have a PhD or ScD in clinical psychology, neuropsychology, and/or neuroscience or have an MD with fMRI expertise. We are committed to diversity, and qualified women and minorities are strongly encouraged to apply. Please email a CV, cover letter of interest, 2-3 written references, and a *brief *writing sample to Ms. Abby Brockman*, (abrock...@partners.org abrock...@partners.org), *Administrative Assistant to Jill Goldstein, PhD, Professor of Psychiatry and Medicine, Harvard Medical School, Director of Research, Connors Center for Women’s Health and Gender Biology, Brigham and Women’s Hospital, Boston, MA 02120. ___ 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] FLASH protocol
Hi, I want to do source localization on 128-channel EEG. For that, I need to create 3-layer head models for our subjects. However, our current MRI protocol only includes MPRAGE. I've talked with the (f)MRI team on our project about adding a single FLASH scan in their protocol. They are mainly concerned about the time requirement. So my questions are: 1) Is it possible to get a decent 3-layer head model just from MPRAGE using FreeSurfer or other tools like SPM? 2) If we have to use FLASH, which protocol we should use? I found one at https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFiledo=gettarget=FreeSurfer_Suggested_Morphometry_Protocols.pdf I don't know if this is the most recent one -- is there a newer FLASH protocol that can produce decent skull boundaries and takes less time to run. 3) Is there a FLASH protocol already imported on Bay 1 (Skyra scanner) at Martinos (where the MPRAGE was run)? If not, is it ok to run FLASH and MPRAGE on different scanners for the same subject? I know this is a lot of questions. I really appreciate any responses. Thanks! Le ___ 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] LGI fails for fsaverage
That is not what Bruce is suggesting. Try to register the post-op to the pre-op using bbregister. You can then map the pre-op surfaces to the post-op brain On 10/29/2014 01:58 PM, Pierre Mégevand wrote: Unfortunately, our pre-implant MR was acquired with double-dose gadolinium and we can't seem to extract the pial surface from it. have you tried using bbregister to register post-op MRI with the pre-op surfaces? On Wed, 29 Oct 2014, Pierre M?gevand wrote: Our usual method for electrode localization remains in the patient's space: co-register post-op MR and CT with pre-op MR brainmask (our reference space) and snap electrodes to patient's outer pial surface. My idea was: register the patient's (crappy) brainmask volume to the Talairach fsaverage volume (not surface), which I can correct manually; use the Talairach.xfm transform to bring the electrodes into that same fsaverage volume, and then snap the electrodes to fsaverage's outer pial surface. But that last step I can't perform. I'm aware that the localization would be pretty inaccurate. I'll look into what you suggest Marie. In case all else fails, the last resort is to show the actual post-op MR and CT slices for electrodes of interest, but that just does not look as appealing as pial surfaces! -- Pierre M?gevand, MD, PhD PLOS Neuro Community editor - Follow us on Twitter Postdoc @?Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter - Read my blog here On Wed, Oct 29, 2014 at 12:29 AM, Marie Schaer marie.sch...@unige.ch mailto:marie.sch...@unige.ch wrote: So what I don't get in your pipeline is how you'll register the post-op brain to fsaverage if you don't have any cortical surface in the post-op?? If I were you, if you want precise registration that includes the sulci, I'd go with the white surface from the pre-op gadolinium scan. And if you just want a rough registration of the skull shape, then you can probably find a way to create the outer surface directly on the gadolinium scan: if your brain mask is good, then mris_fill should work (maybe you need to binarize the data first (in any case a few lines of code in matlab should do the trick). If the brain mask is not good due to gadolinium, then either playing with mri_watershed (and maybe try mri_fill to separate the hemispheres / pons and cerebellum) and then mris_fill for the tessellation. Or if it doesn't work with mri_watershed,?playing a bit with threshold with another skull-stripping program (e.g. MRIcro), then importing the volume back in FreeSurfer and use mris_fill to get a good tessellation. Both solutions will need you to play a bit, but I guess you cannot really afford to simply throw these data and take another subject!? Good luck, Marie On Oct 28, 2014, at 2:57 PM, Pierre M?gevand pierre.megev...@gmail.com mailto:pierre.megev...@gmail.com wrote: You're right, we can't use the post-op surface because of the deformation caused by surgery and the electrode artifacts. Getting a surface right from the brainmask would be OK, if we can't get anything better, but the nice thing about using the fsaverage surface is that you can plot and compare electrode locations from multiple patients. Just in case we have nothing better, though, how would you do it? Thanks again! -- Pierre M?gevand, MD, PhD PLOS Neuro Community editor - Follow us on Twitter Postdoc @?Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter - Read my blog here On Tue, Oct 28, 2014 at 5:23 PM, Marie Schaer marie.sch...@unige.ch mailto:marie.sch...@unige.ch wrote: Hi Pierre, Tricky question. So you can't really use the?post-op cortical surface for this participant, right? Otherwise I would simply use the outer smoothed pial for this subject directly, which would be much more similar to the pre-op than the outer surface from the fsaverage (?).?Otherwise, with the gadolinium MRI, maybe you can still get an adequate white surface, but I'm not sure that it would help you. The other option is to use the brain mask volume (which may work even with gadolinium if you are lucky, otherwise you can play with the watershed parameters), and tesselate a surface directly on this volume. But you'll get the two hemispheres at once (and probably the cerebellum as well), which may not be what you want? Best, Marie On Oct 28, 2014, at 2:10 PM, Pierre M?gevand pierre.megev...@gmail.com mailto:pierre.megev...@gmail.com ?wrote: Thanks Marie. Here is what I'm trying to do. In fact, all I need from LGI are the first few steps, until ?h.pial-outer-smoothed has been generated. I'm not actually interested in the local GI for fsaverage. Our intra-cranial electrode localization method relies on post-implant CT and MRI scans to localize the
Re: [Freesurfer] permission denied
I beleive it should have a lower case X, as in: chmod -R a+x freesurfer/bin -Zeke On 10/28/2014 01:19 AM, Ali Radaideh wrote: Dear Douglas Thanks for your reply. unfortunatey I still get the same error. Here is the terminal output. Is there anything else I can do? freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl imaging@imaging-ThinkCentre-23:~$ tcsh imaging-ThinkCentre-23:~ tkmedit /usr/local/freesurfer/bin/tkmedit: Permission denied. imaging-ThinkCentre-23:~ On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Try chmod -R a+X freesurfer/bin On 10/26/14 1:57 PM, Ali Radaideh wrote: Dear FreeSurfer users, I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest version freesurfer 5.3.0 does not allow me to run any command and everytime I try a command such such as tkmedit i get the following error /usr/local/freesurfer/bin/tkmedit: permission denied. I have tried to change the permission settings sudo chown -R imaging:imaging freesurfer but did not work. Any ideas why is this happening although I have done the same thing to other PCs and they are working fine. Thanks in advance, Ali -- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 390 ext.5422, 5355, 5364 Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 390 ext.5422, 5355, 5364 Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ ___ 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] Venous system on 3D models
Hello my names Rich. I am working on a project that involves creating 3D models of patient brains and placing ECoG (Electrocorticography) leads on these models. I have intra-operative pictures of the leads placed on the subjects and I'm using these pictures to attempt to accurately place the leads. However, as you might guess, the 3D models are very different from looking at a live brain and the true sulcal and gyral pattern is difficult to determine from the pictures. I was wondering if it is possible to have freesurfer create or mark, in some way, the veins on the models so that I can use the venous system as points of reference when placing the leads. If not, is there a better way to do so that you can think of? I am relatively new to freesurfer so I don't fully understand its capability yet. 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.
[Freesurfer] Local gyrification index
Hello, I am trying to obtain estimates for the local gyrification index (LGI) using Freesurfer. I have tried to compute LGI via two different commands... mris_compute_lgi --i lh.pial and recon-all -lgi -s subjectName. Both of these return the same error after running for a while... .. Saving label file //FS/subjects/test/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.029901.label Connecting and filling vertices in path at fillseed 69178 Finding path. done Filling 69178 nlabel 9709 Saving label file //FS/subjects/test/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.030001.label Connecting and filling vertices in path at fillseed 68070 Finding path.Killed ERROR: mri_path2label --confillxfn lh.pial //FS/subjects/test/surf/tmp-mris_compute_lgi-lh.pial/mri_path2label.input failed! I've tried a couple of subjects and I get the error above. Would anyone please be able to offer suggestions regarding how to resolve this issue? Many thanks for taking the time to read my inquiry. Nick ___ 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] 7T reconstruction
Thanks! Best, B On Wed, Oct 29, 2014 at 10:34 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Create a voxel shift map using epidewarp.fsl (only the shift map is needed, don't use this to dewarp the data). Save this in bold/b0dcmap.nii (or nii.gz). When you run preproc-sess and mkanalysis-sess add -b0dc (stands for B0 distortion correction). doug On 10/28/2014 01:14 PM, B V wrote: Hello, I am interested in using functional data collected from 7t using freesurfer and fsfast. We would like to use EPI field maps to warp this data to 3T anatomical space. Can anyone guide me as to how to do this. Best, B ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Unknown problem with fsgd file
Dear Freesurfer Mailing list, I have been attempting to run mri_glmfit using a complicated fsgd file (1 categorical varible with 5 levels, 3 categorical variables with 2 levels, age as covariate). When I run the command, I receive the following error: gdfReadHeader: reading site-gender-group-riskhaplotype.fsgd Input line 5, subjid = 100121, class siteMelbourne-anyRiskAnyRisk-genderFemale-groupControl not defined FSGDF Format Error: file = site-gender-group-riskhaplotype.fsgd, tag=Input I have double checked the fsgd file and confirmed that the class for participant 100121 was specific correctly at the beginning of the file (correct spelling and case was used). So I cannot identify the source of the error. Can you advise me as to what may be going wrong? My full fsgd file begins like this (I have 389 subjects but have provided only the first 20 for brevity): GroupDescriptorFile 1 Title GLM_SiteGender Class siteBrisbane-anyProtNoProt-genderMale-groupCase Class siteBrisbane-anyProtNoProt-genderFemale-groupCase Class siteBrisbane-anyProtNoProt-genderMale-groupControl Class siteBrisbane-anyProtNoProt-genderFemale-groupControl Class siteBrisbane-anyProtAnyProt-genderMale-groupCase Class siteBrisbane-anyProtAnyProt-genderFemale-groupCase Class siteBrisbane-anyProtAnyProt-genderMale-groupControl Class siteBrisbane-anyProtAnyProt-genderFemale-groupControl Class siteMelbourne-anyProtNoProt-genderMale-groupCase Class siteMelbourne-anyProtNoProt-genderFemale-groupCase Class siteMelbourne-anyProtNoProt-genderMale-groupControl Class siteMelbourne-anyProtNoProt-genderFemale-groupControl Class siteMelbourne-anyProtAnyProt-genderMale-groupCase Class siteMelbourne-anyProtAnyProt-genderFemale-groupCase Class siteMelbourne-anyProtAnyProt-genderMale-groupControl Class siteMelbourne-anyProtAnyProt-genderFemale-groupControl Class siteNewcastle-anyProtNoProt-genderMale-groupCase Class siteNewcastle-anyProtNoProt-genderFemale-groupCase Class siteNewcastle-anyProtNoProt-genderMale-groupControl Class siteNewcastle-anyProtNoProt-genderFemale-groupControl Class siteNewcastle-anyProtAnyProt-genderMale-groupCase Class siteNewcastle-anyProtAnyProt-genderFemale-groupCase Class siteNewcastle-anyProtAnyProt-genderMale-groupControl Class siteNewcastle-anyProtAnyProt-genderFemale-groupControl Class sitePerth-anyProtNoProt-genderMale-groupCase Class sitePerth-anyProtNoProt-genderFemale-groupCase Class sitePerth-anyProtNoProt-genderMale-groupControl Class sitePerth-anyProtNoProt-genderFemale-groupControl Class sitePerth-anyProtAnyProt-genderMale-groupCase Class sitePerth-anyProtAnyProt-genderFemale-groupCase Class sitePerth-anyProtAnyProt-genderMale-groupControl Class sitePerth-anyProtAnyProt-genderFemale-groupControl Class siteSydney-anyProtNoProt-genderMale-groupCase Class siteSydney-anyProtNoProt-genderFemale-groupCase Class siteSydney-anyProtNoProt-genderMale-groupControl Class siteSydney-anyProtNoProt-genderFemale-groupControl Class siteSydney-anyProtAnyProt-genderMale-groupCase Class siteSydney-anyProtAnyProt-genderFemale-groupCase Class siteSydney-anyProtAnyProt-genderMale-groupControl Class siteSydney-anyProtAnyProt-genderFemale-groupControl Variables age Input 100105SA sitePerth-anyProtNoProt-genderMale-groupCase 23 Input 100112SA siteBrisbane-anyProtAnyProt-genderMale-groupCase 22 Input 100117SA siteBrisbane-anyProtNoProt-genderMale-groupCase 39 Input 100118 siteBrisbane-anyProtNoProt-genderFemale-groupCase 30 Input 100121 siteMelbourne-anyProtAnyProt-genderFemale-groupControl 21 Input 100122 siteMelbourne-anyProtAnyProt-genderMale-groupControl 53 Input 100151 siteMelbourne-anyProtNoProt-genderFemale-groupControl 58 Input 100185SA siteBrisbane-anyProtNoProt-genderFemale-groupControl 24 Input 100187 siteBrisbane-anyProtNoProt-genderMale-groupCase 24 Input 100189 siteBrisbane-anyProtNoProt-genderFemale-groupCase 21 Input 100190 siteSydney-anyProtNoProt-genderMale-groupControl 41 Input 100191 siteMelbourne-anyProtAnyProt-genderFemale-groupControl 19 Input 100193SA siteSydney-anyProtNoProt-genderMale-groupControl 26 Input 100196 siteBrisbane-anyProtNoProt-genderMale-groupControl 55 Input 100197SA siteBrisbane-anyProtNoProt-genderFemale-groupCase 30 Input 100200SA siteBrisbane-anyProtNoProt-genderMale-groupControl 39 Input 100204 siteSydney-anyProtAnyProt-genderFemale-groupControl 50 Input 100208 siteBrisbane-anyProtNoProt-genderMale-groupControl 25 Input 100209SA siteBrisbane-anyProtAnyProt-genderMale-groupCase 35 Input 100214 siteSydney-anyProtAnyProt-genderMale-groupCase 44 The mri_glmfit command I am using is as follows: mri_glmfit --y site-gender-group-prothaplotype.thick.lh.10.mgh --fsgd site-gender-group-prothaplotype.fsgd dods --C gender.mtx --C group.mtx --C haplotype.mtx --C groupXgender.mtx --C haplotypeXgender.mtx --C groupXhaplotype.mtx --C genderXgroupXhaplotype.mtx --surf fsaverage lh --cortex --glmdir site-gender-group-prothaplotype.thick.lh.glmdir -- Kind regards, Bronwyn Overs Research Assistant
Re: [Freesurfer] adding insula voxels
Hi Bruce, Sorry for not clarifying. A number of subjects in our set have underestimated insula (usually anatomical right insula but sometimes both). I just uploaded an example to the ftp. I don’t think control points or wm edits can help with some of these so I wanted to see how we could go about editing them manually by adding the correct label to the empty voxels with the Edit Segmentation tool in tkmedit. Thank you, Adam ___ 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] Venous system on 3D models
Hi Rich, Do you have a post-operative CT scan of your ECoG patient? If you have that and a high-res T1, you can get very accurate reconstruction of electrode positions on the brain surface by corregistering the two. -zack On Wed, Oct 29, 2014 at 3:32 PM, rwlod...@uic.edu rwlod...@uic.edu wrote: Hello my names Rich. I am working on a project that involves creating 3D models of patient brains and placing ECoG (Electrocorticography) leads on these models. I have intra-operative pictures of the leads placed on the subjects and I'm using these pictures to attempt to accurately place the leads. However, as you might guess, the 3D models are very different from looking at a live brain and the true sulcal and gyral pattern is difficult to determine from the pictures. I was wondering if it is possible to have freesurfer create or mark, in some way, the veins on the models so that I can use the venous system as points of reference when placing the leads. If not, is there a better way to do so that you can think of? I am relatively new to freesurfer so I don't fully understand its capability yet. 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. -- *Zachary Greenberg* *Assistant Imaging Specialist* *Department of Neurological Surgery* *University of California, San Francisco* ___ 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] Venous system on 3D models
I have some post-op CT's for some of my patients but not all, do you have a link or could you explain how to coregister so I can do it for the ones I have? Thank you! On Wed, October 29, 2014 9:18 pm, Zachary Greenberg wrote: Hi Rich, Do you have a post-operative CT scan of your ECoG patient? If you have that and a high-res T1, you can get very accurate reconstruction of electrode positions on the brain surface by corregistering the two. -zack On Wed, Oct 29, 2014 at 3:32 PM, rwlod...@uic.edu rwlod...@uic.edu wrote: Hello my names Rich. I am working on a project that involves creating 3D models of patient brains and placing ECoG (Electrocorticography) leads on these models. I have intra-operative pictures of the leads placed on the subjects and I'm using these pictures to attempt to accurately place the leads. However, as you might guess, the 3D models are very different from looking at a live brain and the true sulcal and gyral pattern is difficult to determine from the pictures. I was wondering if it is possible to have freesurfer create or mark, in some way, the veins on the models so that I can use the venous system as points of reference when placing the leads. If not, is there a better way to do so that you can think of? I am relatively new to freesurfer so I don't fully understand its capability yet. 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. -- *Zachary Greenberg* *Assistant Imaging Specialist* *Department of Neurological Surgery* *University of California, San Francisco* ___ 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
Re: [Freesurfer] Venous system on 3D models
Rich, You need SPM preferably (http://www.fil.ion.ucl.ac.uk/spm/) for matlab, and freesurfer. First run recon-all on the patients T1 (after acpc aligning in Spm). Then take the resultant orig.mgz file (convert to .nii using mri_convert orig.mgz orig.nii), and corregister the post-op CT to it using SPM's normalized mutual info. routine. To do this: 1.) open matlab, 2.)type spm at the prompt, 3.) chose fMRI from the gui pop up, 4.) pick corregister (est. and write) from the top left of the spm gui. Then chose the Orig.nii as the reference image, and the patients pos-op CT as the target. Open the corregisterd CT (rCT.nii), the Orig.nii, and pial surface in freeview. Click on each electrode in the CT, and copy the xyz coords from the bottom left into a text file or matlab matrix (it will list the surface RAS coords in bottem left of freeview, which is what you want to display on the freesurfer pial surface). Let me know when you get that far and I'll send you a link to some code that will help you visualize the pial surface with overlaid electrodes. -zack On Wed, Oct 29, 2014 at 7:28 PM, rwlod...@uic.edu rwlod...@uic.edu wrote: I have some post-op CT's for some of my patients but not all, do you have a link or could you explain how to coregister so I can do it for the ones I have? Thank you! On Wed, October 29, 2014 9:18 pm, Zachary Greenberg wrote: Hi Rich, Do you have a post-operative CT scan of your ECoG patient? If you have that and a high-res T1, you can get very accurate reconstruction of electrode positions on the brain surface by corregistering the two. -zack On Wed, Oct 29, 2014 at 3:32 PM, rwlod...@uic.edu rwlod...@uic.edu wrote: Hello my names Rich. I am working on a project that involves creating 3D models of patient brains and placing ECoG (Electrocorticography) leads on these models. I have intra-operative pictures of the leads placed on the subjects and I'm using these pictures to attempt to accurately place the leads. However, as you might guess, the 3D models are very different from looking at a live brain and the true sulcal and gyral pattern is difficult to determine from the pictures. I was wondering if it is possible to have freesurfer create or mark, in some way, the veins on the models so that I can use the venous system as points of reference when placing the leads. If not, is there a better way to do so that you can think of? I am relatively new to freesurfer so I don't fully understand its capability yet. 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. -- *Zachary Greenberg* *Assistant Imaging Specialist* *Department of Neurological Surgery* *University of California, San Francisco* ___ 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 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] Venous system on 3D models
Thank you so much! This will take me some time, but i'll get back to you when I get that far. On Wed, October 29, 2014 9:47 pm, Zachary Greenberg wrote: Rich, You need SPM preferably (http://www.fil.ion.ucl.ac.uk/spm/) for matlab, and freesurfer. First run recon-all on the patients T1 (after acpc aligning in Spm). Then take the resultant orig.mgz file (convert to .nii using mri_convert orig.mgz orig.nii), and corregister the post-op CT to it using SPM's normalized mutual info. routine. To do this: 1.) open matlab, 2.)type spm at the prompt, 3.) chose fMRI from the gui pop up, 4.) pick corregister (est. and write) from the top left of the spm gui. Then chose the Orig.nii as the reference image, and the patients pos-op CT as the target. Open the corregisterd CT (rCT.nii), the Orig.nii, and pial surface in freeview. Click on each electrode in the CT, and copy the xyz coords from the bottom left into a text file or matlab matrix (it will list the surface RAS coords in bottem left of freeview, which is what you want to display on the freesurfer pial surface). Let me know when you get that far and I'll send you a link to some code that will help you visualize the pial surface with overlaid electrodes. -zack On Wed, Oct 29, 2014 at 7:28 PM, rwlod...@uic.edu rwlod...@uic.edu wrote: I have some post-op CT's for some of my patients but not all, do you have a link or could you explain how to coregister so I can do it for the ones I have? Thank you! On Wed, October 29, 2014 9:18 pm, Zachary Greenberg wrote: Hi Rich, Do you have a post-operative CT scan of your ECoG patient? If you have that and a high-res T1, you can get very accurate reconstruction of electrode positions on the brain surface by corregistering the two. -zack On Wed, Oct 29, 2014 at 3:32 PM, rwlod...@uic.edu rwlod...@uic.edu wrote: Hello my names Rich. I am working on a project that involves creating 3D models of patient brains and placing ECoG (Electrocorticography) leads on these models. I have intra-operative pictures of the leads placed on the subjects and I'm using these pictures to attempt to accurately place the leads. However, as you might guess, the 3D models are very different from looking at a live brain and the true sulcal and gyral pattern is difficult to determine from the pictures. I was wondering if it is possible to have freesurfer create or mark, in some way, the veins on the models so that I can use the venous system as points of reference when placing the leads. If not, is there a better way to do so that you can think of? I am relatively new to freesurfer so I don't fully understand its capability yet. 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. -- *Zachary Greenberg* *Assistant Imaging Specialist* *Department of Neurological Surgery* *University of California, San Francisco* ___ 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 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
