Re: [Freesurfer] LME toolbox - univariate
Thank you Martin! For only one group, would the design matrix be the same but intercept=Group=all ones? Yij = ß1 + ß2*tij +ß3*Group + ß4*Group *tij + ß5*Genderi + ß6*Agei + ß7*ICVi+ b 1i + b2i*tij + eij Regards, Yolanda 2013/5/28 Martin Reuter mreu...@nmr.mgh.harvard.edu Hi Yolanda, since you have the intercept you don't need both group1 and group2 (as one is 1 - the other), so drop beta 5 and 6 terms. If you want to test if the slope is different between the groups differ just look at beta4 which is checking if slope1-slope2 different from zero. If it is negative slope2 is larger, if positive slope1 is larger. Note that if your slopes are negative, e.g. atrophy, then larger means closer to zero = less atrophy. Best, Martin On 05/28/2013 11:57 AM, Yolanda Vives wrote: Dear FreeSurfer experts, I am trying to use the LME toolbox to analyse the hippocampal change over time in a group and also among 2 groups (2 scans per subject). When I estimate the parameters with lme_fit_FS I become a warning saying that the matrix is singular and my results are NaN. I guess that my design matrix X is not correct, can you please help me? I have followed the example from the wiki. My model for the two groups study is the following: Yij = ß1 + ß2*tij +ß3*Group1 + ß4*Group1 *tij + ß5*Group2 + ß6*Group2 *tij+ ß 7*Genderi + ß8*Agei + ß9*ICVi + b1i + b2i*tij + eij 1) intercept (all ones) 2) time (tij) . Here I have 0s for the first scan of each subject and a number in years for the second scans. Is it correct? 3) one for Group1 and zero otherwise 4) colum 3) .* time 5) one for Group2 and zero otherwise 6) colum 5) .* time 7) Gender 8) Age of the subject at each scan moment. 9) ICV (converted to liters). Thank you in advance, Yolanda ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu 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] Post-Doctoral position in brain imaging and computational morphometry – University of Geneva
Applications are invited for a funded Post-Doctoral position in the newly established Brain and Language Lab at the Department of Clinical Neuroscience at the University of Geneva, in collaboration with the Swiss Institute of Technology (EPFL) in Lausanne, Switzerland. Projects will include the development of new data-driven computational morphometry methods for analysis of structural magnetic resonance imaging (MRI) data, and application of these to large datasets in the context of normal variability, disease, and expertise. The work will be supervised by Narly Golestani and Dimitri Van De Ville. Candidates should have a degree in Biomedical Engineering, Computational Neuroscience, or a related field with a strong mathematical and computational background. Ideally they should have experience in brain image analysis, pattern recognition, machine learning, statistics as well as excellent programming skills. We offer a competitive starting salary of 68, 964 CHF/year, or more depending on experience. The position is available immediately, and applications will be considered until the position is filled. Informal inquiries can be addressed to Narly Golestani (narly.golest...@unige.ch). Applications including a CV, a statement of research interests, and the names and full contact details of three referees should be sent to: narly.golest...@unige.ch. ___ 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] LME toolbox - univariate
For only one group you don't need a group variable. you'd drop beta 3 and 4 terms. Yolanda Vives yvi...@pic.es wrote: Thank you Martin! For only one group, would the design matrix be the same but intercept=Group=all ones? Yij = ß1 + ß2*tij +ß3*Group + ß4*Group *tij + ß5*Genderi + ß6*Agei + ß7*ICVi+ b 1i + b2i*tij + eij Regards, Yolanda 2013/5/28 Martin Reuter mreu...@nmr.mgh.harvard.edu Hi Yolanda, since you have the intercept you don't need both group1 and group2 (as one is 1 - the other), so drop beta 5 and 6 terms. If you want to test if the slope is different between the groups differ just look at beta4 which is checking if slope1-slope2 different from zero. If it is negative slope2 is larger, if positive slope1 is larger. Note that if your slopes are negative, e.g. atrophy, then larger means closer to zero = less atrophy. Best, Martin On 05/28/2013 11:57 AM, Yolanda Vives wrote: Dear FreeSurfer experts, I am trying to use the LME toolbox to analyse the hippocampal change over time in a group and also among 2 groups (2 scans per subject). When I estimate the parameters with lme_fit_FS I become a warning saying that the matrix is singular and my results are NaN. I guess that my design matrix X is not correct, can you please help me? I have followed the example from the wiki. My model for the two groups study is the following: Yij = ß1 + ß2*tij +ß3*Group1 + ß4*Group1 *tij + ß5*Group2 + ß6*Group2 *tij+ ß 7*Genderi + ß8*Agei + ß9*ICVi + b1i + b2i*tij + eij 1) intercept (all ones) 2) time (tij) . Here I have 0s for the first scan of each subject and a number in years for the second scans. Is it correct? 3) one for Group1 and zero otherwise 4) colum 3) .* time 5) one for Group2 and zero otherwise 6) colum 5) .* time 7) Gender 8) Age of the subject at each scan moment. 9) ICV (converted to liters). Thank you in advance, Yolanda ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu 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. -- Sent from my phone. Please excuse my brevity.___ 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] Representation of average curvature on subject's curvature
Hi Sophie I'm not sure there's an easy way as those weren't made entirely within freesurfer. I guess you could create a label of all positive curvature and use the outline mode to show multiple labels Bruce On Wed, 29 May 2013, Sophie Maingault wrote: Hi FreeSufer Experts, I would like to do a figure like this one published in High-Resolution Intersubject Averaging and a Coordinate System for the cortical Surface (1999, Fischl et al.). I would to superimpose the isocontour of average curvature (for example fsaverage) on a subject's curvature before and after registration. How can I do this with tksurfer ? [IMAGE] Thanks a lot for your help ! Sophie ___ 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] mri_anatomical_stats on custom 'thickness' file
I mean; if you devide the number of vertices by the area per aparc-parcellation, some parcellations have relatively more vertices per mm^2 as others. If you now would compute the average thickness in for example the lobe-parcellation, the thicknesses of some areas (the parcellations with relatively more vertices per mm^2) get a higher weight in the overal average. Is that true? On Tue, May 28, 2013 at 8:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: what do you mean? That the vertices are not uniform? mri_segstats just computes the mean over the parcellation without reference to non-uniformity. doug On 05/28/2013 02:15 PM, Martijn Steenwijk wrote: Sorry, indeed, my reply was too quick. Seems to work, the results are similar to mri_anatomical_stats. I'm not sure whether this is relevant; but the sampling seems to be not equally dense in the different regions. Does mri_segstats somehow cope with this? Best, Martijn On Tue, May 28, 2013 at 8:03 PM, Martijn Steenwijk martijnsteenw...@gmail.com mailto:martijnsteenwijk@**gmail.commartijnsteenw...@gmail.com wrote: Thanks Doug for your quick reply. But mri_segstats computes the average value inside the cortical region in the volume, right? That's not wat I want to have, I want to know the average value of the data in the volume on the wm/gm surface (i sampled with projfrac = 0). Any thoughts? On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: I would use mri_segstats and specify the --annot option doug On 05/28/2013 01:28 PM, Martijn Steenwijk wrote: Dear all, I've created a custom '.mgh' file containing values on the cortical surface using mri_vol2surf. I would like to compute some statistics on this surface in the aparc-areas computed by freesurfer. Can I then just use mri_anatomical_stats with option -t specifying the custom mgh file as 'thickness' input? Or does mri_anatomical_stats something more complex than just averaging the values inside each region? Best, Martijn __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer 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.**edugr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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. -- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2
Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file
I think it depends on how you do the computation. You would probably weight each vertex by the area then sum then divide by the total area and this is probably not much different than just averaging over vertices without taking the area into account. doug On 5/29/13 9:16 AM, Martijn Steenwijk wrote: I mean; if you devide the number of vertices by the area per aparc-parcellation, some parcellations have relatively more vertices per mm^2 as others. If you now would compute the average thickness in for example the lobe-parcellation, the thicknesses of some areas (the parcellations with relatively more vertices per mm^2) get a higher weight in the overal average. Is that true? On Tue, May 28, 2013 at 8:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: what do you mean? That the vertices are not uniform? mri_segstats just computes the mean over the parcellation without reference to non-uniformity. doug On 05/28/2013 02:15 PM, Martijn Steenwijk wrote: Sorry, indeed, my reply was too quick. Seems to work, the results are similar to mri_anatomical_stats. I'm not sure whether this is relevant; but the sampling seems to be not equally dense in the different regions. Does mri_segstats somehow cope with this? Best, Martijn On Tue, May 28, 2013 at 8:03 PM, Martijn Steenwijk martijnsteenw...@gmail.com mailto:martijnsteenw...@gmail.com mailto:martijnsteenw...@gmail.com mailto:martijnsteenw...@gmail.com wrote: Thanks Doug for your quick reply. But mri_segstats computes the average value inside the cortical region in the volume, right? That's not wat I want to have, I want to know the average value of the data in the volume on the wm/gm surface (i sampled with projfrac = 0). Any thoughts? On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I would use mri_segstats and specify the --annot option doug On 05/28/2013 01:28 PM, Martijn Steenwijk wrote: Dear all, I've created a custom '.mgh' file containing values on the cortical surface using mri_vol2surf. I would like to compute some statistics on this surface in the aparc-areas computed by freesurfer. Can I then just use mri_anatomical_stats with option -t specifying the custom mgh file as 'thickness' input? Or does mri_anatomical_stats something more complex than just averaging the values inside each region? Best, Martijn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://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 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 mailto: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
Re: [Freesurfer] SUMA and FSFAST
sorry, I've never used SUMA. Maybe Ziad can chime in (though he's probably never used FSFAST!) doug On 5/28/13 8:57 PM, Joseph Dien wrote: I was wondering if someone could give me a summary as to how SUMA and FSFAST differ? In other words, user interface aside, what would be reasons to use one or the other? Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com mailto:jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ___ 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] head motion values
fmcpr.mcdat are the motion estimates (mm and degrees). mcprextreg is the motion correction parameters after analysis using a PCA, which is why there is such a huge difference. By default we use the top 4 components. doug On 5/28/13 8:28 PM, Joseph Dien wrote: I have a follow-up question for this thread. I'm currently assessing whether to switch from SPM8 to FSFAST. As part of this process, I did a comparison between the SPM8 and the preproc-sess motion correction outputs but found they were quite different for the example data I looked at. Furthermore, I found that the fmcpr.mcdat output and the mcprextreg output are quite different even though they are both generated by fsfast. The following three charts are for mcprextreg, fmcpr.mcdat, and SPM8 respectively. Finally, I'm including a correlation matrix (I don't see any correspondences). The data are actually two separate sessions with a rest break, resulting in a discontinuity at the midpoint. The SPM realignment was run separately on each and as usual the first volume was the reference volume while FSFAST was run on both sessions as a merged set and I think used the middle volume as its reference volume. This shouldn't have resulted in such a large difference between SPM8 and FSFAST though (Ardekani et al 2001 reported they didn't differ that much in accuracy for SPM99 and AFNI98 versions and my understanding is that FSFAST uses AFNI's routine) and certainly not between the two FSFAST outputs. On the other hand, the magnitude of movement in this example is small so I guess my main concern is the discrepancy between mcprextreg and fmcpr.mcdat. I want to make sure I know what I'm looking at and therefore how to use it properly. I looked up the documentation on AFNI's 3dvolreg (http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dvolreg.html). Would I be correct in thinking that mcprextreg results from the -1Dfile option and fmcpr.mcdat results from the -dfile option? I can take this to the AFNI message board once I'm sure where these files came from. Respectfully, Joe Either fmcpr.mcdat or fmc.mcdat On 09/13/2012 02:07 PM, New Fei Ho wrote: Hi Doug, Can you point out the name of file that I should be looking at? I assumed they were either the mcextreg and mcprextreg output files, but these only have 6 columns. Thanks, New Fei Hi New Fei, I did some digging and found the docs for the output (pasted below). Translations (displacement) are in mm, rotations are in degrees doug 1. n : time point 2. roll : rotation about the I-S axis (degrees CCW) 3. pitch : rotation about the R-L axis (degrees CCW) 4. yaw: rotation about the A-P axis (degrees CCW) 5. dS : displacement in the Superior direction (mm) 6. dL : displacement in the Left direction (mm) 7. dP : displacement in the Posterior direction (mm) 8. rmsold : RMS difference between input frame and reference frame 9. rmsnew : RMS difference between output frame and reference frame 10. trans : translation (mm) = sqrt(dS^2 + dL^2 + dP^2) On 09/13/2012 11:21 AM, New Fei Ho wrote: Hi Doug, To explicitly clarify, does this mean X: L-R Y: Anterior-Posterior Z: Inferior-Superior And are the values of translation/rotation in millimetres? Thanks, New Fei If by XYZ you mean column, row, slice, then yes. The values are with respect to the middle time point (or whatever you used as the template), it is not the relative difference. doug On 09/12/2012 05:37 PM, New Fei Ho wrote: Hi, I would like to compare the mean head motion between two groups. Just to clarify the values found in the mcprextreg file: 1. Do the six columns represent translationX, translationY, translationZ and rotationX, rotationY, rotationZ? 2. Are the values found in each time-point (i) absolute, i.e. the absolute difference in displacement between this time-point and the middle time-point, or (ii) relative i.e. difference between consecutive time-points? Thanks, Newfei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] Contrast of three groups
Hi FreeSurfers, I have a more statistical question: I have three groups of subjects and I want to examine the effect of a continuous variable (cognition). Is it possible to examine three groups? Or should I do pairwise comparisons? What would the contrast than look like? Something like this: 0 0 0 0 0 0 0.33 0.33 0.33 (first three zeros for the three groups; three zeros for age-correction; three weights for cognition scores)?? Thanks! Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jac...@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ___ 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] Contrast of three groups
Hi Doug, Thanks for the answer. How can I examine differences between the groups? Best Heidi Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve [gr...@nmr.mgh.harvard.edu] Verzonden: woensdag 29 mei 2013 17:30 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Contrast of three groups Hi Heidi, That will test the effect of the continuous variable averaged over the 3 groups. doug On 05/29/2013 10:40 AM, Jacobs H (NP) wrote: Hi FreeSurfers, I have a more statistical question: I have three groups of subjects and I want to examine the effect of a continuous variable (cognition). Is it possible to examine three groups? Or should I do pairwise comparisons? What would the contrast than look like? Something like this: 0 0 0 0 0 0 0.33 0.33 0.33 (first three zeros for the three groups; three zeros for age-correction; three weights for cognition scores)?? Thanks! Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jac...@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ___ 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
Re: [Freesurfer] beta weights from FS-Fast analysis
Hi Joe, On 05/29/2013 01:00 AM, Joseph Dien wrote: I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional structure and the fourth dimension appears to be the beta weights. Is there an index somewhere as to which beta weight is which? Or if not, how are they organized? For the first level analysis, the first N beta weights correspond to the N conditions in the paradigm file. The rest are nuisance variables. 2) In order to extract the cluster, it looks like I would use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a volume where the voxels are tagged with the number of the corresponding cluster. Is that from a group analysis? I could then use that to generate masks to extract the information I need for each cluster from beta.nii.gz. If this is from a group analysis, then there should already be a file there (something.y.ocn.dat) that has a value for each subject in the rows and a value for each cluster in the columns. Is that correct? 3) The final information that I would need is the canonical hrf shape generated by FSFAST for a single event. I guess I could generate that by setting up a dummy analysis run with a single event of the desired duration and then look in the X variable in the resulting X.mat file? try this plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf) Sorry for all the questions! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com mailto:jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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] Contrast of three groups
If you want to look for an interaction between your cog score and group, then use the following contrast: 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 1 0 -1 This is an F-contrast with two rows doug On 05/29/2013 11:33 AM, Jacobs H (NP) wrote: Hi Doug, Thanks for the answer. How can I examine differences between the groups? Best Heidi Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve [gr...@nmr.mgh.harvard.edu] Verzonden: woensdag 29 mei 2013 17:30 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Contrast of three groups Hi Heidi, That will test the effect of the continuous variable averaged over the 3 groups. doug On 05/29/2013 10:40 AM, Jacobs H (NP) wrote: Hi FreeSurfers, I have a more statistical question: I have three groups of subjects and I want to examine the effect of a continuous variable (cognition). Is it possible to examine three groups? Or should I do pairwise comparisons? What would the contrast than look like? Something like this: 0 0 0 0 0 0 0.33 0.33 0.33 (first three zeros for the three groups; three zeros for age-correction; three weights for cognition scores)?? Thanks! Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jac...@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ___ 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. -- 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] SUMA and FSFAST
Thanks Ziad, looks like it is similar to FSFAST. doug On 05/29/2013 11:50 AM, Ziad Saad wrote: Hi Joe, As Doug guessed, I never used FSFAST so I can't really tell you much about how they differ. SUMA will require you use FreeSurfer to create the surfaces and warp them to standard spherical space. For the analysis stream, the one difference that comes to mind is that we recreate standard-mesh versions of FreeSurfer's surfaces (via sphere.reg) to make all surfaces isotopic across all the subjects. After that, and aside from the surface-specific procedures such as smoothing or clustering, all level-I and level-II voxel-wise computations can be carried out on surface-based data. A recent description of the analysis stream is in this paper http://afni.nimh.nih.gov/pub/dist/papers/Saad_SUMA_2011.pdf . cheers, z On May 29, 2013, at 09:44 AM, Douglas Greve wrote: sorry, I've never used SUMA. Maybe Ziad can chime in (though he's probably never used FSFAST!) doug On 5/28/13 8:57 PM, Joseph Dien wrote: I was wondering if someone could give me a summary as to how SUMA and FSFAST differ? In other words, user interface aside, what would be reasons to use one or the other? Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com mailto:jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- 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] Reposition Surface
Just a question about the Tools -- Reposition Surface... feature in Freeview. Is that up and running? Is there any accompanying documentation? Thanks. -Derin ___ 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] Defacing with mri_deface
The script mri_deface which is called by recon-all with the -deface flag, requires the existence of two files /usr/local/freesurfer/stable5/average/face.gca /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca The former exists where it should, the latter does not exist at that location, although it can be downloaded from http://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads and gunzipped. When I copy it into a directory and call mri_deface directly, it works OK because it can find that image locally. But when I call recon-all with the -deface flag, it looks for the file where it does not exist, i.e. /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca Could someone with the appropriate permissions please copy that file to where recon-all expects to find it? Second question: If I call recon-all with the -deface flag, does it deface ALL the images in my SUBJECTS_DIR/$subjid/mri directory, or does it only deface a copy of orig.mgz to orig_defaced.mgz? ___ 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] R: Re: very slow analysis with recon-all
Bruce and Sebastian thank you very much. I have checked the files but they are all wrong. These are the image info: data_type FLOAT32dim1 280dim2 240dim3 240dim4 1datatype 16pixdim10.584741pixdim2 1.041269pixdim31.041269pixdim40.00cal_max 0.cal_min0.file_type NIFTI-1+ Waiting for your feedback. Thank you very much. Stefano Messaggio originale Da: sebastian.moell...@rwth-aachen.de Data: 26-mag-2013 21.31 A: Bruce Fischlfis...@nmr.mgh.harvard.edu Cc: std...@virgilio.it, freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] very slow analysis with recon-all Hi Stefano, hi Bruce, sorry to partly high-jack your thread Stafano. In my experience with NHPs I often encounter problems like included cerebellum, so I routinely check the filled.mgz before actually running the surface recon, to confirm that the cerebellum (or other non-white matter) is NOT part of either hemisphere. (In my cases typically I then have to either edit the wm.mgz, the brain mask, or the pons cutting plane, but I guess that is NHP specific). Now wouldn't that filled.mgz check not also work for human recons? best Sebastian On May 26, 2013, at 21:13 , Bruce Fischl wrote: Hi Stefano a defect with over 60K vertices is more than 1/2 the size of a typical hemisphere, so something has gone badly wrong. Have you checked the skull stripping? The aseg? The talairach? There shouldn't be a defect that big - you will need to figure out why cheers Bruce On Sun, 26 May 2013, std...@virgilio.it wrote: Hi list, I'm running recon-all on two T1 but the command is for two days on CORRECTING DEFECT 11 (vertices=55538, convex hull=7811). Is it ok? What's happen? Thanks, Stefano ___ 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] R: R: Re: very slow analysis with recon-all
I apologize. This is the correct info:data_type INT16dim1 280dim2 240dim3 240dim4 1datatype 4pixdim1 0.584741pixdim21.041269pixdim31.041269pixdim4 0.00cal_max0.cal_min0.file_type NIFTI-1+ Messaggio originale Da: std...@virgilio.it Data: 30-mag-2013 0.30 A: sebastian.moell...@rwth-aachen.de, Bruce Fischlfis...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: very slow analysis with recon-all Bruce and Sebastian thank you very much. I have checked the files but they are all wrong. These are the image info: data_type FLOAT32dim1 280dim2 240dim3 240dim4 1datatype 16pixdim10.584741pixdim2 1.041269pixdim31.041269pixdim40.00cal_max 0.cal_min0.file_type NIFTI-1+ Waiting for your feedback. Thank you very much. Stefano Messaggio originale Da: sebastian.moell...@rwth-aachen.de Data: 26-mag-2013 21.31 A: Bruce Fischlfis...@nmr.mgh.harvard.edu Cc: std...@virgilio.it, freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] very slow analysis with recon-all Hi Stefano, hi Bruce, sorry to partly high-jack your thread Stafano. In my experience with NHPs I often encounter problems like included cerebellum, so I routinely check the filled.mgz before actually running the surface recon, to confirm that the cerebellum (or other non-white matter) is NOT part of either hemisphere. (In my cases typically I then have to either edit the wm.mgz, the brain mask, or the pons cutting plane, but I guess that is NHP specific). Now wouldn't that filled.mgz check not also work for human recons? best Sebastian On May 26, 2013, at 21:13 , Bruce Fischl wrote: Hi Stefano a defect with over 60K vertices is more than 1/2 the size of a typical hemisphere, so something has gone badly wrong. Have you checked the skull stripping? The aseg? The talairach? There shouldn't be a defect that big - you will need to figure out why cheers Bruce On Sun, 26 May 2013, std...@virgilio.it wrote: Hi list, I'm running recon-all on two T1 but the command is for two days on CORRECTING DEFECT 11 (vertices=55538, convex hull=7811). Is it ok? What's happen? Thanks, Stefano ___ 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] no hippocampal stats despite running FS 5.3 with -hippo-subfields
I usually use this little bash script (named myrecon) to process my images. #!/bin/bash mkdir ~/freesurfer/subjects/$1/mri/orig -p cp ~/freesurfer/ImgOrig/$1/* ~/freesurfer/subjects/$1/mri/orig/ recon-all -all -s $1 -cw256 -hippo-subfields -qcache With this script I get the entire -all pipeline, plus hippocampal segmentation and the cache for posterior analysis with qdec. All in a once and just typing myrecon subject. You can check if the hippo-subfields were correctly processed reading the recon-all-status.log and with more detail reading hippo-subfields.log. Both files are in freesurfer/subjects/yoursubject/scripts. I attached one of my recon-all-status.log so you can compare. The last line is related to hippo-subfields processing. After recon-all you will see several posterior*.mgz files inside freesurfer/subjects/yoursubject/mri/. BTW, ImgOrig is a custom folder where I have one folder for each subject with the original 00X.mgz file(s). Marcos Em Seg, 2013-05-27 às 09:45 -0700, Salil Soman escreveu: I can add that running the -hippo-subfields flag separately did work: recon-all -s SUBJECTIDENTIFIER -hippo-subfields Is there a reason the order of processing should matter? Is there a way I can change my recon-all call (below) so that hippo-subfields will get processed (so I do not have to make a separate call)? recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all Thank you, Sal On Sun, May 26, 2013 at 2:33 PM, Salil Soman salso...@stanford.edu wrote: Dear Freesurfer Experts, I have been running freesurfer 5.3 without any reported errors using the following command: recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all However, when I look for any of the hippocampal subfield stats (as described on http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation), I do not find any of them. Any suggestions on what I am doing incorrectly? Best wishes, Salil Soman, MD, MS ___ 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. status file for recon-all Thu May 23 01:32:10 BRT 2013 #@# MotionCor Thu May 23 01:32:10 BRT 2013 #@# Talairach Thu May 23 01:35:39 BRT 2013 #@# Talairach Failure Detection Thu May 23 01:37:16 BRT 2013 #@# Nu Intensity Correction Thu May 23 01:37:16 BRT 2013 #@# Intensity Normalization Thu May 23 01:38:35 BRT 2013 #@# Skull Stripping Thu May 23 01:41:00 BRT 2013 #@# EM Registration Thu May 23 02:16:10 BRT 2013 #@# CA Normalize Thu May 23 02:42:59 BRT 2013 #@# CA Reg Thu May 23 02:44:52 BRT 2013 #@# CA Reg Inv Thu May 23 07:28:41 BRT 2013 #@# Remove Neck Thu May 23 07:29:49 BRT 2013 #@# SkullLTA Thu May 23 07:30:59 BRT 2013 #@# SubCort Seg Thu May 23 08:02:06 BRT 2013 #@# Merge ASeg Thu May 23 08:23:51 BRT 2013 #@# Intensity Normalization2 Thu May 23 08:23:51 BRT 2013 #@# Mask BFS Thu May 23 08:28:03 BRT 2013 #@# WM Segmentation Thu May 23 08:28:06 BRT 2013 #@# Fill Thu May 23 08:31:06 BRT 2013 #@# Tessellate lh Thu May 23 08:32:01 BRT 2013 #@# Smooth1 lh Thu May 23 08:32:09 BRT 2013 #@# Inflation1 lh Thu May 23 08:32:14 BRT 2013 #@# QSphere lh Thu May 23 08:32:50 BRT 2013 #@# Fix Topology lh Thu May 23 08:37:40 BRT 2013 #@# Make White Surf lh Thu May 23 09:03:51 BRT 2013 #@# Smooth2 lh Thu May 23 09:10:51 BRT 2013 #@# Inflation2 lh Thu May 23 09:10:55 BRT 2013 #@# Curvature Stats lh Thu May 23 09:13:12 BRT 2013 #@# Sphere lh Thu May 23 09:13:16 BRT 2013 #@# Surf Reg lh Thu May 23 10:08:23 BRT 2013 #@# Jacobian white lh Thu May 23 10:45:12 BRT 2013 #@# AvgCurv lh Thu May 23 10:45:15 BRT 2013 #@# Cortical Parc lh Thu May 23 10:45:17 BRT 2013 #@# Make Pial Surf lh Thu May 23 10:46:15 BRT 2013 #@# Surf Volume lh Thu May 23 11:00:00 BRT 2013 #@# WM/GM Contrast lh Thu May 23 11:00:00 BRT 2013 #@# Parcellation Stats lh Thu May 23 11:00:11 BRT 2013 #@# Cortical Parc 2 lh Thu May 23 11:00:32 BRT 2013 #@# Parcellation Stats 2 lh Thu May 23 11:01:36 BRT 2013 #@# Cortical Parc 3 lh Thu May 23 11:01:56 BRT 2013 #@# Parcellation Stats 3 lh Thu May 23 11:02:52 BRT 2013 #@# Tessellate rh Thu May 23 11:03:09 BRT 2013 #@# Smooth1 rh Thu May 23 11:03:18 BRT 2013 #@# Inflation1 rh Thu May
Re: [Freesurfer] Defacing with mri_deface
Hi Steve I think recon-all -deface only creates the orig_defaced.mgz which you can then use with mri_mask to remove facial features from whatever volumes you want. I don't have write permissions to that directory, but I'll see if I can get help to copy it. cheers Bruce On Wed, 29 May 2013, sle...@nmr.mgh.harvard.edu wrote: The script mri_deface which is called by recon-all with the -deface flag, requires the existence of two files /usr/local/freesurfer/stable5/average/face.gca /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca The former exists where it should, the latter does not exist at that location, although it can be downloaded from http://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads and gunzipped. When I copy it into a directory and call mri_deface directly, it works OK because it can find that image locally. But when I call recon-all with the -deface flag, it looks for the file where it does not exist, i.e. /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca Could someone with the appropriate permissions please copy that file to where recon-all expects to find it? Second question: If I call recon-all with the -deface flag, does it deface ALL the images in my SUBJECTS_DIR/$subjid/mri directory, or does it only deface a copy of orig.mgz to orig_defaced.mgz? ___ 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] mris_divide_parcellation color table error
Hi Tina Did you try visualizing it in tksurfer? Bruce On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: Hello freesurfers, I am trying to create a figure similar to the Hagmann et al 2008 paper with 998 rois overlaid onto the surface, however, I am finding that there is no random, unique color for each parcellation unit like described in the help file for mris_divide_parcellation. I have attached a snapshot of my annotation file overlaid onto the surface, as you can see, the color iterates the same/similar color for a particular label. Can you tell me what I am doing wrong? Is there a pre-existing atlas as described in the Hagmann paper? My input: mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh ./lh.sphere.reg $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010-03-25.gcs ./lh.aparc.998rois.annot mris_divide_parcellation subject_name lh ./lh.aparc.998rois.annot ./splittable.txt ./lh.annotation.998rois_26.annot Many thanks, Tina Jeon, MS UT Southwestern Medical Center ‘14 UT Southwestern Medical Center The future of medicine, today. neonate_buckner40_atlas.png splittable.txt ___ 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] mris_divide_parcellation color table error
Yes same result as with freeview. Sent from my iPhone On May 29, 2013, at 7:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Tina Did you try visualizing it in tksurfer? Bruce On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edumailto:tina.j...@utsouthwestern.edu wrote: Hello freesurfers, I am trying to create a figure similar to the Hagmann et al 2008 paper with 998 rois overlaid onto the surface, however, I am finding that there is no random, unique color for each parcellation unit like described in the help file for mris_divide_parcellation. I have attached a snapshot of my annotation file overlaid onto the surface, as you can see, the color iterates the same/similar color for a particular label. Can you tell me what I am doing wrong? Is there a pre-existing atlas as described in the Hagmann paper? My input: mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh ./lh.sphere.reg $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010-03-25.gcs ./lh.aparc.998rois.annot mris_divide_parcellation subject_name lh ./lh.aparc.998rois.annot ./splittable.txt ./lh.annotation.998rois_26.annot Many thanks, Tina Jeon, MS UT Southwestern Medical Center ‘14 UT Southwestern Medical Center The future of medicine, today. neonate_buckner40_atlas.png splittable.txt ___ 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.
Re: [Freesurfer] mris_divide_parcellation color table error
hmmm, I haven't run that code in a long time. Are the colors different but not visually so? That is, do the rgb values differ by 1 or 2 or something like that? Or are they actualy identical? On Thu, 30 May 2013, Tina Jeon wrote: Yes same result as with freeview. Sent from my iPhone On May 29, 2013, at 7:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tina Did you try visualizing it in tksurfer? Bruce On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: Hello freesurfers, I am trying to create a figure similar to the Hagmann et al 2008 paper with 998 rois overlaid onto the surface, however, I am finding that there is no random, unique color for each parcellation unit like described in the help file for mris_divide_parcellation. I have attached a snapshot of my annotation file overlaid onto the surface, as you can see, the color iterates the same/similar color for a particular label. Can you tell me what I am doing wrong? Is there a pre-existing atlas as described in the Hagmann paper? My input: mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh ./lh.sphere.reg$FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010 -03-25.gcs ./lh.aparc.998rois.annot mris_divide_parcellation subject_name lh ./lh.aparc.998rois.annot ./splittable.txt ./lh.annotation.998rois_26.annot Many thanks, Tina Jeon, MS UT Southwestern Medical Center ‘14 UT Southwestern Medical Center The future of medicine, today. neonate_buckner40_atlas.png splittable.txt ___ 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] beta weights from FS-Fast analysis
On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Joe, On 05/29/2013 01:00 AM, Joseph Dien wrote: I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional structure and the fourth dimension appears to be the beta weights. Is there an index somewhere as to which beta weight is which? Or if not, how are they organized? For the first level analysis, the first N beta weights correspond to the N conditions in the paradigm file. The rest are nuisance variables. Ah, very good! In order to compute the percent signal change statistic (I'm following the MarsBaR approach: http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated) I'm also going to need the beta weights for the session mean regressors. How are the nuisance regressors organized? 2) In order to extract the cluster, it looks like I would use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a volume where the voxels are tagged with the number of the corresponding cluster. Is that from a group analysis? Yes, that's right. I could then use that to generate masks to extract the information I need for each cluster from beta.nii.gz. If this is from a group analysis, then there should already be a file there (something.y.ocn.dat) that has a value for each subject in the rows and a value for each cluster in the columns. I see it. Are these values already scaled as percent signal change? If so, that would be wonderful! :) Is that correct? 3) The final information that I would need is the canonical hrf shape generated by FSFAST for a single event. I guess I could generate that by setting up a dummy analysis run with a single event of the desired duration and then look in the X variable in the resulting X.mat file? try this plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf) Perfect! :) Sorry for all the questions! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com mailto:jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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. Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
