[Freesurfer] Still confused by group analysis..
Dear Freesurfer experts, I very much appreciate your help with an additional set of questions. I feel I'm really close to getting this finished :) 1) In a design with group and gender as discrete factors and age as a continuous factor, why is it that QDEC only displays the contrast Does the avg thickness, accounting for gender, differ between group1 and group2? and not also ..acounting for gender and age,..? 2) In QDEC, if I am left with a cluster after setting the FDR rate to 0.1, does that qualify as a trend towads significance in the same way as when obtaining a p value .1 for a behavioural effect? 3) From the group tutorial, I see that mris_preproc has to be called with flag --cache-in ess.fwhm10thickn.fsaverage. However, after running recon-all (including with the –qcache option) on all my subjects, none of their folders contains a file named ?h.thickness.fwhm10.fsaverage.mgh 4) When comparing two healthy groups, is there anything to gain from using a fsaverage built from the sample (with make_average_subject) as opposed to using the default fsaverage? 5) What is the difference between running make_average_subject and running mris_preproc with --target fsaverage? 6) For my ROI mri_glmfit analysis, I wanted to use the FSGD and contrast files that were automatically created when I did my QDEC whole-brain analysis, since the design will be the same. However, although I identified the FSGD file (qdec.fsgd), I cannot see any plaintext file in the QDEC folder that looks like it contains contrast definitions! Thanks! Tudor ___ 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] Binary volume to surface label
Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. [image: Inline image 2] Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan 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. image.png___ 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] Binary volume to surface label
Hi Jonathan you don't need to register it if it's shown properly in tkmedit or freeview. Can you tell us more about what you are trying to do? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. Inline image 2 Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan 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] Binary volume to surface label
Hi Bruce, I would like to convert the .mgz label volume to a surface label for that subject, but mri_vol2surf requires a registration file. Best, Jonathan On Sunday, May 12, 2013, Bruce Fischl wrote: Hi Jonathan you don't need to register it if it's shown properly in tkmedit or freeview. Can you tell us more about what you are trying to do? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. Inline image 2 Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan 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. ___ 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] Binary volume to surface label
try using --regheader cheers Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, I would like to convert the .mgz label volume to a surface label for that subject, but mri_vol2surf requires a registration file. Best, Jonathan On Sunday, May 12, 2013, Bruce Fischl wrote: Hi Jonathan you don't need to register it if it's shown properly in tkmedit or freeview. Can you tell us more about what you are trying to do? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. Inline image 2 Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan 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] Restricting ROI Analysis
Hi everyone, We are trying to restrict an analysis using Qdec to a region of interest. We have successfully created the ROI mask, however the analysis continues to be run on the entire brain. Any help is greatly appreciated. Thanks, Skyler and Jon -- Skyler G. Shollenbarger Graduate Student - UWM Brain Lab Clinical Psychology Neurospychology University of Wisconsin-Milwaukee ___ 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] Binary volume to surface label
I used the following options: mri_vol2surf --hemi lh --regheader subject01 --cortex --mov label.mgz --o ./label.mgh It ran without error, but I could not open the resulting file in tksurfer as either a label or an overlay: - /Applications/freesurfer/tktools/tksurfer.bin: no data in label file /Users/label.mgh tkmedit: Trying to open /Users/label.dat surfer: Interpreting overlay volume /Users/label.mgh as encoded scalar volume Best, Jonathan On Sun, May 12, 2013 at 1:57 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: try using --regheader cheers Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, I would like to convert the .mgz label volume to a surface label for that subject, but mri_vol2surf requires a registration file. Best, Jonathan On Sunday, May 12, 2013, Bruce Fischl wrote: Hi Jonathan you don't need to register it if it's shown properly in tkmedit or freeview. Can you tell us more about what you are trying to do? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. Inline image 2 Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan 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. ___ 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] using T2* weighted scans to assist with dura stripping in a GE scanner?
This is available online now: http://authors.elsevier.com/sd/article/S1053811913005053 On 5/7/13 3:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: actually Matt Glasser points out that a brief description is in his paper that is coming out soon, and there is also some description in Andre's multi-echo mprage paper Bruce On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] wrote: thanks :-) On May 7, 2013, at 3:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: no, of course not :) On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] wrote: Hi Bruce, Out of curiosity and for reference for my users, do you have a paper on the T2 or FLAIR assisted segmentation? Cheers, Souheil - Souheil Inati, PhD Staff Scientist FMRI Facility NIMH/NIH/DHHS souheil.in...@nih.govmailto:souheil.in...@nih.gov On May 7, 2013, at 2:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Katie I'm really not sure. These days I would recommend a highres (e.g. 1mm isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but it's pretty noisy in brain. cheers Bruce On Tue, 7 May 2013, Katie Surrence wrote: Dear Freesurfer gurus, At the course, André van der Kouwe mentioned in his morphometry methods talk that T2* weighted contrast from MEMPRAGE could be used to further seperate dura from cortex, as also discussed in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. We have a GE scanner in our lab. The internet suggests that a Multi-echo FSPGR/FGRE exists. Would this be the analog? Would it work the same way? Could you also use these images with the mris_make_surfaces command? Thanks very much for your insight -- and I enjoyed the course! /Katie Surrence -- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Correction for multiple comparisons question
Hi Panagiotis, On 5/12/13 9:32 PM, Fotiadis, Panagiotis wrote: Hi Freesurfer experts, I was wondering about three things concerning the use of the mri_glmfit-sim command: 1) I tried running it with the --2spaces flag in order to Bonferroni correct over the two hemispheres but it tells me that the specific flag is not recognized. Is there another way to correct over the two hemispheres? What version are you using? You can just adjust the clusterwise threshold by dividing by 2 (eg, if you want a clusterwise threshold of .05, then set it to .025) 2) I set the cluster-based threshold to 0.999 in order to see all of the clusters and varied the voxel-based threshold in order to see the differences that it would make on the results. Specifically, i set it to be 1.3, 2.0, 2.3, and 3.0. Between the four different occurring cluster summaries, there was only one common cluster that appeared in all four summaries. As expected, the number of voxels of the specific cluster was decreasing as its voxel-wise threshold was increasing. a) However, the reported cluster-wise threshold varied between 0.05 to 0.96 in those four cases. Does this sound reasonable? Shouldn't the cluster wise p values of the same cluster-between the four cases-be less dispersed? I'm not sure what you mean here. At 3.0, the cluster may be very small and so could appear to be very insignificant. b) If there is a cluster reported in only one of the four summaries (i.e. when the voxel-based threshold is 1.3) that say has a cluster-wise p value of 0.03, do I consider that significant or not, since it does not appear in any other summary with such a low cluster wise p value and since the only published p value is the cluster wise one? In principle, it is significant. A lot of reviewers balk at such a liberal voxel-wise threshold since gaussian random fields breaks down at liberal thresholds. However, this uses simulations and not GRF. You should make sure the reviewers know this. There still might be some resistance since you could be picking up some low spatial frequency trends (ie, stuff that is not spatially gaussian) in addition to your true activation. doug Thank you in advance for your time, Panagiotis Fotiadis ___ 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] Restricting ROI Analysis
Hi Skyler, I don't think we have the ability to restrict the analysis to an ROI in QDEC. You can do it with mri_glmfit with the --mask or --label option. doug On 5/12/13 4:25 PM, Skyler Gabriel Shollenbarger wrote: Hi everyone, We are trying to restrict an analysis using Qdec to a region of interest. We have successfully created the ROI mask, however the analysis continues to be run on the entire brain. Any help is greatly appreciated. Thanks, Skyler and Jon ___ 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] Binary volume to surface label
It cannot create a label file directly. What happens when you try to load it as an overlay? Make sure to set the threshold to 0.5. Also, before going to the surface load the binary volume onto the anatomical with the surfaces to make sure that the surfaces pass through the mask. doug On 5/12/13 4:55 PM, Bruce Fischl wrote: Hi Jonathan try -output_type mgh. It should create a volume that is nvertices long. Not sure if it can directly create a label file, maybe Doug knows? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: I used the following options: mri_vol2surf --hemi lh --regheader subject01 --cortex --mov label.mgz --o ./label.mghIt ran without error, but I could not open the resulting file in tksurfer as either a label or an overlay: - /Applications/freesurfer/tktools/tksurfer.bin: no data in label file /Users/label.mgh tkmedit: Trying to open /Users/label.dat surfer: Interpreting overlay volume /Users/label.mgh as encoded scalar volume Best, Jonathan On Sun, May 12, 2013 at 1:57 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: try using --regheader cheers Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, I would like to convert the .mgz label volume to a surface label for that subject, but mri_vol2surf requires a registration file. Best, Jonathan On Sunday, May 12, 2013, Bruce Fischl wrote: Hi Jonathan you don't need to register it if it's shown properly in tkmedit or freeview. Can you tell us more about what you are trying to do? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. Inline image 2 Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan 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
Re: [Freesurfer] thickness
On 5/11/13 7:41 PM, Tudor Popescu wrote: Hi everyone, I resort to asking some questions here again, after feeling increasingly stupid (maybe just tired) after reading the wiki pages relevant for my analysis (ROI, thickness). 1) How should the contrast vector for a group comparison while factoring out age and gender be built? I didn't quite understand the example in the tutorial http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Contrastsbased on intercept/offset. In my case, shouldn't I have 4 elements in the vector (group1, group2, age, gender), with the first two elements receiving perhaps 1 and -1, since they are directly compared, and the last two elements 0 and 0 since I am not directly interested in their effect on the dependent variable? Gender should be two groups (don't code it as a continuous variable). This will give you 8 columns. g1, g2, male, female, g1-age, g2-age, etc. 2) Are the structures described in the .label files produced by mri_annotation2label in common (MNI) or in that subject's individual space? Individual space. 3) For my thickness analysis, I have in mind an ROI for which I have a set of centre coordinates from a meta-analysis of relevant functional studies. What is the best way of defining the mask for this ROI as a function of those coordinates, rather than taking the eponymous region from the Destrieux or the Desikan atlas? Assuming that the coords are in mni152, convert it to mni305 (to do this search for coordinates on the wiki). Then load up fsaverage and find the vertex closest to this coordinate. The draw a label around this vertex. 4) Exactly which of recon-all's outputs has to be inspected, for each subject, in order to tell whether the surface reconstruction has gone well? Load up the surfaces over the nu.mgz or the T1.mgz and see if the surfaces follow the anatomy properly. 5) Is it statistically correct to run the same design both with a DODS FSGD and with a DOSS FSGD? It's not entirely clear to me what assumptions each one (DODS, DOSS) makes of the data, and which one I should select in my case. The DODS allows for interactions between a continuous factor and a discrete factor. Eg, the thickness-age slope could be different between males and females, and you could detect this with DODS. With DOSS, there is only one thickness-age slope for all groups, so there is no way to detect an interaction. doug Thank you very much indeed. Tudor ___ 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] Usage of --area option in estimating the vertex-wise maps of surface area
Hi Xi-Nian, it does not do the same thing, but it does something similar. Anderson found that it gave similar results in a lot of cases, but he has found some differences. If he's still following the FS list, maybe he can comment. doug On 5/11/13 9:53 PM, Xinian Zuo wrote: Hello Doug, I am doing some association studies between functional measures and surface area. In using mris_preproc, there is an option --area. Does this do sth similar to that as Winkler et al. (2012)? Winkler et al., 2012. Measureing and comparing brain cortical surfacearea and other areal quantities. Thank you very much. -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn) Google Scholar Citations: http://scholar.google.com/citations?user=a3-gVGMJhl=en ___ 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.
