Re: [Freesurfer] qdec analysis and covariates
Hi, I have a question related to this post. Besides an age-group interaction, wouldn't it also be neccesary to check for an age-gender interaction? ___ 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] qdec analysis and covariates
Oh, I meant to reply to an older post, but that didn't work apparently. Below the original post. This person does a group analysis, with gender and age as covariates.You adviced to first do a DODS and look for a age-by-group interaction. If there's no interaction, he/she could continue with DOSS. My questions is (since I'm doing a similar analysis) whether it's also necesary to check for a age-by-gender interaction? Or is this not important since gender is a covariate instead of an independent variable? Thanks! Anita Douglas N Greve Mon, 29 Nov 2010 07:27:30 -0800 Yes, that looks fine. The only other thing to decide is whether to use DODS (different offset different slope) or DOSS (different offset same slope). The default is DODS, but if you don't think that there is an age-by-group interaction, then you can get more power using DOSS. If you use DODS, then you should probably de-mean the ages (ie, subtract the grand mean age over all subjects from the age of each individual). doug Roser Sala wrote: Hi, We are doing a group analysis using qdec with two groups, and we would like to include gender and age as covariates. Which is the best option in order to perform a simple t-test (group1>group2 and group2>group1) and including the two covariates? (we would like them to have 'zero' weighting in the contrast matrix) We realized that if we include 'age' as a continous factor in the dialog, qdec is performing rather an interaction analysis than a covariate. So, would it be ok to include group and gender as fixed factors and age as nuisance, and then select the output as 'Does the average thickness accounting for gender differ between group1 and group2' (age as nuisance variable)? By checking all the possibilities this seemed the best option for us, but we would like to get a confirmation that we are doing it right. Many thanks Roser ___ 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] DOSS contrast - one group, 3 covariates
Hi everyone, I want to analyze with DOSS the relationship between performance on a cognitive task (called '15wt') and cortical thickness, in one group, controlling for the effects for age, gender and education. As a Freesurfer-newbie, it be would really great if someone could check my .sfgd file and contrast. .sfgd file: GroupDescriptorFile 1 Class .00 plus blue (this is the gender part) Class 1.00 plus red Variables 15_wt Age Edu Input 0050 .00 52 73 4 Input 0051 .00 38 68 5 Input 0054 1.00 35 57 4 Input 0060 1.00 46 58 6 Input 0062 1.00 46 45 5 etc. contrast: 0 0 .5 0 0 Is this correct? Thanks in advance! Anita ___ 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] DOSS contrast - one group, 3 covariates
Thank you Doug! ___ 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] MRISread error
Hi everyone, I run into an error when I try to do the tutorial on ROI group analysis. I downloaded the tutorial set, but did not put it into FREESURFER_HOME/subjects, because my computer doesn't allow it. I made my own folder and copied everything in there. The error arises when I try to map a label from the fsaverage subject to a target subject: mri_label2label \ > --srcsubject fsaverage \ > --srclabel fsaverage/label/lh.BA45.label \ > --trgsubject 004 \ > --trglabel 004/label/lh.BA45.label \ > --hemi lh \ > --regmethod surface srclabel = fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = 004 trglabel = 004/label/lh.BA45.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/group_analysis_tutorial FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.sphere.reg MRISread(Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.sphere.reg): could not open file No such file or directory ERROR: could not read Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.sphere.reg In related posts I read that it might have to do with the creation of symbolic links. I made sure that in my SUBJECTS_DIR, fsaverage is a symbolic link to my FREESURFER_HOME/subjects directory, in which surf/lh.sphere.reg etc are stored. What am I doing wrong? Does it still have to do with the fact that I put the tutorial data in another folder? Hope you can help me, Thanks in advance, Anita ___ 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] MRISread error
It finally worked! Thank you so much Louis. My SUBJECTS_DIR was pointing to a folder within my TUTORIAL_DATA directory (I thought it was supposed to be like that when I read the instructions), but now they point to the same folder and it works. Thanks again! Anita ___ 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] MNI305 to MNI152 coordinates
Dear FreeSurfers, I have a question regarding conversion from MNI152 coordinates to MNI305 coordinates. I want to take ROIs from a VBM study and use these exact same ROIs in my vertexwise analysis. So I need to translate the x, y, z coordinates from MNI152 space into MNI305 space. In previous posts, I found a matrix that converts from MNI305 coordinates to MNI152: M = [0.9975 -0.00730.0176 -0.0429 0.01461.0009 -0.00241.5496 -0.0130 -0.00930.99711.1840 0001.] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305 However, I want to do it the other way around. I tried to calculate the inverse matrix but haven't succeeded. Does anyone have (or know how to create) the matrix/formula I need? It would be very helpful, thanks in advance. Anita ___ 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] MNI305 to MNI152 coordinates
It worked, thanks. I tried to invert it but the coordinates didn't fully correspond; I must have made an error. Thanks for helping me out! ___ 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] RAS, MNI305, Talairach, MNI-Talairach?
Hi all, I find myself getting quite confused about different coordinates systems. Is the following correct (when viewing in TkSurfer): RAS=MNI Talairach=MNI305 (they are all the same?) Talairach= (non linear) conversion from MNI305 Thanks, Anita ___ 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] Volume-defined ROI 'gone' after vol2surf
Hi all, I want to measure cortical thickness in 7 volume-defined ROIs (created in Marsbar). I followed the tutorial http://freesurfer.net/fswiki/VolumeRoiCorticalThickness. When I want to visualize my surface-based ROI after mri_vol2surf, for some reason ROI 6 and 7 do not appear in tksurfer (and with segstats, no segmentation is found). FreeSurfer does not seem to give any error message: $ mri_vol2surf --mov ~/Desktop/anita-vumc/7Rmidtempgyrus.nii --reg avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest --hemi rh --out rh.fsaverage.7Rmidtempgyrus.mgh --reshape srcvol = /home/guest/Desktop/anita-vumc/7Rmidtempgyrus.nii srcreg = avg152T1_to_fsaverage.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = 0.5 reshape = 1 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 Done loading volume Reading surface /data1/projects/ysbrand-vumc/pddatabase-freesurfer/fsaverage/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 1 using old 2 0.1 0 1 using old 3 0.2 0 1 using old 4 0.3 0 1 using old 5 0.4 0 1 using old 6 0.5 0 1 using old 7 0.6 0 1 using old 8 0.7 0 1 using old 9 0.8 0 1 using old 10 0.9 0 1 using old Done mapping volume to surface Number of source voxels hit = 21723 Reshaping 7 (nvertices = 163842) Writing to rh.fsaverage.7Rmidtempgyrus.mgh Dim: 23406 1 7 Does anyone have an idea about what might have gone wrong? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Cortical thickness/surface area in volume-defined ROIs
Dear Freesurfer experts, I want to use volume-defined ROIs (obtained in a VBM study) to extract mean thickness and surface area, in a total group of 138 participants. I followed the tutorial 'Cortical Thickness of a volume-defined ROI'. I have a few questions regarding this analysis: 1. The volume-defined ROI (i.e. orange dot) appears normal on my avg152_T1 and fsaverage. After the vol2surf-step, however, a few problems arise. The new ROIs look very different: one ROI actually consists of two clusters close to each other, one is very small and two ROIs have completely disappeared. Does anyone know why this happened? 2. When I want to obtain surface area data instead of thickness data, is it sufficient to replace 'thickness' with 'area' in the surf2surf command (it seems to work, but I want to check)? So: --sval lh.area \ --tval lh.area.fsaverage.mgh \ 3. mri_segstats creates separate files for each ROI in each participant. When I want to have all thickness and area ROI data in one file, can I use asegstats2table, meas mean (it seems to work, but I want to check)? Any help would be very much appreciated! Anita ___ 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] Cortical thickness/surface area in volume-defined ROIs
Hi Rujing Zha, Click this link: http://freesurfer.net/fswiki/VolumeRoiCorticalThickness Anita ___ 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] Cortical thickness/surface area in volume-defined ROIs
Hi Bruce, Thank you for your response. Now at least I know what went wrong; I'll try your solution. Thanks! Anita ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Pial surface area
Hi mailinglist, I want to obtain aparc.stats for pial instead of white matter surface area. I read that I therefore should adjust mris_anatomical_stats. However, when I run this command separately, the following error occurs: cannot allocate memory Then I tried to put autorecon3 -parcstats in front in this command, but now it says: Flag mris_anatomical_stats unrecognized. Any help would be greatly appreciated, Anita ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Pial surface area
Hi Bruce, See below. Thank you! Anita First I tried: *aloenhoud@somerenserver:/data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050$ *mris_anatomical_stats -mgz -f stats/lh.aparc.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab 0050 lh pial INFO: assuming MGZ format for volumes. computing statistics for each annotation in label/lh.aparc.annot. reading volume /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/mri/wm.mgz... znzTAGskip: tag=1818326118, failed to calloc 541878272 bytes! Cannot allocate memory Then I tried the following: *aloenhoud@somerenserver:/data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050$*recon-all -autorecon3 -subjid 0050 mris_anatomical_stats -mgz -f stats/lh.aparc.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab 0050 lh pial ERROR: Flag mris_anatomical_stats unrecognized. -autorecon3 -subjid 0050 mris_anatomical_stats -mgz -f stats/lh.aparc.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab 0050 lh pial Linux somerenserver.herseninstituut.knaw.nl 2.6.32-431.5.1.el6.x86_64 #1 SMP Wed Feb 12 00:41:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 0050 exited with ERRORS at Fri Mar 21 14:49:53 CET 2014 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Pial surface area
Hi Bruce, The wm.mgz was created a while ago with an older version, by another student. At the moment I use v5.3.0. Should I recreate wm.mgz with this more recent version, or is there another option? Thank you, Anita ___ 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] Correction multiple comparisons for parcelated areas
Dear FreeSurfers, I’m comparing two groups (patients (N=45) and controls (N=93)) on cortical thickness using 34 parcelated areas in each hemisphere (i.e. 68 areas in total). When correcting for multiple comparisons using Bonferroni, only one area remains significant. Bonferroni is quite conservative (alpha needs to be lower than 0.05/68= 0.000735). Could you recommend any other, more lenient correction statistics for my data? In a search through the literature, I encountered adjusted Bonferroni or Benjamini-Hochberg as alternatives. Do you think these would be useful statistics, or have I missed other, more appropriate ones? Thanks a lot, Anna ___ 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] Interpretation of red/blue clusters in group analysis
Hi FreeSurfers, I'm doing an analysis with two groups: patients and controls. When I look at "Does the average thickness differ between 1 (patients) and 2 (controls)?", I can see blue (negative) and red (positive) correlations. I know that it means that in some cases, the patients have a higher cortical thickness compared to the controls, and in others it's the other way around. But which is which? Since most of the clusters are blue, I assume that blue means: patients have a lower cortical thickness compared to controls, and red means: patients have a higher cortical thickness compared to controls. Is this correct? How does FreeSurfer decide which group to use as the 'reference group' (i.e. the group to which the other group is compared)? Thanks, Anita ___ 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] Significant clusters before and after Monte Carlo
Hi all, When I do a group analysis and check significant clusters after performing a Monte Carlo, I see significant areas that were NOT significant before doing a multiple comparisons correction. Specifically, after Monte Carlo, the parstriangularis is significant, while this area was not significant in the first place (before Monte Carlo). I'm confused; how could that be possible? Am I doing something wrong? Thank you! Anita ___ 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] Significant clusters before and after Monte Carlo
Hi Doug, Thanks for your reply. I was using 1.3 for visualization and 2 for simulation. So that's probably where it went wrong? When I set both thresholds to 2, significant clusters after Monte Carlo were also there before the simulation. Just to double-check: can the values associated with these significant clusters be different before and after Monte Carlo? For example, before Monte Carlo the value of the rostralmiddlefrontal was -4.42, after Monte Carlo it's -2.19. That's normal, right? Thanks again, Anita ___ 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] Significant clusters before and after Monte Carlo
Hi Doug, I mean that before doing any correction, I can press 'Find Clusters and Goto Max', which will show me clusters based on my visualisation threshold. As far as I understood, it will go to the most significant vertex within each cluster and display that value. So before Monte Carlo, I found a cluster in the RMF, and the most significant vertex in there was -4.42. After Monte Carlo, I again see a cluster in the RMF. Now, when I again press 'Find Clusters and Goto Max' it gives me a new value of -2.19. I guess I have a difficulty with interpreting these 'new values' after Monte Carlo. Do I understand correctly from your previous comment that after this correction, they don't correspond to single vertices anymore? If my question is too elaborate for this mailinglist, could you recomment me some literature that might help me? Thanks so much! Anita ___ 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] Significant clusters before and after Monte Carlo
Hi Doug, It is finally starting to make sense to me. It was indeed the case that before Monte Carlo, within a cluster there were different values for each vertex, and after Monte Carlo, each vertex had the same value. I had difficulty understanding the different functions of the color scale min/max threshold and the vertexwise threshold. Is the following correct: The min/max threshold is nothing more than a visualisation threshold; it does not change anything in subsequent analyses that are performed (such as Monte Carlo), it just decides which results are significant enough to be colored or opaque. The vertexwise threshold (the one that is next to Monte Carlo) is the one that decides which vertices should be considered in the simulation. So a vertexwise threshold of 2 only takes vertices into account that have a p value < 0.01. After Monte Carlo, the min/max (visualisation) threshold now decides which cluster wise p-values (cwp's) should be shown in color. So, compared to before Monte Carlo, it now has a slightly different function: it does not decide which individual vertices, but which clusters should be colored/opaque. One last question (if the above is correct): could one decide to set the vertex wise threshold at 1.3 for example, and the visualisation threshold at 2? Or do both threshold always have to be the same? Thanks a lot for your help, Anita ___ 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] Significant clusters before and after Monte Carlo
Great! Thank you! ___ 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.
