[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

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.

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

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

[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

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

[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

[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 ___

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

[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

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] 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

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

[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

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

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.

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

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

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

[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

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

[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

[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