Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

Longitudinal analysis question
by Kairys, Anson 20 Jul '12

20 Jul '12

Hello FS experts, I am running a group up subjects pre/post treatment. When trying to do group analysis, after converting data with the mri_slope command, when I made the long table into a cross table, I noticed in qdec it averaged my "time" variable and only supplies a mean and there is no longer separate timepoints for subjects, just one value per subject. Do I need to define time as something more descriptive than 0 (tp1) and 1 (tp2)? I am so close to analyzing these data, just need a little help with the group analysis Thanks Anson ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

3 6

slice-by-slice predictors
by Caspar M. Schwiedrzik 19 Jul '12

19 Jul '12

Hi! Is it possible to have slice-by-slice predictors in Freesurfer, and if so, how? Thanks, Caspar

2 1

stats
by Oertel, Viola 19 Jul '12

19 Jul '12

Dear Doug, I have a question: when I create the stats tables, there are two tables: lh.aparc.a2005s.thickness.stats and lh.aparc.thickness.stats which one is the right one if I want to get the thickness values of the significant clusters from the main effect (pat. / controls)? Thanks and best regards, Viola

2 1

retroicor
by Caspar M. Schwiedrzik 19 Jul '12

19 Jul '12

Hi! Has someone used retroicor (retroactive correction of physiological noise; Glover at al. 2000) with Freesurfer? I would like to create nuisance regressors for EPI data based on cardiac and respiratory signals. The AFNI version of retroicor produces slice-based regressors, and I am not sure how to use them in Freesurfer. Suggestions for alternative implementations would also be appreciated. Thanks! Caspar

2 9

hippo_subfields questions
by Gabriel Gonzalez Escamilla 19 Jul '12

19 Jul '12

2 1

Automated sub-region segmentation - Amygdala
by Marc Rudolph 18 Jul '12

18 Jul '12

Good afternoon, I am new to freesurfer - is it possible to auto-segment the Amygdala into sub-regions? Thank you for your time, Marc

1 0

mni152.register.dat
by Garikoitz Lerma Usabiaga 18 Jul '12

18 Jul '12

Hi freesurfer experts, I want to use a volume based MNI152 ROI in Freesurfer, when I check it over fsaverage with the following command the ROI is not in the correct position...: tkmedit fsaverage T1.mgz -overlay ROI45.nii -overlay-reg $FREESURFER_HOME/average/mni152.register.dat And I have the same problem when I convert it to surface: cd $SUBJECTS_DIR/fsaverage/surf mri_vol2surf \ --mov ../../ROI2/ROI45.nii \ --reg $FREESURFER_HOME/average/mni152.register.dat \ --projdist-max 0 1 0.1 \ --interp nearest \ --hemi lh \ --out lh.fsaverage.ROI45.mgh \ --reshape - Is this a correct way of using it? Should I get proper results or I am missing anything? and, - Does it make sense creating a new fsaverage using the /spm8/canonical/avg152T1.nii, then applying the ROI which is already in 152 space, and referring the cortical thickness of all the subjects to this "new fsaverage"? (the functional analysis is being carried in SPM as well). Many thanks for your answers, Gari

2 4

Re: [Freesurfer] multiple comparisons correction
by Meng Li 18 Jul '12

18 Jul '12

Dear professor, Thanks for your reply. You said that when drawing conclusions from both hemispheres then I need to use .025, but I found that in qdec interface, the default value of -cwpvalue is 0.05. So are they inconsistent? I also want to find a solution about an ERROR. I tried to run a cortical thickness analysis to look for differences between two groups (patients and controls) with regressing out the gender factor, the patients group have 1 female and 17 male, after analysis, I got the results. But when I add another continuous variable as covariate, I received the message: "ERROR: matrix is ill-conditioned or badly scaled." Then I tried to change the gender composition the patients groups: 2 female/16 male, and the problem was solved. so is it right about what i did, or I need another way to solve this problem? Thanks, Best wishes Meng On 07/06/2012 10:00 PM, Meng Li wrote: > Hi, freesurfer expert, > I performed the statistical analysis between two groups first in left > hemisphere, and got some regions which showed different. > 1) so if I then do multiple correction, i don't need to run the > mri_glmfit-sim command, and just press the button of the monte carlo > null-z simulation in the qdec interface, am i right? correct > 2) Whether mri_glmfit-sim --cache command line and the mc-z in qdec > get the same results, or not? and as to the option --cwpvalthresh, > should i choose 0.05 or 0.025? If you are drawing conclusions from both hemispheres then you need to use .025 > 3) And what is the difference between fdr and mc-z correction? mc-z uses a cluster-wise correction and controls the rate of false positive clusters. FDR is voxel-wise and controls the false discovery rate, which is the number of false positives relative to the total number of positives (as compared to the number of false positives relative to the total number of tests). doug > Thanks, --

4 4

p-val from FDR
by Antonella Kis 18 Jul '12

18 Jul '12

Hi Doug, You mentioned that in my case when FDR found a voxel-wise threshold of 3.8 means p<1.5849e-04. How exactly I you got this p-val? How I can get myp-vals for clusters after FDR? Many thanks. Antonella

2 4

running trac-all -path missing files
by Rui Lavrador 18 Jul '12

18 Jul '12

Hi FS users, I'm running “trac-all –path ” and when running it, it constantly gives the output ERROR: Degenerate spline segment 58 81 24 56 69 24 … But it runs until the end without exiting and says that it ran without errors. It’s normal? Plus, it seems that it fails to create the output files. When looking at the created folder “…/Diff001/dpath” there is only one folder “5cpts”, so I cannot visualize the WM pathways, with freeview, that should be located, for example at “…/dpath/lh.ilf_AS_avg32_mni_flt/path.pd.nii.gz” Any suggestions? -- Rui Lavrador

2 1

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