[Freesurfer] repeated measures ANOVA with two groups

Hi, Is there a way to set up a repeated measures ANOVA and ANCOVA with two different groups (ex: study group v. controls) and each subject has more than two timepoints? Would it be possible to assign each Input in the fsgd file to two classes (ex: timepoint scan and group) or is there another way

Re: [Freesurfer] mri_segstats error

Hi, Doug and all, I wonder if the new version of mri_segstats on the ftp site will change both the ICV and the SupraTentorial volume? Nick seems to mention ICV will be different, the ReleaseNotes says the SupraTentorial Volume will be changed to smaller. Can you explain more on the difference of th

[Freesurfer] Surface statistics for PET

I would like to calculate average PET intensities for specific labels (using the aparc.annot label files). I have coregistered and used mri_vol2surf to assign PET values to the FS generated surface, and viewed the results using qsurfer. The next step is to take the values from the .w files an

Re: [Freesurfer] Tracula question

This probably means that bedpostx didn't process all the slices in your DWIs. Someone else reported something like that recently, not sure what may be causing it, but since it's independent of trac-all, I'd check on the FSL list archives. On Thu, 23 Aug 2012, Natalia Sánchez wrote: they a

[Freesurfer] Whole Brain Volume

Hello All, We are looking into alternative measures for whole brain volume to use for covarying, and the previous topic mentioned mris_volume as a possibility but it isn't located on the top of the aseg file. Has it been moved? Chris McCarthy ___ Frees

Re: [Freesurfer] Tracula question

Can you please check that the x-y-z dimensions of the bedpostx output files are the same as the dimensions of the DWIs? On Thu, 23 Aug 2012, Natalia Sánchez wrote: Thanks for your response!Attached are the requested files The error occurs here are shown on my terminal:  Loading b-values fr

Re: [Freesurfer] Tracula question

Hi Natalia - I'd need to see at which point in the processing the error occurs, since this is a very generic error message. Can you please include your trac-all.log and dmrirc? Thanks, a.y On Thu, 23 Aug 2012, Natalia Sánchez wrote: Hi Anastasia!I finally made tracula -prep work without er

[Freesurfer] REPOST: How to Convert QDEC clusters to standard MNI_152_T1 space

Hi,  I want to overal  my QDEC clusters on the connectivity maps in FSL  on the MNI ( this is the template I use for my connectivity maps). I am not sure how I can mention the label of my clusters, the uncorrected clusters. Should I use the sig.mgh as subject id, my clusters were obtained fro

[Freesurfer] creating a gca file from .mgz files

>From the gcaFormat freesurfer wiki page I know that: The .gca file is composed >of three volumes, which can be extracted like this:mri_convert atlas.gca -nth >0 means.mgz mri_convert atlas.gca -nth 1 labels.mgz mri_convert atlas.gca -nth 2 priors.mgzwhere:means --> the mean intensity of the mo

Re: [Freesurfer] creating labels, new atlas

I found this info on the tksurfer webpage. The label file format is interchangable with TkMedit. You can create a label in TkSurfer, save it, and load it in TkMedit, or vice versa. Jeff Thompson From: jeff_rthomp...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: creating labels, n

[Freesurfer] qdec generate stats data tables

I am trying to use the "generate stats data tables" feature in qdec but am getting the error message below. So based on the error message I know that the trouble subject is SZ0020 and I looked in his file and found the attached aseg.stats file, which looks okay. I reven tried rerunning the segstats

[Freesurfer] resending question about 3rd level analysis

Hi, I'm resending this e-mail, as it didn't seem to go through correctly yesterday: I’m a Freesurfer novice, and I’m confused about how to run a 3rd level cross-subject analysis on the surface using as input cross-run .gfeats from 10 subjects generated from a 2nd level analysis in FSL. Followi

[Freesurfer] How to Convert QDEC clusters to standard MNI_152_T1 space

Hi Doug, Many thanks for your help. Can you please take a look and see if this is the correct way to do it. I want to overal in fact my QDEC clusters on the connectivity maps in FSL but I got them by registering on the MNI 152 so I suppose I can just transform or move my QDEC clusters on t

[Freesurfer] FDR Correction of NHP Surface Data

Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monk

[Freesurfer] creating labels, new atlas

Hello, How can tksurfer be used to create label files for the purpose of making a new atlas, if that atlas is needed to create the surface files needed to view the brain in tksurfer? Would people use FSL to create the masks, and convert them into what is needed for freesurfer or is there anothe