[Freesurfer] autorecon1 with skull stripped image

External Email - Use Caution Dear Free Surfer's team, I have a doubt. I have a sample of patients in which I already have done the skull stripping using specific options with bet, so the skull stripping has been successful. I wonder if I could feed autorecon1 with the skull

[Freesurfer] Ask for your help about freesurfer submillimeter reconstruction!

External Email - Use Caution Dear FreeSurfer Developers, I am now working on the analysis of MRI images with the voxel resolution less than 0.2mm3. I read your webpage about submillimeter reconstruction,

Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

You cannot use QDEC for this. You must use the "command line" stream, ie, create your FSGD file, run mris_preproc, smooth, run mri_glmfit, then mri_glmfit-sim. See the tutorial on the wiki. On 10/17/2018 01:30 PM, Azeez, Azeezat wrote: > > External Email - Use Caution > > Hello, > > I

[Freesurfer] QDEC analysis with more that 2 fixed factors

External Email - Use Caution Hello, I would like to know how I can run statistical analysis in QDEC on a data set where there are 3 fixed factors each with 2 contrast levels. (DEVELOPMENT : old vs young, SEX: male vs female, DIAGNOSE: Control Vs disease ) Any help would be much

Re: [Freesurfer] Longitudinal stream : LME and limits of model

External Email - Use Caution Hi Martin, Thanks for your answer. I actually compare neurospychological scores at baseline between drop-out subjects and subjects with full time-points. If I ever find that drop-out subjects are more severely affected than the subjects with full

Re: [Freesurfer] Adding longitudinal time points to clean dataset {Disarmed}

Hi Molly, no one can really tell you that. My feeling is, that it is pretty safe, given that you have already 4 time points in the base. The base will be very stable and the main reason for the base is that it is an independent space different from any single time point. Which remains true.

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Hi Matthieu, 1) survival analysis is typically used if you want to detect if the time to an event is longer in one group vs the other (e.g. one group gets placebo the other drug and we want to know if recurrence is later in the drug group). Not sure this is what you need. The nice thing is, it

Re: [Freesurfer] Raw Data for Clusters

try mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.ocn.mgh --avgwf mc-z.abs.th13.cluster.ocn.dat --excludeid 0 On 10/17/2018 12:57 AM, WON JONG CHWA wrote: > > External Email - Use Caution > > Dear FreeSurfer Experts, > I am running Qdec 1.4 and I want to extract raw data (in this case,

Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

Hi Amanda what is your command line? And is there any reason you can't convert it back to binary and load it that way if ascii fails? cheers Bruce On Wed, 17 Oct 2018, Worker, Amanda wrote: External Email - Use Caution Hi Bruce, I have the same issue in freeview. The

Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

External Email - Use Caution Hi Bruce, I have the same issue in freeview. The error is: ERROR: could not determine type of /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc mri_read(): couldn't determine type of file

[Freesurfer] license format error

External Email - Use Caution Dear FreeSurfer Developers, I have a installed freesurfer (6.0.0-centos6_x86_64) on 2 of our linux servers. One the first server: platform: ubuntu 16.04 uname -a: Linux fermi 4.4.0-133-generic #159-Ubuntu SMP Fri Aug 10 07:31:43 UTC 2018 x86_64