[Freesurfer] Welch's t-test for HOV violation

2019-03-11 Thread Hannah CK
External Email - Use Caution We are conducting t-test comparisons across groups in which there is a large discrepancy in group sizes. HOV is violated. I've searched for ways to run Welch's t-test in FreeSurfer (or a similar analysis that does not assume homogeneity of variance) but

Re: [Freesurfer] Welch's t-test for HOV violation

2019-03-11 Thread Greve, Douglas N.,Ph.D.
I used to have this about 20 years ago, but I stopped supporting it when it did not fit cleanly into the GLM ... The shortest route is probably to do two separate analyses with mri_glmfit, one for each group. This will output means and variances for each group. Then use fscalc to compute maps o

[Freesurfer] Changing Thresholds in dmri_pathstats: --pthr option not changing results

2019-03-11 Thread Adam Schadler
External Email - Use Caution Dear freesurfer community, I have been trying to experiment a bit with the dmri_pathstats command that TRACULA uses to compute tract statistics. I read previously that one could change the default threshold value that stats are computed with by using

[Freesurfer] Trouble updating free surfer

2019-03-11 Thread Shana Adise
External Email - Use Caution Hello, I originally ran into some hiccups with AFNI’s @SUMA_make_spec_FS, which stems from a freesurfer error: 1. Error one: Abort dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/

[Freesurfer] Error with FSGD format

2019-03-11 Thread Jennifer Legault
External Email - Use Caution Hi Freesurfer experts, I am trying to run the mris_preproc command, however I keep getting the following error: ERROR: format for not recognized. Even when I create files in linux (using vi), TextEdit, or Notepad, and make sure that there are no extr

Re: [Freesurfer] Trouble updating free surfer

2019-03-11 Thread Shana Adise
External Email - Use Caution Of note, I forgot to add that disabling SIP does not fix the problem: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ On Mar 11, 2019, at 5:29 PM, Shana Adise mailto:shana.ad...@uvm.edu>> wrote: Exter

Re: [Freesurfer] Error with FSGD format

2019-03-11 Thread Greve, Douglas N.,Ph.D.
Can you send your command line and full terminal output? On 3/11/19 6:03 PM, Jennifer Legault wrote: External Email - Use Caution Hi Freesurfer experts, I am trying to run the mris_preproc command, however I keep getting the following error: ERROR: format for not recognized. Even whe