[Freesurfer] fsPALM - Path Issue?

2019-09-19 Thread Harikumar, Amritha
Hello,

I had emailed the Freesurfer Forum a few weeks back about trying the PALM 
analysis for permutation testing. I recently tried fsPalm again on running some 
of our subcortical analyses for the caudate, putamen, and nucleus accumbens, 
and we performed the following steps:


  *   Set our respective ROIs (e.g. caudate, putamen, nucleus accumbens)
  *   Set the paths for fsPalm to run for each of the ROIs
  *   Ran mri_glmfit as noted in the Freesurfer Help documentation for fsPalm 
for the three ROIs

We ran into several issues. When we looked in the ‘run_palm.m’ output file 
under the subfolder for our first ROI that we tried to run PALM analysis for, 
it mentions ‘error in run_palm: zthresh = fast_p2z(pthresh)'. We are not sure 
where this function fast_p2z is supposed to be called from, as it is not 
located in any of the Matlab scripts when downloading the package for fsPalm 
(e.g. the palm-alpha115 file from Freesurfer). My question is - are we missing 
a path, or several paths that we have to put into the Matlab script, or does 
fsPalm no longer work for running such analyses? fsPalm has worked in the past 
for one of my colleagues using the palm-alpha112 file, but we are now having 
trouble running this using the palm-alpha115 file version. Any help would be 
greatly appreciated.

Thanks,
Amritha


Amritha Harikumar
Clinical Research Coordinator
Holt Emotion and Social Neuroscience Lab
Department of Psychiatric Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
___
149 13th Street, Rm 2620A
Charlestown, MA 02129
Phone: 617-724-3283



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[Freesurfer] PALM Analysis

2019-09-04 Thread Harikumar, Amritha
Hello,

Thanks for letting me know regarding running fsPalm in your previous message. 
My next question is - what command can we use in Freesurfer that can run 
multiple comparison testing for subcortical regions? If not fsPalm, is there 
another function that will perform this?

Thanks,
Amritha


Amritha Harikumar
Clinical Research Coordinator
Holt Emotion and Social Neuroscience Lab
Department of Psychiatric Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
___
149 13th Street, Rm 2620A
Charlestown, MA 02129
Phone: 617-724-3283



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> Today's Topics:
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>   1. OHBM International Mentoring Programme Sign-up   {Disarmed}
>  (Meena M. Makary)
>   2. PALM Analysis (Harikumar, Amritha)
>   3. Re: PALM Analysis (Greve, Douglas N.,Ph.D.)
>   4. Discrepancy between thresholded surface and cluster  labels
>  (Bronwyn Overs)
>   5. Reconall with no-MPRAGE T1w image? (Rovai Antonin)
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[Freesurfer] PALM Analysis

2019-09-02 Thread Harikumar, Amritha
Hi there,

I am trying to run a Permutation Analysis of Linear Models (PALM) for analyzing 
subcortical areas in the nucleus accumbens, caudate, and putamen. Upon trying 
to run the script after reading the Freesurfer wiki, I am not sure what it is 
referring to regarding applying fsPalm in MATLAB. My questions are - do we a.) 
copy paste the existing fspalm command in Matlab and run it after setting the 
two Freesurfer paths listed in the wiki, or what is the correct procedure to 
run it? I tried running it in terminal as well, but didn’t have any luck. My 
existing Matlab script has set up the two Freesurfer paths, and is trying to 
run the fsPalm command for each subcortical area of the three ROIs mentioned 
above, but that isn’t working either. Any help in running fsPalm would be 
greatly appreciated!

Thanks,
Amritha 

Amritha Harikumar
Clinical Research Coordinator
Holt Emotion and Social Neuroscience Lab
Department of Psychiatric Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
___
149 13th Street, Rm 2620A
Charlestown, MA 02129
Phone: 617-724-3283




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