Re: [Freesurfer] PALM Analysis

[Greve, Douglas N.,Ph.D.]

Sorry, fsplam is only for surfaces.

On 9/2/2019 7:46 PM, Harikumar, Amritha wrote:
> 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
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] PALM Analysis

[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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[Freesurfer] OHBM International Mentoring Programme Sign-up {Disarmed} {Disarmed}

[Meena M. Makary]

External Email - Use Caution

Hi all,

Between September 1st and September 31st 2019, registration for the fourth
round of the Online International Mentoring Programme organized and
coordinated by the OHBM Student and Postdoc Special Interest Group

will take place. In the programme, every OHBM member can become an (online)
mentor or a mentee to another OHBM member(s) for a period of approximately
one year (October-June). During this time, the mentor can support the
mentee to grow in academia by providing advice on topics such as—but not
limited to—personal development, grant writing, and work-life balance. In
response to the feedback from previous participants and the increased
interest of mentees in industry, we have also invited a number of mentors
from industry to join us for this new round.

If you are interested in being a mentor and/or mentee, please fill out this
short registration form

and
you will be contacted with further details.

If you participated in any of the previous rounds and would like to further
take part in the programme, you have two possible ways (It is possible to
choose both options):

   1. If you would like to continue being paired with your current
   mentors/mentees, please first discuss this with your mentoring partner. In
   this case, please do not re-subscribe for the programme and please delegate
   the mentee to fill in this feedback form
   

for us.
   2. If you would like to apply for new mentors/mentees, you will be able
   to do so using the registration link above.

Please feel free to forward this message to your colleagues. Please also
forward this email to former researchers working in industry, if you know
any, as we are still looking for more industry representatives to join the
programme as mentors this year.

We would like to thank all the OHBM mentors and mentees who participated in
the previous three rounds of the programme! The third round of the
programme is now ending. We hope that most of you had an opportunity to
meet in person during the OHBM Annual Meeting in Rome. If you have feedback
for us, please contact us at ohbmtrain...@gmail.com
.
Please share any comments which might help to further improve our
programme!


To find out more about the programme, please visit the OHBM Student and
Postdoc SIG website

and check our previous publication
.
If you have any questions about the programme, please contact us at
ohbmtrain...@gmail.com

.


We hope to welcome you in the programme very soon!

Best regards,
—
*Meena M. Makary, Ph.D.*
Assistant Professor | Cairo University 
Postdoctoral Fellow | Radiology, Harvard Medical School

Postdoctoral Fellow | Athinoula A. Martinos Center, MGH

Career Development and Mentoring Manager | OHBM Student and Postdoc SIG

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[Freesurfer] Compare vertexwise correlation maps

[Matthieu VANHOUTTE]

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Dear experts,

I would like now to determine if there is statistically difference 
between vertexwise correlation maps (whether one is statistically 
"stronger" than the other). Would there be a way to do this with 
Freesurfer? (r-to-z Fisher transformation and statistical method?)

Best regards,

Matthieu

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[Freesurfer] Two questions about flac_desmat.m for retinotopy analysis in fsfast

[Caspar M. Schwiedrzik]

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Hi Doug,
I have two quick questions about the analysis of polar angle maps:
1. Does the analysis take the HRF (lag etc.) into account?
2. Our stimulation starts at 12 for clockwise and counter clockwise. I
found this older post
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-August/025241.html
specifying changes to flac_desmat.m to account for that. I was wondering
whether to change case {'fourier'} and/or case {'abret'}?

This is using version 5.3.
Thank you!
Caspar
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