Dear FreeSurfer,
I am comparing two groups of my subjects together in qdec and when I want
to visualize each subject, I can see two different regions for inferior
parietal lobe and supramarginal gyrus. But in the normal pial surface, it
seems like that the labels of both overlap with each other.
Hello doug,
Should I add --label-src in addition to --label-trg or should I replace the
latter with the former? Thanks. Also, Just to conform, I should run
mri_glmfit-sim after mri_mcsim.
Best,
Paul
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From: Douglas N Greve
Sent:
The FreeSurfer group is offering a four-day FreeSurfer Tutorial and
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Charlestown, MA. You can register for the course on our course website:
https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription
Details about the content of
1. It is not a problem that some of the demeaned ICV values are
negative; this is what happens when you demean a set of numbers; you
must leave the negative numbers there. Are you doing a paired analysis
or do you just have two groups? I don't think you can do a paired
analysis in QDEC.
2.
Can you send me the aparc.annot.ctab and label files?
On 08/03/2016 12:25 PM, Caroline Beelen wrote:
> My command line is:
> mris_label2annot --subject fsaverage --hemi lh --ctab aparc.annot.ctab
> --annot myaparc --l lh.fusiform.label
>--l lh.inferiorparietal.label (etc.) --nhits
Great, will do that - thank you very much for your help!
Psychiatric Services University of Bern (UPD)
University Hospital of Psychiatry
Division of Systems Neuroscience of Psychopathology
Translational Research Center
Dr. Martina Papmeyer, Postdoctoral Fellow
Bolligenstr. 111, CH-3000 Bern 60
There are several things that need to be changed as I've indicated below
On 08/01/2016 10:09 PM, miracle ozzoude wrote:
> Thanks doug. Also, Please can you verify if this are the right codes
> for performing ROI surface based analysis using the command line. I
> tried to reverse the whole brain
Please remember to include previous correspondence in your email.
On 08/01/2016 04:22 AM, 連 志浩 wrote:
>
> Dear Douglas,
>
> Thanks for your explanation. These information are helpful to me.
>
> >I'm not sure what you mean. How can it be a delay if it is after
> thetrial is over?
>
> I’m sorry
We don't have a spearman analysis in FS. You can load the data into
matlab and do it, something like
ymri = MRIread('yourdata.mgh');
y = fast_vol2mat(ymri);
% y is now a matrix that is nsubjects by nvertices
% Do spearman analysis on each vertex
sp = yourspearman(y,X); % sp should be a
Dear all,
I'm running into the following error when running "recon-all -s
-lgi" using the latest version of FreeSurfer and Matlab R2016a:
ERROR: make_roi_paths did not complete successfully!
It seems like this is a common issue when using more recent versions of
Matlab, so I editted the
Dear FS experts
I would like to examine associations between cortical thickness and sum scores
of a scale (ordinal scale). Accordingly, I would need to conduct Spearman
rather than Pearson correlation analyses. I found the following post to this
email list, indicating that the GLM model in FS
Hi Freesurfer (FS) users,
I am a new user in the world of FS and I am trying to normalize rsfMRI EPI
series to CVS MNI space. I would like to do it without resampling the EPI
images to 1*1*1mm3 resolution.
I've registered EPI series to FS T1 space by using following command (after
bbregister),
Dear users,
Many of you have recently experienced problems with the hippocampal subfield
and brainstem substructure segmentation modules. These modules have been broken
in the dev version for a couple of weeks. All the problems have now been fixed
internally. The updates will be incorporated
Dear Freesurfers and TRACULA experts,
Thank you for your help so far. I am trying to map the endpoints of the
tract probability distributions onto the cortical surface (as mentioned
in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos).
I've somehow gathered that I need to do this (example
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