And, a minor clarification on one of the ROIs in question--
I should have phrase the comment about ROI #80 as follows:
80 non-WM-hypointensities ---> *should be in list of FS_nongm?
... since the name clearly implies that it is non-WM.
Basically, I am first wanting to check that the ab
Hi again Eugenio,
Sorry for the picky follow-up question regarding the longitudinal hippocampal
subfields processing, but do you suggest that when the official version 6 comes
out, we rerun everything (including the standard FS long processing) or would
it be ok to just rerun the hippocampal
Dear Christian,
Both options are OK, as long as you report on your paper how you obtained your
results. Rerunning everything with 6.0 has the advantage that the results are
easier to reproduce but, if you’ve already QCed large amounts of data processed
with 5.3, not rerunning in understandable a
Hi Bruce,
Thanks for your answer.
What do you think would be better, run recon-all on the original data (with
lesions) then edit the aseg for the juxtacortical lesions or use a lesion
filling on the T1 and then run recon-all on it.
Thanks again.
Cheers,
Ismail
PhD candidate
Neurocentre Magendie
the former I think, but it's an empirical question
Bruce
On Mon, 12 Dec 2016, Ismail Koubiyr wrote:
> Hi Bruce,
> Thanks for your answer.
> What do you think would be better, run recon-all on the original data (with
> lesions) then edit the aseg for the juxtacortical lesions or use a lesion
> fill
Would you please give me the reasons why the former would be better ?
Ismail
PhD candidate
Neurocentre Magendie, INSERM
Bordeaux, France
2016-12-12 15:47 GMT+01:00 Bruce Fischl :
> the former I think, but it's an empirical question
> Bruce
> On Mon, 12 Dec 2016, Ismail Koubiyr wrote:
>
> > Hi
Hi Bruce,
We re-ran these subjects using recon-all -all -autorecon2-cp -aurorecon3
-subjid freesurferfolder.
We got no output files from that, but I'm wondering if freesurfer didn't run
only because we incorrectly ran this command with the '-all', or do you think
there was some other reason? We
because filling in the T1 may cause artifacts
On Mon, 12 Dec 2016, Ismail
Koubiyr wrote:
Would you please give me the reasons why the former would be better ?
Ismail
PhD candidate
Neurocentre Magendie, INSERM
Bordeaux, France
2016-12-12 15:47 GMT+01:00 Bruce Fischl :
the former I thin
Hi Batool
you don't need -all and -autorecon2-cp -aurorecon3 (-all is both of those
and more). It must have generated some output. Is there a recon-all.log in
the freesurferfolder/scripts dir?
cheers
Bruce
On Mon, 12 Dec 2016,
Rizvi, Batool wrote:
>
> Hi Bruce,
> We re-ran these subjects usi
Hi Bruce,
I noticed I did it incorrectly, so I started running an hour ago just recon-all
-autorecon2-cp -autorecon2 without the -all, about an hour ago. It's starting
to generate output now, not sure why it didn't at all last time (may have to do
with our new cluster). Will let you know if anyt
Alright, thanks a lot for your help Bruce.
Best,
Ismail
PhD candidate
Neurocentre Magendie, INSERM
Bordeaux, France
2016-12-12 17:33 GMT+01:00 Bruce Fischl :
> because filling in the T1 may cause artifacts
>
> On Mon, 12 Dec 2016, Ismail Koubiyr wrote:
>
> Would you please give me the reasons
Hi Doug et al,
I would like to get a different cluster summary stat out of mri_glmfit-sim.
Rather than size, I'd like to use the "sum of t-scores" (after Maris &
Oostenwald 2007, for example). That is, set a cluster inclusion threshold,
and then for each cluster of adjacent vertices that clear the
Hi Doug,
Thank you for your note and my apologies for a delayed response. To create the
sig.mgh file we used a volume specific mri_glmfit analysis, omitting the --surf
flag and using our volume specific input (ces.nii.gz in
SIRP_LoadRegression_Stable5.3_012616_sm5_mni305). I don't know if this
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