Hi Lily - No, you should search for dmri_pathstats in the log file
(scripts/trac-all.log) and follow the syntax for the command that you'll see
there. Only change the threshold, and potentially the output file, if you don't
want to overwrite the existing one.
a.y
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Hello Liam,
Have you tried following the “Setup Instructions”
under, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall. ?
For the 6.0.0 release:
If you are on the Mac, running the .pkg installer should give you the
distribution under /Appli
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Hi there,
I have been trying to learn and set-up Freesurfer for a research project I
am working on, but I am having trouble with the set-up/installation process.
Once Freesurfer is set-up, I will be using it to measure hippocampal
volumes post-ablatio
Hi Ricky
how did you try to load the defect_labels? The end of the recon-all.log
file lists a defect with 26K vertices, which is probably too big to fix
(it's about 1/5 of a normal surface). You should be able to visualize it
by loading the lh.defect_labels file as an overlay on the
lh.inflat
Hi Doug
Thanks for your reply.
Yes, I did.
I run the command from the folder where my analysis which I call loom.lh is
located.
selxavg3-sess -s $subj -d ../all_subjects -analysis loom.lh -force
On Mar 13, 2020, at 6:41 PM, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
Did you pass
Can you say more about how the 10mm, th 1.3 is different than the others?
On 3/11/2020 2:48 PM, Purcell, Juliann wrote:
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Hi FreeSurfer Experts,
I am running permutation simulations with several smoothing levels and
cluster forming thresholds to evaluate th
Are you asking how to do subcortical analysis or are you asking how to
account for subcortical analysis during correction for multiple
corrections? For the latter, use --3spaces
On 3/12/2020 2:03 PM, Hengameh Marzbani wrote:
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thank you for your detailed an
can you send the command line and terminal output?
On 3/12/2020 3:07 PM, Renew Andrade wrote:
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>
> Dear FreeSurfer experts:
> I cannot fix the problem that I mention in the subject. I put the output of
> the terminal below. I was doing functional connectivit
Did you pass it an analysis? There is not one in that command line
On 3/12/2020 11:28 AM, Nasiriavanaki, Zahra wrote:
Hi Freesurferers
I am trying to run selxavg3-sess for a single subject (3T fMRI data).
Oddly, the terminal output shows that it doesn't need updating for
preprocessing and en
It looks like you are using gender as a continuous variable. You should
set up two classes, one for male one for female. You can then test for
the AT slope with a contrast of
0 0 0 0 0.5 0.5
you don't need separate pos and neg contrasts
For mri_glmfit-sim, a threshold of 1.3 (p<.05) is way too
are you looking at
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
?
did you download the patch?
On 3/11/2020 8:19 PM, Edith Botchway wrote:
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Hi,
I’m new to FreeSurfer and working my way through the tutorial on
cluster co
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Also, when I run the lme_mass_fit_EMinit, lme_mass_RgGrow, lme_mass_fit_Rgw,
I get a warning: Matrix is close to singular or badle scaled. Results may be
inaccurate. RCOND=3e-21/ In
parallel_function>make_general_channel/channel_general (line 914)
Hi,
I am trying to get voxel by voxel stats for fmajor on a threshold that's not
the 0.2 default because when I looked at merged nii, fmajor is constructed
correctly but on a different threshold. This is the command I used:
dmri_pathstats --intrk fmajor_PP_avg33_mni_bbr/path.pd.trk --dtbase
..
Hi Bo
looks like you are running out of memory, no?
cheers
Bruce
On Fri, 13 Mar 2020, ZhangBo
wrote:
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Hi team,
I encountered an error when running the test "Candal" dataset.
For some patients' files, I found the error information in the log file.
Hi Fraser
if you look at the mris_register help there is an option to specify a
manual label that corresponds to an atlas parcel:
-L
Specify a manual label to align with atlas label
in the past I have used this to draw a central sulcus and force it to align
using the
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Hi there
I have a clear parcellation error with one participant who does look to
have an atypical structure around the right post-central gyrus (looks split
in two).
Both the pre and post central gyri are shifted significantly backwards –
but only for
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