Dear Freesurfer Mailing list,
I have been attempting to run the following command in freesurfer v5.3.0:
mri_glmfit --y site-gender-group-prothaplotype.thick.lh.10.mgh --fsgd
site-gender-group-prothaplotype.fsgd dods --C me_site-BrisVsMelb.mtx --C
me_site-BrisVsPer.mtx --C me_site-MelbVsPer.mtx
It says that C has only one column. Make sure that you created the C
matrix as a simple text file. Don't create it on Windows or with a word
processor. An easy way to create it is
echo 1 -1 > con.mtx
doug
On 11/26/14 9:44 PM, Xinfa Shi wrote:
Hi everyone,
I get this error when running grou
Hi everyone,
I get this error when running group analysis of cortical thickness by
command-line:
xin-fa@xinfa--PC:/media/E/FREESURFER/VisualData$ mri_glmfit --y
lh.group_differ.thickness.10.mgh --fsgd group_differ.fsgd dods --C con.mtx
--surf fsaverage lh --cortex --glmdir lh.group_differ.glmdir
It looks like there is something wrong with that label file (there
should not be 1.7 million lines). Check to see whether the first couple
of lines look similar to the other labels. it might be that mergelabels
is not quite doing the right thing.
doug
On 11/26/14 11:38 AM, Anna Jonsson wro
It is there again. I don't know what the status if it is in terms of
the version. Try it and let me know
doug
On 11/25/14 4:34 PM, Morgan Hough wrote:
Hi Doug,
Could you put the epidewarp.fsl script back on your ftp site? I don’t
see it at the link in the archives:
ftp://surfer.nmr.mgh.h
Specify the cluster-wise p-value to be 1 (ie, --cwpvalthresh 1)
doug
On 11/26/14 2:05 AM, Jürgen Hänggi wrote:
Dear FS experts
We would like to force FS's mri_glmfit-sim function of FS 5.3.0 to
report all results and not only the significant results.
This was the behavior of this function
Through the file drop at the end of this email. But you might want to
wait until next week as I will be out of the office until Dec 4.
doug
On 11/26/14 12:50 AM, Bronwyn Overs wrote:
Hi Douglas,
How exactly should I upload the glmdir?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscie
Thanks Douglas, I will upload it then.
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.ed
You can use mri_segstats with the annotation (--annot) and the cluster
sig map as a mask (--mask , --maskthresh, --masksign), use the --y input
to mri_glmfit as the input (--i) to mri_segstats, and specify --avgwf
roiaverages.txt --sum roi.sum.txt
roi.sum.txt will have the list of parcellati
Hi, Could you use a colormap for your aseg? It is really hard to see the
different ROIs on a grayscale image.
Thanks, Lilla
On Wed, 26 Nov 2014, Octavian Lie wrote:
Dear Lilla,
Here is a snapshot of the aseg volume, which rescues some gray matter not
included in the pia. I am not sure if t
Hi Octavian,
If you have an OK aseg volume, you could try to fit a
surface over it using mris_make_surfaces with the -cover_seg flag.
Lilla
On Tue, 25 Nov 2014, Bruce Fischl wrote:
>
>
> -- Forwarded message --
> Date: Tue, 25 Nov 2014 08:05:55 -0600
> From: Octavian Lie
> R
hi the full error message is
reading input surface /XX/surf/lh.pial...
reading input pial surface /XX/surf/lh.pial...
reading input white surface //X/surf/lh.white...
mris_anatomical_stats: could not parse 1697283th line '60529 -5.365 -17'
in label file
subj: could not rea
Thank you for clarifying this.
Mihaela
On Tue, Nov 25, 2014 at 11:16 PM, Bruce Fischl
wrote:
> No, I don't think so
> Bruce
>
>
>
> On Nov 25, 2014, at 11:05 PM, Mihaela Stefan
> wrote:
>
> Hi Bruce,
>
> I've heard people saying that FS 5.3 is focusing on better output for
> cortical thickness
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