Hello,
We have been trying to analyze some longitudinal structural data using the
FreeSurfer Mixed Effects Model toolbox and have been running into some
issues.
We have 2-3 timepoints per individual imaged across adolescence and 3
groups of interest. We set up a design matrix to examine potential
Hey Bruce et al, any update on this?
Thanks,
Jared
> On Apr 28, 2017, at 2:48 PM, Jared P Zimmerman
> wrote:
>
> Here’s the script that I’m running and the merged stderr stdout. I’ve also
> tried various permutations of mris_sample_parc using the -t flag and using
> different LUTs than the
The spatiotemporal lme model is more advanced than the traditional vertex-wise
lme but it's also more difficult to setup with the current scripts.
So I'd suggest you simply use the easier traditional vertex-wise lme:1-Read
your label eg.:
lhcortex =
fs_read_label('freesurfer/subjects/fsaverage
Hi Knut
where is it being filled? If it is the occipital horn we may soon have a
patch for it
cheers
Bruce
On Thu, 4 May 2017, Knut J Bjuland wrote:
Hi
Are there any options that I can use in Freesurfer 6.0 that can prevent lef
t lateral ventricle from being filled with WM? Should I send th
Hi Shane
if you upload this subject I will take a look
cheers
Bruce
On Thu, 4 May 2017, Shane
Schofield wrote:
Hi,
In my dataset, the lateral ventricles are filled in the wm.mgz (picture).
However the aseg.mgz shows that these voxels were correctly classified as
lateral ventricles. In anot
Hi Jared
it looks like it couldn't find the lookup tbale:
reading input surface
/data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white...
could not open translation file
/share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt
cheers
Bruce
On Thu,
4 May 2017, Jared P
Zimmerman
can you try it with -ct
and send us the output if that doesn't work? That's what we use
internally
cheers
Bruce
On Thu, 4 May 2017, Jared P
Zimmerman wrote:
Yeah I see that, but the cma_parcellation_colors.txt isn’t distributed with FS
5.3, yet it is the default LUT called by mris_sample_
That’s what I did below, see the script and log.txt attached to a previous
email. This is the output from the mris_sample_parc step
> reading parcellation volume from
> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/s111_bla_8mm_orig2.nii.gz...
> reading input surface
>
fwiw, this problem persists in FS6.0
-jared
> On May 4, 2017, at 12:11 PM, Jared P Zimmerman
> wrote:
>
> That’s what I did below, see the script and log.txt attached to a previous
> email. This is the output from the mris_sample_parc step
>
>> reading parcellation volume from
>>
sorry, I don't see the mris_sample_parc command line. Can you just send
it and the entire screen output?
On Thu, 4 May 2017, Jared P Zimmerman
wrote:
That’s what I did below, see the script and log.txt attached to a previous
email. This is the output from the mris_sample_parc step
reading
mris_sample_parc ${sub} \
lh ${targ}.nii.gz \
${targ}_fs6_annot.annot \
-ct ${SUBJECTS_DIR}/${sub}/bla_test_table.txt
This is the call from my script, which didn’t get written to stdout. The
bla_test_table.txt exists, and is just a space delimited file with “index name
I see. This is the problem - mris_sample_parc is one of the binaries that
requires all options come before the mandatory arguments. Move the -ct
part to the beginning and it should work
cheers
Bruce
On Thu, 4 May 2017, Jared P
Zimmerman wrote:
mris_sample_parc ${sub} \
lh ${targ}.n
Hello FreeSurfer community,
I am having an issue with the icon graphics displaying properly in freeview
(Linux virtual machine - Ubuntu). I receive the following warning when opening
the application:
"libpng warning: Application built with libpng-1.2.7 but running with 1.6.25"
The newer versi
Thanks Bruce, this did it.
-jared
> On May 4, 2017, at 12:33 PM, Bruce Fischl wrote:
>
> I see. This is the problem - mris_sample_parc is one of the binaries that
> requires all options come before the mandatory arguments. Move the -ct
> part to the beginning and it should work
>
> cheers
Freesurfer experts,
QDEC won't allow me to type any information in on the subjects of Display
page--i.e. in the FDR rate box, or in either threshold box. I found some emails
regarding this from 2013, but no information that helps vis a vis the newest
version.
Is there a reason this is happen
Dear Freesurfer list,
We have been using Freeview's "transform volume" functionality to do AC-PC
alignment on some of our T1 scans before processing with recon-all. We had
previously been using SPM, but wanted to move to an entirely free method rather
than relying on MATLAB. It turns out that
The cutoff is only on screen visually for faster interaction. When you save the
transformed volume, it should be complete.
Best,
Ruopeng
> On May 4, 2017, at 5:28 PM, Hamilton, Liberty
> wrote:
>
> Dear Freesurfer list,
>
> We have been using Freeview's "transform volume" functionality to do
Does freeview still run? If it does, you can just ignore the warning.
Best,
Ruopeng
> On May 4, 2017, at 12:39 PM, Kanoff, Kristen Elise
> wrote:
>
> Hello FreeSurfer community,
>
> I am having an issue with the icon graphics displaying properly in freeview
> (Linux virtual machine – Ubuntu
Hi all,
We also have the same issue, any idea/suggestion?
Thanks.
Yann
> On 27 Apr 2017, at 9:43 am, Bronwyn Overs wrote:
>
> Hi Mailing List,
>
> Still trying to solve the below medial surface problem. Does anyone have any
> ideas?
> Kind regards,
> Bronwyn Overs
> Research Assistant
>
>
if someone can upload a dataset as well as the exact coordinates of the
problem I'll take a look
cheers
Bruce
On Fri, 5 May 2017, Yann Quidé wrote:
Hi all,
We also have the same issue, any idea/suggestion?
Thanks.
Yann
On 27 Apr 2017, at 9:43 am, Bronwyn Overs
wrote:
Hi Mail
It didn't crash. I got the following line in the terminal window:
Invalid argument
WARNING: 319 NaNs found in subjid.map.mgh
When the NaNs were common in all the subjects, mri_glmfit did not end
successfully. After I omitted the common NaN values, there were still a few
subjects with NaN values
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