Yes, it works now!
Thank you so much.
Have a great weekend,
Elissa
On Fri, Nov 13, 2015 at 12:40 PM, Martin Reuter wrote:
> Hi Elissa,
>
> this is the real error:
> SyntaxError: Missing parentheses in call to 'print'
>
> those scripts use the Python 2 print command and you are running them with
Can you run the following commands and tell me what happens?
cd /path/to/subject/surf
mris_calc -o lh.area.mid lh.area add lh.area.pial
On 11/12/15 11:39 AM, Nicole Zurcher wrote:
Hi Bruce/hi all,
Yes I am sure that I did not run out of disk space and I still get this
error message for mris_
Use foldind
On 11/12/15 12:06 PM, Eryilmaz, H. Hamdi wrote:
> Thanks Doug for the quick reply! Is there an option in aparcstats2table that
> allows to make a table with the folding index measure? If so, what variable
> should I use in the flag -meas?
>
> Best,
> Hamdi
>
>
>
hmmm, not sure. Can you send me your selxavg3-sess command and the
folder your ran it from and the $SUBJECTS_DIR ?
doug
On 11/13/15 4:16 PM, Afzal, Afsana wrote:
Hi,
I'm doing first level analysis in FSFAST and I'm consistently getting
the following error when running fast_selxavg3():
Savin
That does make sense Andrew. But would that be the case even if I weren't
correcting for ICV? In other words, the analysis works when I don't correct for
it. The GLM still looks for variance in group differences regardless if you're
correcting for something or not...right?
From: freesurfer-bo
Hi,
I'm doing first level analysis in FSFAST and I'm consistently getting the
following error when running fast_selxavg3():
Saving to
/autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz
SmoothOnly requested, so exiting now
Found 0 voxels with cor
I believe your issue is you are trying to do a between group analysis but you
only have 1 subject in group B. There is no way to estimate the variance in the
measure if there is only one subject in the group.
-Andrew
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Hirsch, G
Hi Elissa,
this is the real error:
SyntaxError: Missing parentheses in call to 'print'
those scripts use the Python 2 print command and you are running them
with Python 3.
In 3, print needs to be like
print("Hello world!")
in 2 it was simply
print "Hello world!"
so make sure you run them wit
Dear Freesurfer support,
I am very new to freesurfer and I thank you in advance for your assistance.
I have been trying to run the group analysis tutorial (qdec) and I have
encountered the following error messages. I was unable to generate the
stats data tables in the tutorial and received the fol
Hi Andrew, the values I'm using are already mean centered -- similarly, I've
never been able to use the full ICV values. Even with David's suggestion of
reducing the number of digits (effectively making the numbers smaller), it
still doesn't work...
Gabriella
From: freesurfer-boun...@nmr.mg
Try mean centering your ICV values (I.e. Subtract the mean value from each
individual value). This has worked for me to bypass this error.
-Andrew
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Hirsch, Gabriella"
mailto:gabriella_hir...@meei.harvard.edu>>
Reply-To:
"frees
Thanks for the suggestion David. I tried it but I still got the same error :/
Gabriella
From: David Vazquez [mailto:dvazq...@ucr.edu]
Sent: Friday, November 13, 2015 12:36 PM
To: Hirsch, Gabriella
Subject: Re: [Freesurfer] qdec analysis with ICV
Hi Gabriella.
I'm not an expert, but I've had th
In your log:
"- Launching hardi_mat -
Number of measurement points: 6
"
6 directions will not be enough for a hardi/Qball reconstruction. There
is something wrong with your selected gradient table. Which did you choose?
On 11/13/2015 10:16 AM, Alan Francis wrote:
Are your 83 regions set up in a single file with different indices for
each ROI? If so, you can run mri_segstats; the summary file will
indicate how many voxels are in each ROI.
On 11/13/15 11:45 AM, André Schmidt wrote:
Dear FS experts,
Using recon-all I defined 82 regions for a probabilisti
Dear FS experts,
Using recon-all I defined 82 regions for a probabilistic tractography analysis.
To address volume differences across regions, I like to normalize the obtained
streamlines by the number of voxels in each regions. Is there an easy way to
count voxels within each of my 82 regions?
Hi Freesurfer Experts,
I am hoping someone can help me solve this error I'm experiencing while
conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying
to analyze for volume differences using a demeaned ICV as a nuisance factor
(see attached fsgd file - note I changed the
Hi Daniel
do you mean the white and pial surfaces? You can certainly compute the
surface normals for them, or use mris_convert to do it:
mris_convert -n lh.white lh.white.normals.asc
will compute and write out the surface normals (using an outwards-pointing
convention) for the white surface t
Hi Bruce,
That was very quick! Yes, I do believe this is what I am looking for. Thank
you so much!
Best
Daniel
On Fri, Nov 13, 2015 at 4:53 PM, Bruce Fischl
wrote:
> Hi Daniel
>
> do you mean the white and pial surfaces? You can certainly compute the
> surface normals for them, or use mris_con
Hi,
I am looking for a way of figuring out the orientation vector of the
neurons within a voxel. That is, in which direction is the dipole of the
neurons pointing at. This could be possible to calculate if there is a way
of determining the position of the inner and outer layer for each voxel,
whic
Hi Ruopeng:
These brains have been run on Tracula and they look good. As a post
processing step, I wanted to look at the connectivity between the DACC and
anterior insula using DTK and Trackvis. Here is what I did:
1. I used the Imaging model HARDI/Q-Ball since these were acquired using
the HARDI
Hi Amanda,
there can always be individual outliers (in both the longitudinal and
even more so in the cross sectional stream). These can be causes by low
image quality or motion artifacts etc, or by failure of some steps in
the processing stream. That is why we recommend to do QC (e.g. check
s
Dear all,
when I run the recon-all -localGI command.
I encaunter the same problem as previous described by Meenal (see email
below).
It seems that the processing stops at the matlab command*make_roi_paths*.
Does anybody encaunter a similar problem and somehow solved it?
Thanks in advance.
Ge
Hello,
I am running TRACULA on one subject, I ran trac-all -prep without problem.
However, when I run trac-all -bedp, it is not successfully completed.
Although it says, all slices processed, it gives the error:
bedpostx_mgh: line 345: kill: (18735) - No such process
I am missing many outputs suc
Hi,
At the very beginning of the hippocampal subfields segmentation
the following message window popped up:
segmentSubjectT1_autoEstimateAlveusML cannot be opened
because of a problem.
Check with the developer to make sure
segmentSubjectT1_autoEstimateAlveusML works with this version
of Mac OS X.
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