Hi,
I am trying to run trac-all using
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
If I set up the configuration file with just one subject as a test,
trac-all runs without errors. However, when I update the configuration file
for more than one subject, I get the following error:
mv -f /scr
Hi all- Is there a command we can have screenshots (similar to one employed in
fsl) of fucntional--> structural registration in FSFAST to visually check the
registration on top of the BBR cost?
Cheers,
Sabin Khadka
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Hi All,
I have been using the quantifyHippocampalSubfields.sh from build 20150507
with no problems.
However when I try to run the script in the new build (20150610) it fails
if I run with the "T1" flag or without.
here is the result with T1:
*vermisii:RBrain ca
It is hard to say from those slices, but the registration does not look
great to me. It will really rely on you to make the final call though
because it is very hard for me to say from a few slices of a partial
volume image. You can try changing the intensity (click in the image and
hit the 'i'
What command did you type?
On Wed, Jun 10, 2015 at 5:32 PM, Mohammed Goryawala wrote:
> Hello All,
>
> I am trying to read .mgz files into matlab on MacOSX using the MRIread
> command.
>
> It returns me the following error:
>
> SWITCH expression must be a scalar
> or string constant.
>
> Error i
Hello All,
I am trying to read .mgz files into matlab on MacOSX using the MRIread
command.
It returns me the following error:
SWITCH expression must be a scalar
or string constant.
Error in load_mgh (line 126)
switch type
Error in MRIread (line 88)
[mri.vol, M, mr_parms, volsz] =
load_mgh(
Hi,
> We had the same problem with importing scans into Freesurfer that had been
> converted from PAR/REC to NIFTI using nipy. The problem only affected a
> subset of the data. When visualising the data with Fiji the brain appeared
> highly skewed. Upon closer inspection of the header data of the
Thanks a lot, it worked!
2015-06-08 21:23 GMT+02:00 Aaron Schultz :
> You may need to reinstall XQuartz and/or fix symlinks:
>
> e.g.: sudo ln -s /opt/X11 /usr/X11R6 ; sudo ln -s /opt/X11 /usr/X11
>
> -Aaron Schultz
>
>
> > On Jun 8, 2015, at 9:31 AM, Bruce Fischl
> wrote:
> >
> > Hi J
Hi Jung, I don't understand what you did or what you are trying to do.
Can you elaborate?
doug
On 6/9/15 1:46 PM, Park, Jung Mi wrote:
Hello Freesurfer team
I got a warning message when I checked tkregister2 after I did
mni152.reg, mri_matrix_multiply command.
I got warning messages and fou
You can use mri_label2label to create a binary mask of the label
(--outmask), then use mris_apply_reg, something like
mris_apply_reg --src lh.label.bin.mgh --trg lh.label.bin.on-rh.mgh
--streg lh.sphere.reg.fsaverage_sym rh.sphere.reg.fsaverage_sym --no-rev
Then use mri_cor2label to convert i
It is hard to tell from that image what is going on. Can you post pics
of the white surface (green line) on the actual functional instead of
the noise image? Also, for the sagittal view, show a slice that is not
right on the midline (where there is no surface).
doug
On 6/9/15 1:22 PM, lucas ho
I never used Analyse HDR/IMG format before so I can't tell if the conversion
with dcm2nii works, but it may be worth a shot.
Are you on Linux or Mac OS X? If you send me the output of the command `head
-c350 | hexdump -Cv`, where is the
path to your NIFTI file, I could have a look for you if
Hi Jalmar,
Thanks, that's very helpful because the files I am working with have been
transformed more than once, and were originally par/rec files. I do not have
those original files - I only have the analyze files which I was trying to
convert to .nii, since the hdr file gives a different erro
Hi Jennifer,
We had the same problem with importing scans into Freesurfer that had been
converted from PAR/REC to NIFTI using nipy. The problem only affected a subset
of the data. When visualising the data with Fiji the brain appeared highly
skewed. Upon closer inspection of the header data of
Dear Freesurfer experts,
I would like to study the cortical thickness difference between two
groups (two different genotypes) and include age and years of
education as covariates. I processed my data with Freesurfer 5.3.0 und
I am now running analysis in Qdec.
I don't know how to set the design
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