Hi all,
I have seen others post a similar problem on the freesurfer mailing list but I
could not find a solution.
When I edit a volume using control points, I am noticing that the use of CP
edits adversely effects the wm/gm surfaces in the resulting re-processed image.
Like others have reporte
Hi all,
Ah, good to know that there is a Talairach accuracy problem. What have
other groups been doing about this? Do you think it makes sense to
manually edit much of our data? From what we've seen so far (registering
to ages 3-9 so more errors expected) about 25% of our data have the
registrat
If you upload the subject to our FTP site I will take a look
Bruce
On Oct 10, 2012, at 9:29 PM, EK Kim wrote:
> Thank you for your answer.
> I'm not sure I understand your question right,
> but I just processed the file using following procedures.
> 1. recon-all -autorecon1 -nuintensitycor-3T
Thank you for your answer.
I'm not sure I understand your question right,
but I just processed the file using following procedures.
1. recon-all -autorecon1 -nuintensitycor-3T (because mine was 3T)
2. skullstripping brain mask using gcuts
3. adding control points (only on the left hemisphere)
4. re
I think 5.1 specifically has a problem with Talairach accuracy (is that
right Nick?). Should be much better with the next release
On Wed, 10 Oct
2012, Eric Cunningham wrote:
Hi Bruce,
I am running version 5.10
Thanks,
-Eric
On Wed, Oct 10, 2012 at 3:13 PM, Bruce Fischl
wrote:
Hi Eric
Hi Bruce,
I am running version 5.10
Thanks,
-Eric
On Wed, Oct 10, 2012 at 3:13 PM, Bruce Fischl wrote:
> Hi Eric
>
> what version are you running?
> Bruce
>
> On Wed, 10 Oct 2012, Eric Cunningham wrote:
>
> Greetings,
>>
>> I am trying to determine how bad a talairach.xfm registration has to be
Hi Eric
what version are you running?
Bruce
On Wed, 10 Oct 2012, Eric Cunningham wrote:
Greetings,
I am trying to determine how bad a talairach.xfm registration has to be to
warrant a manual edit. I have found that even minor edits can have
noticable (9%) effects on major subcortical volumes
Greetings,
I am trying to determine how bad a talairach.xfm registration has to be to
warrant a manual edit. I have found that even minor edits can have
noticable (9%) effects on major subcortical volumes (such as thalamus or
hippocampus). Very few registrations seem to have completely failed, b
Hi Greg, you can do something like
mri_concat --o lh.surf.mgh $SUBJECTS_DIR/*/surf/winkler.mgh
doug
On 10/10/2012 04:52 PM, Gregory Kirk wrote:
> a have a bunch of data stored in the subj_id directories of the subjects for
> convieniance but
> it is already in the average surface space, but i w
a have a bunch of data stored in the subj_id directories of the subjects for
convieniance but
it is already in the average surface space, but i want to assemble it into one
file so i can
run the glm.
mris_preproc --fsgd subset.fsgd --target subset_average --hemi lh --meas
winkler.mgh --out lh.
Sorry, it was the first command that failed. Run these two commands,
then the mris_anatomical_stats
mri_annotation2label --subject vol17 --hemi lh --lobesStrict lobesfile
mri_annotation2label --subject vol17 --hemi rh --lobesStrict lobesfile
On 10/10/2012 12:24 PM, Carolina Valencia wrote:
> Hi D
you need to register them.
cheers
Bruce
On Wed, 10 Oct 2012, dgw wrote:
> Hi,
>
>> From the wiki (http://www.freesurfer.net/fswiki/mri_ms_fitparms), I
> can see that mri_ms_fitparms can accept and afi map. Can someone tell
> me what assumptions the -afi subcommand makes about the position of
> th
Hi,
>From the wiki (http://www.freesurfer.net/fswiki/mri_ms_fitparms), I
can see that mri_ms_fitparms can accept and afi map. Can someone tell
me what assumptions the -afi subcommand makes about the position of
the afi map relative to the flash volumes? does it calculate
everything in scanner coor
Dear Freesurfers,
presumably this is quite a newbie's question but I was wondering
whether my recon-all times can be plausible if it takes less then 10
or 12 hours to perform the entire routine on a local machine. I'm
using freesurfer 64 bit on Debian testing equipped with 16GB of RAM
and Intel Co
Hello again,
I'm sorry about all these questions.
My analysis is being based on Morey et al. and I would like to know why do
they not divide the study in left hippocampus and right hippocampus? Is it
related with the type of comparison, once they are only worried about the
comparison between meth
Hi Douglas,
I've tried your suggestion, but I don't succeed, first I look for all the
option of the command mris_anatomical_stats and I don't understand some of
them, like the last word white and the -cortex option.
If I finally succeed, where I can find the values? Can I visualize a
colored brain
Hi Aimi, this is not possible with nifti since 163842 > 32768 (2^15)
which is the limit for nifti. It should have worked with mgh output and
--noreshape. Can you confirm that it does not?
doug
On 10/10/2012 11:15 AM, Aimi Watanabe wrote:
> Hello,
>
> My input to freesurfer is:
>
> mri_surf2sur
Hello,
My input to freesurfer is:
mri_surf2surf
--cortex --fwhm-src 5 --noreshape --hemi rh --tval [$output file] --sval
[$input file] --srcsubject [$subject id] --trgsubject fsaverage --tfmt nii
When I reopen the resulting image with Nibabel, the dimensions are 27307
x 1 x 6 x 296. While 296
Hi Hugh,
no attachments came through. Do you mean the segmentation of the
hippocampus in the aseg? What version are you running?
cheers
Bruce
On Wed, 10 Oct 2012, Hugh Pemberton wrote:
> Dear freesurfer crew,
> I'm having a few issues with segmentation around the hippocampus, I have
> included
what was the name of the file that you transferred?
On Wed, 10 Oct 2012, EK
Kim wrote:
I already uploaded this problem 2 days ago, reprocessing the subject to make
sure about control points.
However when I added the control points to the left hemisphere,
the right hemisphere surface was change
Dear all,
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