Hi Francisco,
you are *much* better off avoiding going through analyze. Once you do
that all bets are off. Can you reprocess directly from the dicoms and see
if the left/right issue goes away?
cheers,
Bruce
On Thu, 12 Feb 2009, Francisco Robles
wrote:
Hello free Surfer communities,
I'm
what files are in [subject path]/mri/*aseg*.mgz?
On Fri, 13 Feb 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Sorry to post this again, but I am still having issues with surfaces exiting
with errors. These are the two outputs that I have gotten:
MRI_fill: could not read segmentation from aseg.
Nathan,
Can you send me the recon-all.log file for that subject? Its found in
the /scripts dir.
Nick
On Fri, 2009-02-13 at 15:15 -0500, Dankner, Nathan (NIH/NIMH) [F] wrote:
> Sorry to post this again, but I am still having issues with surfaces exiting
> with errors. These are the two outputs
Sorry to post this again, but I am still having issues with surfaces exiting
with errors. These are the two outputs that I have gotten:
MRI_fill: could not read segmentation from aseg.auto_noCC.mgz
reading segmented volume aseg.auto_noCCseg.mgz...
ERROR: cannot find [subject path]/aseg.auto_noCC
Hi Corey,
if the talairach transform has been computed (as it is in recon-all),
then loading one of the standard anatomicals will bring it up. Something
like:
tkmedit norm.mgz lh.pial -aux ct.anat.nii
where is the name you gave to recon-all .
cheers,
Bruce
On Fri, 13 Feb 2009, Keller, C
you have to give it the actual name of the subject (it has to have been
analyzed in freesurfer)
Keller, Corey J. wrote:
Hi Freesurfers,
We have an MRI coregistered with a CT scan using spmregister. I have converted
the CT to the anatomical volume using mri_vol2vol. We are then trying to view
Hi Freesurfers,
We have an MRI coregistered with a CT scan using spmregister. I have converted
the CT to the anatomical volume using mri_vol2vol. We are then trying to view
the anatomical ct in tkmedit and output talairach coordinates but as of now can
only see RAS coordinates. Is there a way to
Chris,
talairach_avi is a wrapper script around the registration tools created
by Avi Snyder of Washington University, namely the tool imgreg_4dfp,
which is the heart of talairach_avi. The wrapper script handles all the
conversions (4dfp,t4 to mgz, concluding with the output of the
talairach.xfm
Nick,
Just a clarification question. I read the wiki regarding the new eTIV and
it says that the registration to
$FREESURFER_HOME/average/711-2C_as_mni_average_305.4dfp.img is done with
talairach_avi as opposed to imgreg_4dfp. I am guessing imgreg_4dfp is
correct because the template has 4df
hi Dev,
You might have wrong SUBJECTS_DIR,
check it using echo $SUBJECTS_DIR
> Hi,
> I have been running into an error while using Qdec.
> *Error in Analyze: Couldn't open file
> <$SUBJECT_DIR>//surf/lh.thickness.fwhm10.fsaverage.mgh*
>
> I checked and the file is there in that folder. I know t
Hi,
I have been running into an error while using Qdec.
*Error in Analyze: Couldn't open file
<$SUBJECT_DIR>//surf/lh.thickness.fwhm10.fsaverage.mgh*
I checked and the file is there in that folder. I know this file is created
when recon-all is run with -qcache option. I have run that twice and i
Juergen,
Are you running v4.2.0 of linux centos 32b, or asking if this problem
was fixed in that version? ie., which version are you running now? I'm
not aware of this problem currently (that is, I too thought it was fixed
some time ago).
Nick
On Fri, 2009-02-13 at 16:22 +0100, J=?ISO-8859-1?
Gabriel,
Running mri_segstats will not cause any trouble, it just reads files,
and doesnt modify anything.
You can run v4.2.0 on your subjects manually segmented with v4.0.5, that
is, you can safely run:
recon-all -s subj -all
and it will keep and use all your edits. Only when the -clean flag
Jose,
bbregister was released in v4.2.0. For usage, type bbregister --help.
Nick
On Fri, 2009-02-13 at 14:15 +0100, Jose Luis Cantero Lorente wrote:
> Dear all,
>
> I would like to automatically corregister PET to MRI by using the command
> bbregister. I am not sure what is going on since Fre
Mike,
Another piece of info: the talairach.xfm transform is a registration to
an image _with_ skull, to this image:
$FREESURFER_HOME/average/711-2C_as_mni_average_305.4dfp.img
The utility imgreg_4dfp is used to perform this registration. So the
eTIV should not be as subject to changes due to at
Dear FS experts
I tried to make an average subject of 52 subjects, but it seems that an
already fixed error is back:
Checking 47
/usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po
laris_Male_48.mgh
Checking 48
/usr/local/freesurfer/subjects/average/tmp/make_average_vol
Dear freesurfers: I have two questions:
1. I have FS v4.0.5 and i've downloaded the new mri_segstats to calculate the
eTIV,
this new calculation may cause any trouble in my group of manual segmented
subjects?
2. I have 60 subjects manual segmentated on FreeSrufer 4.0.5, i want to know
if i
Dear freesurfers:
I have 60 subjects manual segmentated on FreeSrufer 4.0.5, i want to know if i
run the recon2 or recon3 in the new FS 4.2.0, will have any problem?
the diferences between versions can cause any trouble with the analisis because
imcompability or something?
Regards Gabriel
Dear all,
I would like to automatically corregister PET to MRI by using the command
bbregister. I am not sure what is going on since Freesurfer (release 4.0.5)
always says "Command not found" when I try to run this function. Any help with
this issue would be very welcome.
Thanks in advance.
B
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