Hi,
I am trying to resample two volumetric data onto freesurfer individual
subjects. The volume images are NIFTI format from SPM results (spmT_0001.img
and con_0001.img). I used the following command to resample spmT map onto
the surface:
> mri_vol2surf --mov 3t0499/model/ravol/spmT_0001.img --re
Dear Free Surfers,
I wonder if something went wrong with transitioning FS-FAST and/or
unpacksdcmdir from 4.5 to 5.0. Our functional analysis stream is set to
work in 4.5 and it was working fine. However, since the default version
was changed to 5.0, our analyses have stopped working despite that
Hi Doug,
Thanks for the reply. I have tried using the method you've suggested,
however, I'm stuck because mri_label2annot which I use to turn my label
into a annot file only works in one hemisphere while mri_aparc2aseg
works for the whole brain. Do you know a work around for this?
Can I merge th
Hi,
in the meantime the 5.0 longitudinal stream has been fixed and tested.
See:
http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalChangeLog
for links to download the fixed binaries and updated recon-all script.
Note, that we recommend to wait with any large scale longitudinal
processing for t
The problem is that mri_label2volume just does not work all that well on
surface labels. Another way to do this is to create an annotation from
the single label using mris_label2annot, then create a segmentation/mask
volume using mri_aparc2aseg.
doug
Prapti Gautam wrote:
>
> Dear freesurfers,
HI Roberto, I can't quite tell what the problem is that you are trying
to fix. What is actually going wrong? If it displays correctly in
tkmedit, then the coordinates are probably write. I don't know what you
mean when you say the the Volume RAS coords are swapped.
doug
roberto.vivi...@uni-ulm
For cortex volumes, use the values in the aparc.stats file. In version
5, the ctx volumes should not be listed in the wmparc.stats file.
doug
Ed Gronenschild wrote:
> Hi,
>
> In the wmparc.stats file a large number of ctx structures
> and the corresponding volumes, like ctx-lh-parahippocampal.
>
Hi,
In the wmparc.stats file a large number of ctx structures
and the corresponding volumes, like ctx-lh-parahippocampal.
For some of these structures the volumes are also listed
in the ?h.aparc.stats files.
Which volumes are correct?
Ed
___
Freesurfer
You can also use mri_surfcluster if you want to do it from the command
line.
doug
On 9/15/10 8:54 AM, Bruce Fischl wrote:
> click on it in tksurfer and use the custom fill to fill up to and
> including the functional threshold, then save the resulting label.
>
> cheers
> Bruce
> On Wed, 15 Se
click on it in tksurfer and use the custom fill to fill up to and
including the functional threshold, then save the resulting label.
cheers
Bruce
On Wed,
15 Sep 2010, Gabriel Go.Es. wrote:
>
>
> Hello
>
>
>
> I'm wondering about how to create a label from a cluster wich is significant
> from a
Dear list,
I am using mri_convert to prepare my pipeline for FreeSurfer, and,
yes, I have been struggling for a couple of days to get it done.
After conversion, I have no problem using tkmedit to display the file;
however, the Volume RAS coordinates are swapped -- the numbers aren't
wrong,
Hello
I'm wondering about how to create a label from a cluster wich is significant
from a group comparison, I mean, I have made group somparisons and i get some
significant clusters, and I want to susbtract that significative cluster and
transform it to a label file.
Best Regards
Gabr
Dear freesurfers,
I am trying to convert a label that I have hand drawn into tksurfer into
a volume file using mri_label2volume and succeed in transforming into a
volume file but the volume looks splotchy and the ends are not connected
, i.e. instead of a smooth bit of cortex I get disjoi
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