On 03/06/2014 10:34 AM, krista kelly wrote:
> Hi Doug,
>
> Maybe I was mistaken. In your previous email when you said "do not
> spec --label-thresh", I thought that you were saying not to use that
> option and to just use --slabel for the V1.thresh.label. I've done
> that using this command:
>
not sure what you mean, those are not mutually exclusive
On 03/05/2014 06:05 PM, krista kelly wrote:
> Ok thanks!
>
> Also, for the lh.cortex pial_lgi, should I stick to --label-thresh .5
> rather than --slabel?
>
>
> On Wed, Mar 5, 2014 at 5:59 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvar
Right, one more thing. add --excludeid 0
On 03/05/2014 05:59 PM, krista kelly wrote:
> Thanks Doug! That fixed it. But now I have two numbers in each file,
> which do I use (see also attached file)?
>
> ColHeadersIndex SegId NVertices Area_mm2StructName
> Mean
> StdD
Thanks Doug! That fixed it. But now I have two numbers in each file, which
do I use (see also attached file)?
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max
Range 1 0 124241 81007.3 Seg 2.7306 0.6613 1.4985 4.4779 2.9795 2 1
3540 2225.6 Seg0001 2.4966 0.3254 2.0
Sorry, I gave you some bad advice. Only use --label-thresh with labels
that have a statistic that is non-zero (this is the last column of the
label file). Eg, in lh.V1.thresh.label, the stat is always 0 (but it is
non-zero in lh.V1.label). The stat is the probability that the vertex is
in the
Thanks Doug! I did that and it worked, but now here's another problem: the
values that I obtained for V1, V2, and cortex for each subject are all the
same. For example, BV20 left hemisphere values for V1, V2, and cortex are
all 2.7241 (same thing happens for the right hemisphere). Maybe I can tell
use asegstats2table (I know, it's confusing:)
doug
On 03/05/2014 01:42 PM, krista kelly wrote:
> Hi again,
>
> My apologies for the barrage of emails! I was able to do mri_segstats
> on V1 labels for pial_lgi using the following:
>
> mri_segstats --label-thresh .5 --slabel $s lh
> $SUBJECTS_DI
Hi again,
My apologies for the barrage of emails! I was able to do mri_segstats on V1
labels for pial_lgi using the following:
mri_segstats --label-thresh .5 --slabel $s lh
$SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
$SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
$SUBJECTS_DIR/$s/stats/lh.V1.thresh.la
Perfect, it works thanks!
On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve
wrote:
> sorry, it is --slabel
> btw, there is documentation. If you run it without options it gives you a
> list of arguments as well as examples
> doug
>
> On 03/05/2014 11:32 AM, krista kelly wrote:
>
>> Thanks Doug, b
sorry, it is --slabel
btw, there is documentation. If you run it without options it gives you
a list of arguments as well as examples
doug
On 03/05/2014 11:32 AM, krista kelly wrote:
> Thanks Doug, but when I try this I get the following error: Option
> --label unknown
>
>
> On Wed, Mar 5, 2014 a
Thanks Doug, but when I try this I get the following error: Option --label
unknown
On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve
wrote:
>
> try
> mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i
> $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
>
> On 03/0
try
mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i
$SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
On 03/05/2014 11:15 AM, krista kelly wrote:
> Hello,
>
> I would like to extract the pial_lgi data from Freesurfer's V1.thresh
> labels but can't quite figur
Hello,
I would like to extract the pial_lgi data from Freesurfer's V1.thresh
labels but can't quite figure it out. I've tried adapting the commands from
the LGI Freesurfer tutorial as such:
mri_segstats --label-thresh BV20 lh V1.thresh.label --i
$SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thr
13 matches
Mail list logo
