On Wed, Mar 5, 2014 at 7:13 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

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)?

ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range
1 0 124241 81007.3 Seg0000 2.7306 0.6613
1.4985 4.4779 2.9795
2 1 3540 2225.6 Seg0001 2.4966 0.3254
2.0502 3.0296 0.9794

On Wed, Mar 5, 2014 at 5:07 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>

<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:

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 label, so you can
choose the
threshold based on that. The lh.V1.thresh.label is for
when the
stat is the max for V1 relative to the other labels (eg,
V2). If
you select thresh=.5, you may miss places where V1 is the most
likely but still less than .5. I would probably use
lh.V1.thresh.label (and then do not spec --label-thresh)

doug

On 03/05/2014 03:40 PM, krista kelly wrote:

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 you
what I did step by step to see if you can find where
I went
wrong.

First, I did a for loop to run mri_segstats for each
participant for each label per hemisphere (here is an
example
of V1):

foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27
BV28 BV29
BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40
BV41
BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14
MB15
MB16 MB17 MB18 MB19 MB20) <<hit enter>>
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.label.LGI.stats
<<hit enter>>
end <<hit enter>>

for left V2 I ran:

foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27
BV28 BV29
BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40
BV41
BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14
MB15
MB16 MB17 MB18 MB19 MB20) <<hit enter>>
mri_segstats --label-thresh .5 --slabel $s lh
$SUBJECTS_DIR/$s/label/lh.V2.thresh.label --i
$SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
$SUBJECTS_DIR/$s/stats/lh.V2.thresh.label.LGI.stats
<<hit enter>>
end <<hit enter>>

and for left cortex I ran:
foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27
BV28 BV29
BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40
BV41
BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14
MB15
MB16 MB17 MB18 MB19 MB20) <<hit enter>>
mri_segstats --label-thresh .5 --slabel $s lh
$SUBJECTS_DIR/$s/label/lh.cortex --i
$SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
$SUBJECTS_DIR/$s/stats/lh.cortex.LGI.stats
end <<hit enter>>

This is where the problem must be occurring since all
files
created during these commands show the same files per
hemisphere. I've attached three files created during
mri_segstats (left V1, V2, cortex.stats) for one
participant.
I've also attached files created during asegstats2table to
show how all values are the same for each label for all
participants (V1, V2, cortex.LGI.txt).

If anyone has any insight into the problem, that would
be great!

Best,
Krista

On Wed, Mar 5, 2014 at 1:54 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>> wrote:

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
$SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
$SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
$SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats

However, now I'm having trouble with bringing
all of
the data
into one table using aparcstats2table. I found
online
how to
get the data for aparc annotation
(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033069.html)
and tried to adapt to the labels. Here is what
I've tried:

aparcstats2table --subjects BV20 BV21 BV22
BV23 BV24
BV25 BV26
BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35
BV36 BV37
BV38
BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09
MB10 MB11
MB12
MB13 MB14 MB15 MB16 MB17 MB18 --hemi lh --meas
thickness
--parc V1.thresh.label.LGI --tablefile
lh.V1.thresh.label.LGI.txt

I get the following output when I do this:

SUBJECTS_DIR : /Applications/freesurfer/subjects
Parsing the .stats files
Traceback (most recent call last):
File
"/Applications/freesurfer/bin/aparcstats2table", line
371, in <module>
parc_measure_map = parsed.parse(options.meas)
File
"/Applications/freesurfer/bin/fsutils.py", line
207, in
parse
val =
float(strlist[self.measure_column_map[measure]])
ValueError: could not convert string to float:
Seg0000

I've attached an example of the file created
during
mri_segstats in case that helps.

Thanks!
Krista

On Wed, Mar 5, 2014 at 1:21 PM, krista kelly
<krista.kelly16@gmail.com
<mailto:krista.kelly16@gmail.com>
<mailto:krista.kelly16@gmail.com
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<mailto:krista.kelly16@gmail.com
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<mailto:krista.kelly16@gmail.com>
<mailto:krista.kelly16@gmail.com
<mailto:krista.kelly16@gmail.com>>>>> wrote:

Perfect, it works thanks!

On Wed, Mar 5, 2014 at 11:35 AM, Douglas N
Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
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<mailto:greve@nmr.mgh.harvard.edu>>
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<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
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<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
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<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>> 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, 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
<greve@nmr.mgh.harvard.edu
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<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>

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<mailto:greve@nmr.mgh.harvard.edu
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<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>>> 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 03/05/2014 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 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.thresh.label.stats
>
> I've also tried
>
> mris_anatomical_stats -l
lh.V1.thresh.label -f
>
BV20/stats/lh.V1.thresh.label.stats
BV20 lh
pial_lgi
>
> but I've had no luck with
either.
>
> I would appreciate any help!
>
> Thanks,
> Krista
>
>
>
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<tel:617-726-7422 <tel:617-726-7422>>>>

Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop:
https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
<tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
<tel:617-724-2358>>>
Fax: 617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422
<tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>

Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
<tel:617-726-7422>>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/