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 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
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
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/

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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contains patient information, please contact the Partners
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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...) 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.comwrote:

Perfect, it works thanks!

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

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
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/

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.

harvard.edu>

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.

-- 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/

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.eduwrote:

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.commailto: 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>> 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
        <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
            >
            >
            > _______________________________________________
            > Freesurfer mailing list
            > Freesurfer@nmr.mgh.harvard.edu
        <mailto:Freesurfer@nmr.mgh.harvard.edu>
            <mailto:Freesurfer@nmr.mgh.harvard.edu

        <mailto:Freesurfer@nmr.mgh.harvard.edu>>

            >
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

            --
            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/

            _______________________________________________
            Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
        <mailto:Freesurfer@nmr.mgh.harvard.edu>
        <mailto:Freesurfer@nmr.mgh.harvard.edu

        <mailto:Freesurfer@nmr.mgh.harvard.edu>>

        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


            The information in this e-mail is intended only for
        the person to
            whom it is
            addressed. If you believe this e-mail was sent to you
        in error and
            the e-mail
            contains patient information, please contact the Partners
            Compliance HelpLine at
        http://www.partners.org/complianceline . If the e-mail was
        sent to
            you in error
            but does not contain patient information, please
        contact the
            sender and properly
            dispose of the e-mail.



    --         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/

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.eduwrote:

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> 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

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


                    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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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.eduwrote:

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> 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>>> 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
    <mailto:krista.kelly16@gmail.com>>
            <mailto:krista.kelly16@gmail.com
    <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>
            <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
    <mailto:greve@nmr.mgh.harvard.edu>
            <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>>>
                        <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
    <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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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:

mri_segstats --slabel BV20 lh $SUBJECTS_DIR/BV20/label/lh.V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats add --excludeid 0

Was this incorrect? It seemed to work fine.

So then for the cortex.label, I realize it is not thresholded the way V1.thresh.label is because it takes into account every vertex for the whole hemisphere, so do I keep both --label-thresh .5 and --slabel in the mri_segstats command? Or should I only use --slabel similar to the command above?

mri_segstats --label-thresh .5 --slabel BV20 lh $SUBJECTS_DIR/BV20/label/lh.cortex.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.cortex.stats add --excludeid 0

Thanks! Krista

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

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
    <mailto:krista.kelly16@gmail.com>>
            <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>
            <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>>>
                    <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>
            <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>>

                    <mailto:krista.kelly16@gmail.com
    <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>
            <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
    <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:

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

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Great! Thanks so much for all your help! :)

On Thu, Mar 6, 2014 at 11:48 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:

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:

mri_segstats --slabel BV20 lh $SUBJECTS_DIR/BV20/label/lh.V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats add --excludeid 0

Was this incorrect? It seemed to work fine.

Yes, that is correct. You would only use --label-thesh if the label has a valid statistic that can be thresholded (the last column in the label file)

...

So then for the cortex.label, I realize it is not thresholded the way V1.thresh.label is because it takes into account every vertex for the whole hemisphere, so do I keep both --label-thresh .5 and --slabel in the mri_segstats command? Or should I only use --slabel similar to the command above?

mri_segstats --label-thresh .5 --slabel BV20 lh $SUBJECTS_DIR/BV20/label/lh.cortex.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.cortex.stats add --excludeid 0

Don't use --label-thresh here because the cortex label does not have a valid statistic

...

Thanks! Krista

On Wed, Mar 5, 2014 at 7:13 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: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>
    <mailto: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
    <tel:2.4966%20%200.3254>
             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>>
            <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:


                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>>>
                    <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
    <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... )

...

                            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
    <mailto:krista.kelly16@gmail.com>>
                    <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>
            <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>>>
                    <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>
            <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>>
                    <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>
            <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>>>>
                            <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>
            <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>>
                    <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>
            <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>>>

                            <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>
            <mailto:krista.kelly16@gmail.com
    <mailto:krista.kelly16@gmail.com>>
                    <mailto:krista.kelly16@gmail.com
    <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>
            <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
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            <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
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            <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
    <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>>>>>

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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>>>>


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


                                            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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                                            Douglas N. Greve, Ph.D.
                                            MGH-NMR Center
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            <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>

     <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
            <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>>
                    <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
            <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
                            <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
            <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>>
                    <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
            <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>


     <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
            <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>>
                    <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
            <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
                            <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
            <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>>
                    <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
            <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>>

    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


                                            The information in
    this e-mail
            is intended
                            only for
                                        the person to
                                            whom it is
                                            addressed. If you
    believe this
            e-mail
                    was sent
                            to you
                                        in error and
                                            the e-mail
                                            contains patient
    information,
            please
                    contact
                            the Partners
                                            Compliance HelpLine at
    http://www.partners.org/complianceline . If the e-mail was
                                        sent to
                                            you in error
                                            but does not contain
    patient
                    information, please
                                        contact the
                                            sender and properly
                                            dispose of the e-mail.



                                    --         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>>>
                    <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
    <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>
            <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
    <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>>>
                    <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 <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> <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 <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>>>
                    <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 <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>
    <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 <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>

     <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>
     <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>>>
                    <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
    <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>>>
                    <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 <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>>> <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 <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/

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer