Hi all,
I was able to work around this by providing the path to lh.thickness and not
to the .label. (Paths relative since I've cd'd to subjects/myguy/label
before running it. )
ERROR'd attempt:
Cmd: mri_segstats --i lh.thickness --slabel <myguy> lh ./lh.BA3a.label --id
1 --sum table.dat
Using Freesurfer version 5.1.
Subjects Directory is /blah/Freesurfer/subjects/
Sessions Directory is /stuff/sessions
$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
cwd
cmdline /opt/freesurfer5.1/bin/mri_segstats --i lh.thickness --slabel
<myguy> lh ./lh.BA3a.label --id 1 --sum table.dat
sysname Linux
hostname london.v21.med.va.gov
machine x86_64
user vhasfcbuckls
Constructing seg from label
Loading lh.thickness
mri_read(): couldn't determine type of file
/blah/Freesurfer/subjects/<myguy>/label/lh.thickness # that path won't exist
because it's in myguy/surf/
ERROR: loading lh.thickness
Apparently successful attempt:
Cmd: mri_segstats --i ../surf/lh.thickness --slabel
<myguy> lh ./lh.BA3a.label --id 1 --sum table.dat
Using Freesurfer version 5.1.
Subjects Directory is /blah/Freesurfer/subjects/
Sessions Directory is /stuff/sessions
$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
cwd
cmdline /opt/freesurfer5.1/bin/mri_segstats --i ../surf/lh.thickness
--slabel <myguy> lh ./lh.BA3a.label --id 1 --sum table.dat
sysname Linux
hostname london.v21.med.va.gov
machine x86_64
user vhasfcbuckls
Constructing seg from label
Loading ../surf/lh.thickness
Vertex Area is 0.647859 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
0 1 2512 1731.59
Reporting on 1 segmentations
[/blah/Freesurfer/subjects/<myguy>/label]
The Resulting table.dat:
cat table.dat
# Title Segmentation Statistics
#
# generating_program /opt/freesurfer5.1/bin/mri_segstats
# cvs_version $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
# cmdline /opt/freesurfer5.1/bin/mri_segstats --i ../surf/lh.thickness
--slabel <myguy> lh ./lh.BA3a.label --id 1 --sum table.dat
# sysname Linux
# hostname london.v21.med.va.gov
# machine x86_64
# user me
# anatomy_type surface
#
# SUBJECTS_DIR /blah/Freesurfer/subjects/
# subjectname <myguy>
# Label <myguy> lh ./lh.BA3a.label
# InVolFile ../surf/lh.thickness
# InVolFileTimeStamp 2012/09/21 20:53:03
# InVolFrame 0
# ExcludeSegId
# Only reporting non-empty segmentations
# VertexArea_mm2 0.647859
# TableCol 1 ColHeader Index
# TableCol 1 FieldName Index
# TableCol 1 Units NA
# TableCol 2 ColHeader SegId
# TableCol 2 FieldName Segmentation Id
# TableCol 2 Units NA
# TableCol 3 ColHeader NVertices
# TableCol 3 FieldName Number of Vertices
# TableCol 3 Units unitless
# TableCol 4 ColHeader Area_mm2
# TableCol 4 FieldName Area
# TableCol 4 Units mm^2
# TableCol 5 ColHeader Mean
# TableCol 5 FieldName Intensity Mean
# TableCol 5 Units unknown
# TableCol 6 ColHeader StdDev
# TableCol 6 FieldName Itensity StdDev
# TableCol 6 Units unknown
# TableCol 7 ColHeader Min
# TableCol 7 FieldName Intensity Min
# TableCol 7 Units unknown
# TableCol 8 ColHeader Max
# TableCol 8 FieldName Intensity Max
# TableCol 8 Units unknown
# TableCol 9 ColHeader Range
# TableCol 9 FieldName Intensity Range
# TableCol 9 Units unknown
# NRows 1
# NTableCols 9
# ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max
Range
1 1 2512 1731.6 Seg0001 1.7868 0.4464 0.8637
3.5082 2.6445
Hope this helps,
~ShannonB.
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Thursday, January 08, 2015 11:35 AM
To: Salil Soman
Cc: free surfer
Subject: Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 131, Issue 13
Try giving it the full path to the label
On 01/08/2015 02:17 PM, Salil Soman wrote:
> Dear Doug,
>
> Thank you for your email. I am running into trouble using mri_segstats
> - the command you sent (mri_segstats --i lh.thickness --slabel subject
> lh lh.BA3a.label --id 1 --sum table.dat) gave me the error:
>
> "No such file or directory
> mri_segstats: could not open label file lh.BA3a.label"
>
> I tried substituting a single subject in place of "subject" in the
> command you sent I get the same error.
> I confirmed that the lh.BA3a.label file is in the label subfolder for
> the individual subject.
>
> I would like to output the volume, thickness, and area for all the
> broadman areas (especially 35). Any advice you can provide on how to
> do this would be a great help.
>
> Thank you for all your help.
>
> Sal
>
> Date: Thu, 08 Jan 2015 11:37:11 -0500
> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu
> < <mailto:gr...@nmr.mgh.harvard.edu> mailto:gr...@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] Possible to generate table of statistics for
> specific label?
> To: <mailto:freesurfer@nmr.mgh.harvard.edu>
freesurfer@nmr.mgh.harvard.edu
> < <mailto:freesurfer@nmr.mgh.harvard.edu>
mailto:freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <54aeb237.9010...@nmr.mgh.harvard.edu
> < <mailto:54aeb237.9010...@nmr.mgh.harvard.edu>
mailto:54aeb237.9010...@nmr.mgh.harvard.edu>>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
> Yep, you can use somehting like
>
> mri_segstats --i lh.thickness --slabel subject lh lh.BA3a.label --id 1
> --sum table.dat
>
> doug
>
>
> On 01/08/2015 08:50 AM, Salil Soman wrote:
> > Dear List Members,
> >
> > Is it possible to generate tables of volume / area / thickness
> > information for a specific label that is not included in aparcstats
> > or asegstats using command line code in freesurfer (e.g. the
> > broadman areas)? If so, could someone point me to the instructions?
> >
> > Thank you for your time and consideration.
> >
> > Best wishes,
> >
> > Sal
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
<mailto:gr...@nmr.mgh.harvard.edu> gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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