Thanks Martin,
Yes, the label is from Qdec in first time point space I have done the
following:
1) mri_label2label --srclabel rh_roi --srcsubject fsaverage --trgsubject
1003_1.long.temp_1003 --trglabel rh_roi --regmethod surface --hemi rh
(For all the subj_1.long.temp_subj and subj_2.long.temp_subj)
2) mris_anatomical_stats -l rh.roi -t rh.thickness -b -f
$subs/stats/rh.parsopercularis.stats $subs rh
And at the end when I am trying to extract the thickness from each subject
I get the following error:
amir% aparcstats2table --hemi lh --subjects `cat list5.txt` --parc
transversetemporal --meas thickness --skip --tablefile lh.Cth.roi.txt
SUBJECTS_DIR : /Applications/freesurfer/subjects/longBO
Parsing the .stats files
Skipping
/Applications/freesurfer/subjects/longBO/1003_1.long.temp_1003/stats/lh.transversetemporal.stats
Skipping
/Applications/freesurfer/subjects/longBO/1005_1.long.temp_1005/stats/lh.transversetemporal.stats
Skipping
/Applications/freesurfer/subjects/longBO/1003_2.long.temp_1003/stats/lh.transversetemporal.stats
Skipping
/Applications/freesurfer/subjects/longBO/1005_2.long.temp_1005/stats/lh.transversetemporal.stats
Building the table..
Traceback (most recent call last):
File "/Applications/freesurfer/bin/aparcstats2table", line 388, in
<module>
rows, columns, table = sanitize_table(options, pretable)
File "/Applications/freesurfer/bin/aparcstats2table", line 303, in
sanitize_table
_spec, _parc_measure_map = dt[0]
IndexError: list index out of range
The lh.tranverstemporal.stats looks like this:
# Table of FreeSurfer cortical parcellation anatomical statistics
#
# CreationTime 2015/05/27-11:57:08-GMT
# generating_program mris_anatomical_stats
# cvs_version $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks
Exp $
# mrisurf.c-cvs_version $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05
nicks Exp $
# cmdline mris_anatomical_stats -l lh.transversetemporal.label -t
lh.thickness -b -f 1003_1.long.temp_1003/stats/lh.transverstemporal.stats
1003_1.long.temp_1003 lh
# sysname Darwin
# hostname Cerebro.local
# machine x86_64
# user amir
#
# SUBJECTS_DIR /Applications/freesurfer/subjects/longBO
# anatomy_type surface
# subjectname 1003_1.long.temp_1003
# hemi lh
# AnnotationFile lh.transversetemporal.label
# AnnotationFileTimeStamp 2015/05/27 12:22:37
# Measure Cortex, NumVert, Number of Vertices, 134133, unitless
# Measure Cortex, WhiteSurfArea, White Surface Total Area, 89551.4, mm^2
# NTableCols 10
# TableCol 1 ColHeader StructName
# TableCol 1 FieldName Structure Name
# TableCol 1 Units NA
# TableCol 2 ColHeader NumVert
# TableCol 2 FieldName Number of Vertices
# TableCol 2 Units unitless
# TableCol 3 ColHeader SurfArea
# TableCol 3 FieldName Surface Area
# TableCol 3 Units mm^2
# TableCol 4 ColHeader GrayVol
# TableCol 4 FieldName Gray Matter Volume
# TableCol 4 Units mm^3
# TableCol 5 ColHeader ThickAvg
# TableCol 5 FieldName Average Thickness
# TableCol 5 Units mm
# TableCol 6 ColHeader ThickStd
# TableCol 6 FieldName Thickness StdDev
# TableCol 6 Units mm
# TableCol 7 ColHeader MeanCurv
# TableCol 7 FieldName Integrated Rectified Mean Curvature
# TableCol 7 Units mm^-1
# TableCol 8 ColHeader GausCurv
# TableCol 8 FieldName Integrated Rectified Gaussian Curvature
# TableCol 8 Units mm^-2
# TableCol 9 ColHeader FoldInd
# TableCol 9 FieldName Folding Index
# TableCol 9 Units unitless
# TableCol 10 ColHeader CurvInd
# TableCol 10 FieldName Intrinsic Curvature Index
# TableCol 10 Units unitless
# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv
GausCurv FoldInd CurvInd
lh.transversetemporal.label 1759 1138 3029 2.424 0.552
0.101 0.026 11 2.0
Best regards,
Amirhossein Manzouri
On Thu, May 28, 2015 at 6:40 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu>
wrote:
> Hi Amirhossein,
>
> where exactly is your label. If it is in the first time point, then how
> did it get there?
> I think it is probably in fsaverage space (where the first time points
> were mapped to perform your QDEC analysis). In that case use
> mri_label2label from fsaverage to the individual base spaces for all
> subjects.
>
> Best, Martin
>
> On 05/27/2015 04:32 PM, Douglas N Greve wrote:
>
>> Use mri_label2label. Run it with --help to get more info
>> doug
>>
>> On 05/27/2015 05:08 AM, amirhossein manzouri wrote:
>>
>>> Hi All,
>>> I have created two ROIs from first time point Qdec group comparison. I
>>> need to use this ROI labels to extract the thickness from tp1 and tp2
>>> registered to base (template) subjects(from longitudinal pipeline).
>>> Would you please let me how can I convert the label from 1st time
>>> point space to longitudinal template space?
>>>
>>> Best regards,
>>> Amirhossein Manzouri
>>>
>>>
>>>
> --
> Dr. Martin Reuter
>
> Instructor in Neurology
> Harvard Medical School
> Assistant in Neuroscience
> Dept. of Radiology, Massachusetts General Hospital
> Dept. of Neurology, Massachusetts General Hospital
> Research Affiliate
> Computer Science and Artificial Intelligence Lab,
> Dept. of Electrical Engineering and Computer Science,
> Massachusetts Institute of Technology
>
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
>
> Phone: +1-617-724-5652
> Email:
> mreu...@nmr.mgh.harvard.edu
> reu...@mit.edu
> Web : http://reuter.mit.edu
>
>
>
>
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