However, I'm afraid I still have a problem with my stats files. So my pipeline at the moment is:
- creation of a manual label (i.e. rh.MRQI_Tmppole.label) with QDEC - automatic creation of the corresponding label (i.e. *subj_1*/label/rh.MRQI_Tmppole.label) for each subject with File > Map Label to Subjects... - computing of the corresponding statistics with mris_anatomical_stats –l rh.MRQI_Tmppole.label –t rh.pial_lgi –b –f *subj_1*/stats/rh.MRQI_Tmppole.stats *subj_1 *rh, which creates a file *subj_1*/stats/rh.MRQI_Tmppole.stats - calling of aparcstats2table --hemi rh -s *subj_1 *-m thickness -p aparc.MRQI_Tmppole -t rh.map.txt, which causes me this error:
ERROR: The stats file /home/.../stats/rh.aparc.MRQI_Tmppole.stats is not found or is too small to be a valid statsfile
Could you please help me finding what's wrong with my stats file?
Thank you
Best elisa
2014-10-15 16:28 GMT+02:00 elisa veronese dovreipensarci@gmail.com:
Great, thank you Douglas, now it's not confusing :)
Best, elisa
2014-10-15 16:26 GMT+02:00 Douglas Greve greve@nmr.mgh.harvard.edu:
It is a little confusing, but when you pass a map with -t lh.map, then the values in the map go into the column labeled "thickness" regardless of what the map is. When you then run aparcstats2table and specify "thickness" you get whatever is in the thickness column regardless of whether it is thickness or not.
On 10/15/14 7:44 AM, elisa veronese wrote:
Thank you Douglas, but I'm afraid I'm still missing the point. The -m option allows me measuring area (default), volume, thickness, thicknessstd, meancurv, gauscurv, foldind, curvind. Anyway my problem regards gyrification index, so I cannot understand why you suggested me to use -m thickness.
Thank you. Best,
elisa
2014-10-14 17:50 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
That call to aparcstats2table will give you the surface area. Use "-m thickness". With this, it will report whatever you passed as the -t option to mris_anatomical_stats (rh.pial_lgi in this case).
doug
On 10/13/2014 07:49 AM, elisa veronese wrote:
Dear FreeSurfers,
I'm facing a problem with the estimation of local gyrification index. I've already performed the analysis with QDEC and the insertion of the MEASURE1 = pial_lgi line in the .Qdecrc file, but I'd like to see if it is possible to use the /aparcstats2table /command in order to have more concise and easy-to-read results.
From the QDEC GUI I've drawn a label in the temporal pole, and applied it to all my subjects (/mris_anatomical_stats -l rh.MR_TmpPole.label -t rh.pial_lgi -b -f s1/stats/rh.MR_TmpPole.stats s1 rh/)
The problem is that when I call the /aparcstats2table --hemi rh --subjects s1 s2 ... --parc MR_TmpPole -t GI_MR_TmpPole.txt/ / / I get a .txt file like this:
rh.MR_TmpPole.arearh_rh.MR_TmpPole.label_arearh_WhiteSurfArea_area s1 6623.096171.8 s2 6257.085247.3 ...
but I'm not sure what those numbers stand for. I'm afraid they have nothing to do with the gyrification index.
Thank you,
best
elisa
-- Elisa Veronese - PhD
/ Research Unit on Brain Imaging and Neuropsychology (RUBIN) / / Inter-University Center for Behavioral Neurosciences (ICBN) University of Udine and University of Verona, Italy / ICBN Website: http://icbn.uniud.it/tiki-index.php /
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-- Elisa Veronese - PhD
Research Unit on Brain Imaging and Neuropsychology (RUBIN) *
Inter-University Center for Behavioral Neurosciences (ICBN) University
of Udine and University of Verona, Italy ICBN Website: http://icbn.uniud.it/tiki-index.php http://icbn.uniud.it/tiki-index.php *
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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.
-- Elisa Veronese - PhD
*Research Unit on Brain Imaging and Neuropsychology (RUBIN)*
*Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php http://icbn.uniud.it/tiki-index.php*