Hello, I was trying to get the cortical thickness in the table format for all of my subjects on which I had run recon all. I see the stats folder with rh/lh.aparc.stats files. My command was: aparcstats2table --subjects AA471.T1 AA471.T2 AA471.T3 AA474.T0 AA476.T0 AA479.T0 AA483.T0 AA483.T2 AA483.T3 AA486.T0 AA492.T1 AA492.T3 AA495.T0 AA495.T1 AA495.T2 AA495.T3 AA499.T0 AA534.T0 AA539.T0 AA543.T2 AA543.T3 AA549.T1 AA549.T2 AA549.T3 AA550.T1 --hemi rh --meas thickness --tablefile rh.aparc.thick.txt The message came: SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files ERROR: The stats file /opt/freesurfer/subjects/AA471.T1/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files
I used the skip option only to find this message SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files Skipping /opt/freesurfer/subjects/AA471.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA471.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA471.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA474.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA476.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA479.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA483.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA483.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA483.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA486.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA492.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA492.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA499.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA534.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA539.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA543.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA543.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA549.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA549.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA549.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA550.T1/stats/rh.aparc.stats Building the table.. Traceback (most recent call last): File "/opt/freesurfer/bin/aparcstats2table", line 338, in <module> rows, columns, table = sanitize_table(options, pretable) File "/opt/freesurfer/bin/aparcstats2table", line 253, in sanitize_table _spec, _parc_measure_map = dt[0] IndexError: list index out of range
Please advise. Rashmi.
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Hi Rashmi, Could you check that the ?h.aparc.stats for the subjects exist and contain actual measurements? If not, check the <subjid>/scripts/recon-all.log to see if the -parcstats step failed. Also, double-check your SUBJECTS_DIR path is correct. -Louis
On Wed, 25 Jan 2012, Rashmi Singh wrote:
Hello, I was trying to get the cortical thickness in the table format for all of my subjects on which I had run recon all. I see the stats folder with rh/lh.aparc.stats files. My command was: aparcstats2table --subjects AA471.T1 AA471.T2 AA471.T3 AA474.T0 AA476.T0 AA479.T0 AA483.T0 AA483.T2 AA483.T3 AA486.T0 AA492.T1 AA492.T3 AA495.T0 AA495.T1 AA495.T2 AA495.T3 AA499.T0 AA534.T0 AA539.T0 AA543.T2 AA543.T3 AA549.T1 AA549.T2 AA549.T3 AA550.T1 --hemi rh --meas thickness --tablefile rh.aparc.thick.txt The message came: SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files ERROR: The stats file /opt/freesurfer/subjects/AA471.T1/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files
I used the skip option only to find this message SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files Skipping /opt/freesurfer/subjects/AA471.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA471.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA471.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA474.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA476.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA479.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA483.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA483.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA483.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA486.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA492.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA492.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA499.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA534.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA539.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA543.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA543.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA549.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA549.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA549.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA550.T1/stats/rh.aparc.stats Building the table.. Traceback (most recent call last): File "/opt/freesurfer/bin/aparcstats2table", line 338, in <module> rows, columns, table = sanitize_table(options, pretable) File "/opt/freesurfer/bin/aparcstats2table", line 253, in sanitize_table _spec, _parc_measure_map = dt[0] IndexError: list index out of range
Please advise. Rashmi.
This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.
Did you look at the file to see if it looks reasonable? Eg, it might be completely empty if you ran out of space during the processing. doug
Rashmi Singh wrote:
Hello, I was trying to get the cortical thickness in the table format for all of my subjects on which I had run recon all. I see the stats folder with rh/lh.aparc.stats files. *My command was:* aparcstats2table --subjects AA471.T1 AA471.T2 AA471.T3 AA474.T0 AA476.T0 AA479.T0 AA483.T0 AA483.T2 AA483.T3 AA486.T0 AA492.T1 AA492.T3 AA495.T0 AA495.T1 AA495.T2 AA495.T3 AA499.T0 AA534.T0 AA539.T0 AA543.T2 AA543.T3 AA549.T1 AA549.T2 AA549.T3 AA550.T1 --hemi rh --meas thickness --tablefile rh.aparc.thick.txt *The message came:* SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files ERROR: The stats file /opt/freesurfer/subjects/AA471.T1/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files
*I used the skip option only to find this message* SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files Skipping /opt/freesurfer/subjects/AA471.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA471.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA471.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA474.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA476.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA479.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA483.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA483.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA483.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA486.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA492.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA492.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA499.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA534.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA539.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA543.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA543.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA549.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA549.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA549.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA550.T1/stats/rh.aparc.stats Building the table.. Traceback (most recent call last): File "/opt/freesurfer/bin/aparcstats2table", line 338, in <module> rows, columns, table = sanitize_table(options, pretable) File "/opt/freesurfer/bin/aparcstats2table", line 253, in sanitize_table _spec, _parc_measure_map = dt[0] IndexError: list index out of range
Please advise. Rashmi.
This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.
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