[Freesurfer] IndexError: list index out of range
Hello everyone, I am trying to run a cortical thickness analysis in QDEC. I have recon-all and qcache but while trying to run asegstats2table, I keep getting the error-list index out of range. asegstats2table --subjects 101 102 103 INSP104 INSP105 INSP107 INSP108 INSP109 112 113 114-S 115-S 116-S 117-S INSP119 INSP120 INSP121 INSP122 123 INSP124 125 126 INSP-127 INSP-129 INSP130 INSPD131 INSPD132 133 INSPD134 136 INSP137 INSP138 INSP139 INSP140 INSP141 INSP143 INSP144 --meas volume --tablefile Vol_HV_stats.txt SUBJECTS_DIR : /Applications/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File "/Applications/freesurfer/bin/asegstats2table", line 548, in id_name_map, measurelist = parsed.parse(options.meas) File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse seg = strlst[1] # segmentation id is in the 2nd field IndexError: list index out of range. This does not happen when I run the same command for a separate group of subjects. The recon-all and qcache ran without error. So I was hoping you could help me resolve this issue. Warm Regards Ayushi Shukla Research Assistant National Institute of Mental Health and Neurosciences Bangalore, India ___ Freesurfer mailing list 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.
Re: [Freesurfer] Qdec error in analysis
Hi, Thank you for your response. Yes, I checked, and I do have the permission to read the file. Warm Regards Ayushi On Thu, 6 Jul 2017 at 09:42, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > Do you have read permission to that file? > > On 6/29/17 7:04 AM, AYUSHI SHUKLA wrote: > > Hi, > > I'm a new user of qdec and I'm trying to run a cortical thickness analysis > in qdec between Schizophrenic patients and healthy controls. > I have run "recon-all -i" and "recon-all -s -qcache" on my data > and it says that this has run successfully without any errors. > > But when I hit analyze on the qdec GUI, I get the following error- "Error > in Analyze: Couldn't open > /Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz > or .mgh file." > > I went through the old questions with the same issue, however I could not > figure a solution for my problem as when I check in the directory, the file > is present. I have tried to re-run recon-all and recon-all -s as well, but > it is still giving the same error. I was wondering if someone could help me > with this issue. > > > Warm Regards > > Ayushi Shukla > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > 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. > ___ Freesurfer mailing list 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.
[Freesurfer] Qdec error in analysis
Hi, I'm a new user of qdec and I'm trying to run a cortical thickness analysis in qdec between Schizophrenic patients and healthy controls. I have run "recon-all -i" and "recon-all -s -qcache" on my data and it says that this has run successfully without any errors. But when I hit analyze on the qdec GUI, I get the following error- "Error in Analyze: Couldn't open /Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file." I went through the old questions with the same issue, however I could not figure a solution for my problem as when I check in the directory, the file is present. I have tried to re-run recon-all and recon-all -s as well, but it is still giving the same error. I was wondering if someone could help me with this issue. Warm Regards Ayushi Shukla ___ Freesurfer mailing list 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.
[Freesurfer] QDEC Error in Analysis
Hi, I'm a new user of qdec and I'm trying to run a cortical thickness analysis in qdec between Schizophrenic patients and healthy controls. I have run "recon-all -i" and "recon-all -s -qcache" on my data and it says that this has run successfully without any errors. But when I hit analyze on the qdec GUI, I get the following error- "Error in Analyze: Couldn't open /Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file." I went through the old questions with the same issue, however I could not figure a solution for my problem as when I check in the directory, the file is present. I have tried to re-run recon-all and recon-all -s as well, but it is still giving the same error. I was wondering if someone could help me with this issue. Warm Regards Ayushi Shukla ___ Freesurfer mailing list 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.
