Hi Dr. Greve,
Please find the attached qdec file, along with diagnosis file which I used in QDEC, and this is the same qdec file I trying to use for the aparcstats2table command.
Thanks.
PS: I was also wondering (a) how can I average thickness stats (b) are these in fsaverage (standard) space and (c) how can I display it on standard fsaverage for publications purpose?
On Wed, Nov 9, 2016 at 10:52 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you send the qdec file with variables?
On 11/09/2016 11:51 AM, Martin Juneja wrote:
Hi Dr. Greve,
Somehow even after adding variables, it's not working, although same qdec file works fine when I perform GLM in qdec. So I replaced the flag with subjectsfile and provided subject list.txt file. So in that way, it's working fine now.
I was also wondering (a) how can I average these thickness stats (b) are these in fsaverage (standard) space and (c) how can I display it on standard fsaverage for publications purpose?
Thanks a lot.
On Wed, Nov 9, 2016 at 7:39 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Appears to be having problems reading the qdec table. It might be expecting the qdec table to actually variables in it. Can you try adding variables? Also, try it without the --qdec flag instead specifying the subjects with --subjects HC003_1 HC004_1 ... On 11/8/16 8:09 PM, Martin Juneja wrote:Hi everyone, I am trying to use following command to save stats from a set of subjects in a table format: aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t zzz.txt But after I run this, I get following error: Traceback (most recent call last): File "/usr/local/freesurfer/bin/aparcstats2table", line 353, in <module> subj_listoftuples = assemble_inputs(options) File "/usr/local/freesurfer/bin/aparcstats2table", line 228, in assemble_inputs fsid=row['fsid'].strip() KeyError: 'fsid' My qdec.dat file looks like below: fsidHC003_1 HC004_1 HC006_1 HC015_1 This command works fine if I use subject IDs individually here e.g. aparcstats2table --subjects HC_Example HC003_1 HC004_1 HC006_1 HC015_1 --hemi lh --meas thickness -t zzz.txt Another question I have here is: How can I average these thickness stats and display it on standard fsaverage? Any help would be really appreciated. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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.
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