Can you send the new qdec table file? On 08/05/2015 04:05 AM, Clara Kühn wrote: > no worries! > sadly, though, deleting the empty line wasn't the answer to the problem :( > Cheers, Clara > > ----- Ursprüngliche Mail ----- > Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Dienstag, 4. August 2015 20:43:47 > Betreff: Re: [Freesurfer] cannot find qdec file > > oops, sorry for the delay, thanks for the reminder. The problem is that > you have a blank line at the end of your long.qdec.table.dat file. > Remove the line and see if it works. > doug > > On 08/04/2015 12:42 PM, Clara Kühn wrote: >> Hi Doug, >> did the fordoug.log file give any information about why FreeSurfer can't >> find my qdec file? >> >> Cheers and thanks for working on this! >> Clara >> >> ----- Ursprüngliche Mail ----- >> Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> >> An: freesurfer@nmr.mgh.harvard.edu >> Gesendet: Montag, 3. August 2015 17:16:18 >> Betreff: Re: [Freesurfer] cannot find qdec file >> >> can you run >> >> mris_preproc --debug --qdec-long >> /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 >> --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh >> |& tee fordoug.log >> >> and send me fordoug.log ? >> >> >> On 8/3/15 10:38 AM, Clara Kühn wrote: >> >> >> >> the command line is this: >> mris_preproc --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat >> --target 7kids_template_sc1 --hemi lh --meas thickness --out >> /scr/etsch2/kids/ct/qdec/lh.thickness.mgh >> >> the terminal output is this: >> nsubjects = 22 >> ERROR: cannot find /scr/etsch2/kids/ct/.long. >> >> and the actual qdec file is attached. >> Cheers, Clara >> >> ----- Ursprüngliche Mail ----- >> Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> An: >> freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:35:24 >> Betreff: Re: [Freesurfer] cannot find qdec file >> >> Can you send your command line, full terminal output, and your >> long.qdec.table.dat file? >> >> On 8/3/15 10:31 AM, Clara Kühn wrote: >> >> >> >> ok, it can only access the file if I type >> ls /scr/etsch2/kids/ct/qdec/long.qdec.table.dat (so with the forward slash) >> >> but if I then use that path for the mris_preproc command I get >> nsubjects = 22 >> ERROR: cannot find /scr/etsch2/kids/ct/.long. >> >> >> >> ----- Ursprüngliche Mail ----- >> Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> An: >> freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:23:48 >> Betreff: Re: [Freesurfer] cannot find qdec file >> >> that is probably not the full path. Try typing >> >> ls scr/etsch2/kids/ct/qdec/long.qdec.table.dat >> >> If it says it cannot find the file, then it is not the full path. Maybe >> you need a forward slash (ie, "/") in the beginning? >> >> On 8/3/15 10:18 AM, Clara Kühn wrote: >> >> >> >> then I get the error ERROR: cannot find >> scr/etsch2/kids/ct/qdec/long.qdec.table.dat >> >> I had tried that. Sorry, no luck with that. >> >> ----- Ursprüngliche Mail ----- >> Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> An: >> freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:16:58 >> Betreff: Re: [Freesurfer] cannot find qdec file >> >> you have to give it the entire path to the file >> >> On 8/3/15 10:14 AM, Clara Kühn wrote: >> >> >> >> Dear FS-experts, >> >> I want to analyze my longitudinal data with your suggested LME models and am >> therefore following the walkthrough by J. Bernal. I get an error though very >> early on when using the command >> mris_preproc --qdec-long qdec/long.qdec.table.dat --target >> 7kids_template_sc1 --hemi lh --meas thickness --out qdec/lh.thickness.mgh >> >> It always says >> ERROR: cannot find qdec/long.qdec.table.dat >> >> Yes, the walkthrough asks for an input file named just qdec.table.dat, but I >> haven't got that. So far in the longitudinal stream there are >> long.qdec.table.dat and cross.qdec.table.dat files but no simple >> qdec.table.dat files. So I figured I'd use the long.qdec file because FS >> needs to get the information about the long timepoints. >> But it cannot find the file, even though I see it. I've also tried copying >> the long.qdec file and naming it qdec.table.dat but it still doesn't find it. >> >> The entire path to the file is scr/etsch2/kids/ct/qdec/long.qdec.table.dat >> and my SUBJECTS_DIR is scr/etsch2/kids/ct >> >> Can you help me see what I'm missing? >> Thanks a lot in advance, >> Clara >> _______________________________________________ >> Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu >> https://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 >> _______________________________________________ >> Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu >> https://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 >> _______________________________________________ >> Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu >> https://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 >> >> >> _______________________________________________ >> 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 >> >>
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