/ really? So if you run ls -l /Users/nnidementia/Documents/PDFS/FSVASE_002/surf/lh.thickness.fwhm10.fsaverage.mgz/
what do you get? On 11/11/2015 07:59 PM, Heidi Foo wrote: > Hi Dr Greve, > > Yes it does, for all base templates, there > are lh(rh).long.thickness-avg(pc1, rate, and > spc).fwhm0(5,10,20,25).fsaverage.mgh files. > > I did the following steps in preprocessing: > > 1. recon-all -all -s <tpNid> -i path_to_tpN_dc m > 2. recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all > 3. recon-all -long <tpNid> <templateid> -all > 4. long_mris_slopes --qdec > /Users/nnidementia/Documents/PDFS/long.qdec.table.txt --meas thickness > --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label > --time years --qcache fsaverage --sd /Users/nnidementia/Documents/PDFS > 5. long_mris_slopes --qdec > /Users/nnidementia/Documents/PDFS/QDEC/long.qdec.table.txt --meas > thickness --hemi lh --sd /Users/nnidementia/Documents/PDFS --do-pc1 > --do-label --generic-time --fwhm 10 --qcache fsaverage --stack-pc1 > /Users/nnidementia/Documents/PDFS/QDEC/lh.cross.qdec.table.txt.thickness-pc1.stack.mgh > > --isec-labels > /Users/nnidementia/Documents/PDFS/QDEC/lh.cross.qdec.table.txt.fsaverage.cortex.label > > Thanks. > > Regards, > Heidi Foo > > > > > On Wed, Nov 11, 2015 at 11:57 PM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > does that file exist? Did you run recon-all -qcache ? > > > On 11/11/15 7:54 AM, Heidi Foo wrote: >> Apologies, the error message should be /Error in >> analyze: couldn't open >> >> /Users/nnidementia/Documents/PDFS/FSVASE_002/surf/lh.thickness.fwhm10.fsaverage.mgz >> or .mgh file./ >> >> On Wed, Nov 11, 2015 at 8:48 PM, Heidi Foo <heidifo...@gmail.com >> <mailto:heidifo...@gmail.com>> wrote: >> >> Hi Dr Greve, >> >> Thank you for your advice, it is deeply appreciated. I >> removed the blank lines of wmh.levels and included a carriage >> return at the end of the long.qdec.table.txt. >> >> However, there is still /error in analyze: Couldn't open >> >> /Users/nnidementia/Documents/PDFS/FS_PD002_1.nii/surf/lh.thickness.fwhm10.fsaverage.mgz >> or .mgh file./ >> / >> / >> I checked my qdec.table.txt (both cross and long) but I did >> not see any fsaverage included in the list of subjects. Am I >> missing something? >> >> Thank you. >> >> Regards, >> Heidi Foo >> / >> / >> >> On Wed, Nov 11, 2015 at 12:28 AM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> Also, try removing the blank line at the end of >> wmh.levels, and make sure you have a carriage return at >> the end of long.qdec.table.txt. This may fix the 2nd error >> >> On 11/09/2015 10:38 PM, Heidi Foo wrote: >> >> Dear Dr Greve, >> >> Thanks for your reply. I have already linked >> fsaverage to my SUBJECTS_DIR but the error still >> persists. >> >> Attached is my qdec (long and cross) files. >> >> Thanks. >> >> Regards, >> Heidi Foo >> >> >> >> On Tue, Nov 10, 2015 at 6:36 AM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >> >> >> >> On 11/06/2015 09:35 PM, Heidi Foo wrote: >> >> Dear FreeSurfer experts, >> >> I am trying to compare between stable WMH >> group and rapid >> progressed WMH group in regards to the >> cortical thickness as >> well as volume changes in the gray matter. >> The nuisance >> variable in my case is age. I ran my analysis >> using QDEC but >> encountered a few problems: >> >> 1. There is error in analyze: couldn't open file >> >> It looks like it cannot find fsaverage. Link it >> to your >> SUBJECTS_DIR if you have not already. >> >> 2. If this error doesn't appear, another one >> does. >> QdecGlmDesign::Create: zero factors! >> (Attached the screenshot of the errors for >> your perusal) >> >> please send the qdec file >> >> >> I am hoping that you could give me a solution >> to my problems. >> >> Thank you so much. >> >> Regards, >> Heidi >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: >> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> >> 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. >> >> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
