Hi Martin, When doing cross-sectional analysis on a longitudinal data set and the qdec table is ordered as followed:
fsid Gender Group Age d115a.long.d115_base 1 1 19 d120a.long.d120_base 0 1 22 Why does the presmoothing not have to be: recon-all -s d115a.long.d115_base -qcache recon-all -s d120a.long.d120_base -qcache instead of recon-all -long d115a d115_base -qcache recon-all -long d120a d120_base -qcache Cheers, Kasper 2016-03-11 17:52 GMT+01:00 Martin Reuter <[email protected]>: > Hi Kasper, > > That needs to be the cross-sectinal name (whenever you also pass a base, > it will automatically create the ..long.. names internally). > > cheers, Martin > > > > On 03/11/2016 08:51 AM, Kasper Jessen wrote: > > Hi Martin, > > Thanks for the answer :-) > > To presmooth the data onto target, with the following command: > > recon-all -long <tpid> <baseid> -qcache > > The <tpdi>, does that have to be the longitudinal name ( > d115a.long.d115_base) or the cross-sectional name (d115a)? > > Best wishes > Kasper > > 2016-03-09 22:38 GMT+01:00 Martin Reuter <[email protected]>: > >> Hi Kasper, >> >> short answer: yes. >> >> long answer >> 1. yes >> 2. yes (you need to create a table in cross sectional format (no >> fsid-base column) and the fsid needs to be the tp.long.base names for >> baseline visit. the path should point to where these *.long.* directories >> are located). >> 2. yes (fsaverage should be linked there anyway, right?) >> 3. yes >> >> ;-) Martin >> >> >> On 03/09/2016 03:42 PM, Kasper Jessen wrote: >> >> Dear FreeSurfer experts, >> >> We have a longitudinal study design with up to 5 time points. However, we >> both want to do a baseline cross-sectional analysis and later a >> longitudinal analysis. All subjects have been run through the longitudinal >> pipeline (only the base was edited). We want to start analysing baseline >> cross-sectionally using QDEC. I have read through the wiki guides but would >> like to make sure that we are doing it correctly. We have done/plan to do >> the following: >> >> 1. The [CROSS], edited [BASE] and [LONG] is processed. >> >> 2. We will create a qdec table called qdec.table.dat. However, because we >> want to use the improved longitudinal runs [LONG] (i.e., because the [BASE] >> has been edited] the first column in the QDEC table (i.e., fsid) has been >> changed to include the longitudinal names (please see below). In addition, >> we have included the line *SUBJECTS_DIR /my/path/to/subject/data* to let >> FreeSurfer know that it is the longitudinal directories that should be used >> (is this the correct why to let FreeSurfer know that it is the >> "longitudinal runs" which should be used?). >> >> SUBJECTS_DIR /my/path/to/subject/data >> fsid Gender Group Age >> d115a.long.d115_base 1 1 19 >> d120a.long.d120_base 0 1 22 >> ... >> >> 2. We transfer the default fsaverage to the subject directory. >> 3. To presmooth the data onto the target we run the following command: >> *recon-all >> -long <tpid> <baseid> -qcache* >> >> When the above steps are done we plan to load it into QDEC. >> >> Is the above steps correct for doing a cross-sectional group analysis in >> QDEC? >> >> Best regards, >> Kasper Jessen >> MD, PhD student >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing >> [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- >> Martin Reuter, PhD >> Assistant Professor of Radiology, Harvard Medical School >> Assistant Professor of Neurology, Harvard Medical School >> A.A.Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> Research Affiliate, CSAIL, MIT >> Phone: +1-617-724-5652 >> Web : http://reuter.mit.edu >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> 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. >> >> > > > -- > Kasper Jessen, > MD, PhD student > Center for neuropsychiatric Schizophrenia Research (CNSR) > Mental Health Centre Glostrup > Nordre Ringvej 29-67 > 2600 Glostrup > Tlf.: 24430136 > E-mail: [email protected] eller <[email protected]> > [email protected] > > > _______________________________________________ > Freesurfer mailing > [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web : http://reuter.mit.edu > > > _______________________________________________ > Freesurfer mailing list > [email protected] > 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. > > -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: [email protected] eller [email protected]
_______________________________________________ Freesurfer mailing list [email protected] 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.
