mri_label2label needs to be called with --surfreg fsaverage_sym.sphere.reg
Martin, can you modify long_mris_slopes to add this? But another question is exactly what you want to do in the end. What function of the slopes and hemisphere are you trying to compute? doug On 03/21/2014 01:20 PM, Peggy Skelly wrote: > I tried your suggestion (using subjTP/xhemi in place of subjTP) in the > qdec table. I doesn't work because long_mris_slopes uses subjTP and > subjBase to create "subjTP.long.subjBase", the directory of the actual > data. Extra slashes "/" in the name create an incorrect name (i.e. > subjTP/xhemi.long.subjBase/xhemi). > > So I tried copying the contents of the /xhemi subdirectories into a > different $SUBJECTS_DIR with timepoint and base names the way > long_mris_slopes expects them: > subjdir_xhemi/subjTP1.long.subjbase > subjdir_xhemi/subjTP2.long.subjbase > subjdir_xhemi/subjbase > > This works to create appropriate path/filenames for long_mris_slopes. > But ... > > The problem now is when long_mris_slopes calls mri_label2label > (mapping cortex labels to fsaverage_sym), the file surf/rh.sphere.reg > is not found. It's not in the /xhemi/surf directory. It is in the > original subject directory. xhemi/surf/ only > contains rh.fsaverage_sym.sphere.reg. > > Any suggestions? Am I approaching this problem (combining healthy > hemispheres in a longitudinal study) correctly? > > Peggy > > > > On Mon, Mar 17, 2014 at 3:35 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > I'm not sure this will work but try entering the subjectids in the > qdec > table as subjectTP and subjectTP/xhemi and use subject as the base (TP > is just a shorthand for time point, use whatever you used) > doug > > On 03/17/2014 01:09 PM, Peggy Skelly wrote: > > The patch works! Thank you. > > > > Now, to compute the longitudinal measures: I don't see > 'long_mris_slopes > > --help' mentioning xhemi, so I suppose > > it won't be able to find the flipped subjects. Is there a way to > > copy/rename the <subj>/xhemi/ directory > > to $SUBJECTS_DIR so I could run long_mris_slopes? > > > > Peggy > > > > On 3/14/14, 7:13 PM, Peggy Skelly wrote: > >> Thanks -- (I thought I might not have understood the processing > >> pipeline properly.) > >> > >> I'm running 5.3, I'll try the patch and let you know how it works. > >> > >> Peggy > >> > >> > >> On 3/14/14, 16:07 , Douglas N Greve wrote: > >>> Actually, I don't think this will work. What version of FS are you > >>> running? > >>> > >>> I've created a patch of the 5.3 recon-all here > >>> > >>> > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch > >>> > >>> > >>> Copy this to $FREESURFER_HOME/bin/recon-all (after making a > backup!) > >>> > >>> then re-run > >>> > >>> doug > >>> > >>> > >>> On 03/14/2014 03:57 PM, Douglas N Greve wrote: > >>>> You have uncovered a bug. I don't think anyone has tried to run > >>>> xhemi on > >>>> a longitudinal data set before. There is a work-around. First run > >>>> > >>>> xhemireg --s subject --no-tal > >>>> > >>>> Then run > >>>> > >>>> surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh > --xhemi > >>>> > >>>> I think this should work > >>>> > >>>> doug > >>>> > >>>> > >>>> On 03/14/2014 03:39 PM, Peggy Skelly wrote: > >>>>> Hi All, > >>>>> > >>>>> Although the question of flipping hemispheres has come up > before, I > >>>>> still struggling with it. > >>>>> I'm working on a longitudinal study with stroke subjects > (half with lh > >>>>> lesions, half with rh lesions). We want to compare only the > >>>>> non-lesioned, healthy, hemispheres at 2 timepoints (pre- and > >>>>> post-therapy). > >>>>> > >>>>> Using the tutorial > >>>>> > (http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview) > >>>>> as > >>>>> a guide, I've completed the longitudinal analysis > (cross-base-long > >>>>> steps) for both lh- and rh-lesioned subjects. > >>>>> > >>>>> I've done the thickness data qcache for the right/healthy > hemi for the > >>>>> lh-lesioned group: > >>>>> long_mris_slopes --qdec > long_qdec_lh_lesion_subjects_table.dat --meas > >>>>> thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc > --do-stack > >>>>> --do-label --time my_time_var --qcache fsaverage_sym --sd > >>>>> $SUBJECTS_DIR > >>>>> > >>>>> Convert the long_qdec_lh_lesion_subjects_table.dat into a > >>>>> cross.qdec.table.dat to use in qdec. This works well---I can > look for > >>>>> clusters where athe average thickness-rate is different from 0. > >>>>> > >>>>> How can I combine the rh-lesioned group with the first group? > >>>>> > >>>>> I thought I could flip hemispheres of the results at each > subject's > >>>>> longitudinal output timepoint with: > >>>>> surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh > --xhemi > >>>>> > >>>>> but this terminated with an error: > >>>>>> recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi > -talairach > >>>>>> > >>>>>> ERROR: Are you trying to run or re-run a longitudinal time > point? > >>>>>> If so, please specify the following parameters: > >>>>>> > >>>>>> \' -long <tpNid> <templateid> \' > >>>>>> > >>>>>> where <tpNid> is the time point id (SAME as cross > sectional > >>>>>> ID) and <templateid> is the ID created in the > -base run. > >>>>>> The directory <tpNid>.long.<templateid> will be > created > >>>>>> automatically or used for output, if it already > exists. > >>>>> I know it's recommended to flip hemispheres after processing > >>>>> > > (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html). > >>>>> > >>>>> When (and how) is it best done? > >>>>> > >>>>> Thanks, > >>>>> Peggy > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>>>> 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 > > > > > > -- > 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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 -- 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
