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 greve@nmr.mgh.harvard.eduwrote:
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
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