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
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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
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