I have found and fixed the problem. You will need a new version of
mris_apply_reg from here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg
Copy it to $FREESURFER_HOME/bin (after making a backup copy of the one
that is there)
On 1/7/19 2:10 PM, James Michael Roe wrote:
>
> External Email - Use Caution
>
> Thanks for the quick reply. Have sent the file to you now
>
>
> - James
>
>
> ------------------------------------------------------------------------
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
> N.,Ph.D. <dgr...@mgh.harvard.edu>
> *Sent:* 07 January 2019 17:42
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] mris_apply_reg failing for area/volume
> What is $SUBJECTS_DIR/${template}/surf/lh.sphere.reg ? If template is not
> fsaverage_sym, can you send this file to me too?
>
>
> On 1/7/19 5:21 AM, James Michael Roe wrote:
>> External Email - Use Caution
>>
>> Dear freesurfer experts
>>
>> I am still unable to register RH area and volume files to the LH of a
>> symmetrical template for a number of longitudinally processed subs. This is
>> only the case when using the --jac flag (all run fine without).
>> There appears to be quite good correspondence (although not perfect) between
>> whether the LONG sub fails and whether the BASE of that sub fails with the
>> same error. Some CROSS subs also fail, though there appears to be little
>> correspondence.
>>
>> I would greatly appreciate any help you can give me.
>>
>> To recap, the command I am running is:
>>
>> #right to left
>> mris_apply_reg \
>> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>> --trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \
>> --streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg
>> $SUBJECTS_DIR/${template}/surf/lh.sphere.reg \
>> --jac
>>
>>
>> #right to right
>> mris_apply_reg \
>> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>> --trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \
>> --streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg
>> $SUBJECTS_DIR/${template}/surf/rh.sphere.reg \
>> --jac
>>
>>
>> Attached is the output for one CROSS sub (with fsaverage_sym as template)
>> and one LONG (with another symmetrical template) to show that the error is
>> not template-specific.
>>
>>
>> Thank you in advance!
>>
>>
>> - James
>>
>>
>>
>> ________________________________________
>> From:freesurfer-boun...@nmr.mgh.harvard.edu
>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of James Michael
>> Roe<j.m....@psykologi.uio.no>
>> Sent: 12 November 2018 10:52
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>>
>> External Email - Use Caution
>>
>> Hi again Doug
>>
>> FYI have sent the files as requested
>>
>> James
>>
>> ________________________________________
>> From:freesurfer-boun...@nmr.mgh.harvard.edu
>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
>> N.,Ph.D.<dgr...@mgh.harvard.edu>
>> Sent: 08 November 2018 15:01
>> To:freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>>
>> Not sure what is going on. Can you send me the input rh.area file as
>> well as lh.40tvs8ref_sym_20.sphere.reg and
>> 40tvs8ref_sym_20/surf/lh.sphere.reg? You can post them here
>>
>> https://gate.nmr.mgh.harvard.edu/filedrop2
>>
>> When it asks you for an email, usegr...@nmr.mgh.harvard.edu and not my
>> email above
>>
>>
>>
>>
>>
>>
>> On 11/08/2018 08:21 AM, James Michael Roe wrote:
>>> External Email - Use Caution
>>>
>>> Hi Doug
>>>
>>> Here is the output file
>>>
>>>
>>> James Michael Roe
>>> PhD. Candidate
>>> Center for Lifespan Changes in Brain and Cognition
>>> Department of Psychology
>>> University of Oslo
>>> PB 1094 Blindern
>>> 0317 Oslo
>>> Mobile: 958 49 437
>>>
>>> ________________________________________
>>> From:freesurfer-boun...@nmr.mgh.harvard.edu
>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
>>> N.,Ph.D.<dgr...@mgh.harvard.edu>
>>> Sent: 07 November 2018 19:02
>>> To:freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>>>
>>> Can you send the terminal output that includes the error?
>>>
>>> On 11/06/2018 06:36 PM, James Michael Roe wrote:
>>>> External Email - Use Caution
>>>>
>>>> Hi Bruce
>>>>
>>>> I realise that my last message made it sound as though the problem was
>>>> fixed.
>>>> However, I was only confirming that the files load fine in freeview (are
>>>> not corrupted) as asked.
>>>> The issue of many subs area and volume files failing to register when
>>>> using --jac is still unsolved
>>>>
>>>> Appreciate the support.
>>>>
>>>> Thanks
>>>>
>>>> James
>>>>
>>>> ________________________________________
>>>> From: James Michael Roe
>>>> Sent: 31 October 2018 19:45
>>>> To: Freesurfer support list
>>>> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>>>>
>>>> Hi Bruce
>>>>
>>>> Can confirm that both files (rh.area & rh.volume) load fine in freeview
>>>>
>>>> Thanks for the help!
>>>>
>>>> James
>>>> ________________________________________
>>>> From:freesurfer-boun...@nmr.mgh.harvard.edu
>>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce
>>>> Fischl<fis...@nmr.mgh.harvard.edu>
>>>> Sent: 29 October 2018 15:43
>>>> To: Freesurfer support list
>>>> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>>>>
>>>> Hi James
>>>>
>>>> can you verify that the various files (e.g.
>>>> /cluster/projects/p23/projects/Memory_Project/James/AgeSym/long_recons_FXhemi/010_NDev/1000409_02_10_02_11.long.base_1000409_11/surf/rh.area)
>>>>
>>>> are intact by loading them into freeview? For the area file you will of
>>>> course have to load it as an overlay not as a surface (since it isn't a
>>>> surface)
>>>>
>>>> cheers
>>>> Bruce
>>>> On Mon, 29 Oct 2018, James Michael Roe wrote:
>>>>
>>>>> External Email - Use Caution
>>>>>
>>>>>
>>>>> Dear freesurfer experts
>>>>>
>>>>>
>>>>>
>>>>> I’m running the following commands to register RH area and volume files
>>>>> per sub to both hemispheres
>>>>> of a symmetrical template following Xhemi routines.
>>>>>
>>>>> The commands have already worked for many subs, but are failing to write
>>>>> the target file for a
>>>>> number of others (and all run fine without the –-jac flag)
>>>>>
>>>>>
>>>>> #right to left
>>>>>
>>>>> mris_apply_reg \
>>>>>
>>>>> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>>>>>
>>>>> --trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \
>>>>>
>>>>> --streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg
>>>>> $SUBJECTS_DIR/${template}/surf/lh.sphere.reg \
>>>>>
>>>>> --jac
>>>>>
>>>>>
>>>>>
>>>>> #right to right
>>>>>
>>>>> mris_apply_reg \
>>>>>
>>>>> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>>>>>
>>>>> --trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \
>>>>>
>>>>> --streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg
>>>>> $SUBJECTS_DIR/${template}/surf/rh.sphere.reg \
>>>>>
>>>>> --jac
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> The error is not template-specific as the output is the same using
>>>>> fsaverage_sym
>>>>>
>>>>> Attached is the log file.
>>>>>
>>>>>
>>>>>
>>>>> Thanks in advance!
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> - James
>>>>>
>>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
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>>> Freesurfer@nmr.mgh.harvard.edu
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>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
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>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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