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:
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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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of James Michael Roe
<j.m....@psykologi.uio.no><mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: 08 November 2018 15:01
To: freesurfer@nmr.mgh.harvard.edu<mailto: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, use
gr...@nmr.mgh.harvard.edu<mailto:gr...@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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: 07 November 2018 19:02
To: freesurfer@nmr.mgh.harvard.edu<mailto: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:
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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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Bruce Fischl
<fis...@nmr.mgh.harvard.edu><mailto: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
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