Re: [Freesurfer] mris_apply_reg failing for area/volume
External Email - Use Caution
Hi Doug
Thank you very much for this. I am unfortunately not able to get the new
version to work with our system.
Is it possible to send a version built for centos6/rhel6?
Thanks again!
- James
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
Sent: 10 January 2019 00:27
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
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
> on behalf of Greve, Douglas
> N.,Ph.D.
> *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
>> on behalf of James Michael
>> Roe
>> 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
>> on behalf of Greve, Douglas
>> N.,Ph.D.
>> 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
>>>
>>>
>>>
Re: [Freesurfer] mris_apply_reg failing for area/volume
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
> on behalf of Greve, Douglas
> N.,Ph.D.
> *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
>> on behalf of James Michael
>> Roe
>> 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
>> on behalf of Greve, Douglas
>> N.,Ph.D.
>> 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
>>> on behalf of Greve, Douglas
>>> N.,Ph.D.
>>> 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
>>
Re: [Freesurfer] mris_apply_reg failing for area/volume
External Email - Use Caution
Thanks for the quick reply. Have sent the file to you now
- James
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of James Michael Roe
<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>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<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>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<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:
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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Bruce Fischl
<mailto:fis...@nmr.mgh.harvard.edu>
Sent: 29 October 2018 15:43
To: Freesurfer support list
Subje
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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of James Michael Roe
<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>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<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>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<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:
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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Bruce Fischl
<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 no
Re: [Freesurfer] mris_apply_reg failing for area/volume
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
on behalf of James Michael Roe
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
on behalf of Greve, Douglas N.,Ph.D.
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, use 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
> on behalf of Greve, Douglas N.,Ph.D.
>
> 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
>> on behalf of Bruce Fischl
>>
>> 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 comma
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
on behalf of Greve, Douglas N.,Ph.D.
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, use 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
> on behalf of Greve, Douglas N.,Ph.D.
>
> 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
>> on behalf of Bruce Fischl
>>
>> 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
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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___
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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 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
> on behalf of Greve, Douglas N.,Ph.D.
>
> 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
>> on behalf of Bruce Fischl
>>
>> 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
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Re: [Freesurfer] mris_apply_reg failing for area/volume
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
on behalf of Greve, Douglas N.,Ph.D.
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
> on behalf of Bruce Fischl
>
> 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
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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subexample_slurm.log
Description: subexample_slurm.log
___
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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
> on behalf of Bruce Fischl
>
> 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
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Re: [Freesurfer] mris_apply_reg failing for area/volume
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
on behalf of Bruce Fischl
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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Re: [Freesurfer] mris_apply_reg failing for area/volume
External Email - Use Caution
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
on behalf of Bruce Fischl
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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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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[Freesurfer] mris_apply_reg failing for area/volume
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
subexample_slurm.log
Description: subexample_slurm.log
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Re: [Freesurfer] mris_apply_reg
Dear Mohamad, You're right, after I use version 6.0, it works. Thanks for your help. best, Lanbo On Fri, Nov 3, 2017 at 3:12 PM, Alshikho, Mohamad J. < malshi...@mgh.harvard.edu> wrote: > Hi Lanbo, > > You need Freesurfer 6 to run this command. The flag --src-label is not > part of FS5.3 > > > > Best, > > M_ > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@ > nmr.mgh.harvard.edu] *On Behalf Of *lanbo Wang > *Sent:* Friday, November 3, 2017 11:49 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] mris_apply_reg > > > > Dear Freesurfer experts, > > I try run this code according to Xhemi： > mris_apply_reg --src-label label/rh.V1_exvivo.thresh.label --trg > rh-on-lh.V1_exvivo.thresh.label \ > > --streg xhemi/surf/lh.fsaverage_sym.sphere.reg > surf/lh.fsaverage_sym.sphere.reg > > However, error shows: Option --src-label unknown. And also mris_apply_reg > --help didn't show how to correctly use -label. > > What's the correctly code. > > Thanks for your advices. > > Best, > > Lanbo > > > > > ___ > Freesurfer mailing list > 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 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.
Re: [Freesurfer] mris_apply_reg
Hi Lanbo, You need Freesurfer 6 to run this command. The flag --src-label is not part of FS5.3 Best, M_ From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of lanbo Wang Sent: Friday, November 3, 2017 11:49 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mris_apply_reg Dear Freesurfer experts, I try run this code according to Xhemi： mris_apply_reg --src-label label/rh.V1_exvivo.thresh.label --trg rh-on-lh.V1_exvivo.thresh.label \ --streg xhemi/surf/lh.fsaverage_sym.sphere.reg surf/lh.fsaverage_sym.sphere.reg However, error shows: Option --src-label unknown. And also mris_apply_reg --help didn't show how to correctly use -label. What's the correctly code. Thanks for your advices. Best, Lanbo ___ Freesurfer mailing list 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.
Re: [Freesurfer] mris_apply_reg
Hi Lanbo Doug (who knows the answer to this question) is on vacation. Can you repost next week? thanks Bruce On Fri, 3 Nov 2017, lanbo Wang wrote: Dear Freesurfer experts, I try run this code according to Xhemi： mris_apply_reg --src-label label/rh.V1_exvivo.thresh.label --trg rh-on-lh.V1_exvivo.thresh.label \ --streg xhemi/surf/lh.fsaverage_sym.sphere.reg surf/lh.fsaverage_sym.sphere.reg However, error shows: Option --src-label unknown. And also mris_apply_reg --help didn't show how to correctly use -label. What's the correctly code. Thanks for your advices. Best, Lanbo ___ Freesurfer mailing list 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] mris_apply_reg
Dear Freesurfer experts, I try run this code according to Xhemi： mris_apply_reg --src-label label/rh.V1_exvivo.thresh.label --trg rh-on-lh.V1_exvivo.thresh.label \ --streg xhemi/surf/lh.fsaverage_sym.sphere.reg surf/lh.fsaverage_sym.sphere.reg However, error shows: Option --src-label unknown. And also mris_apply_reg --help didn't show how to correctly use -label. What's the correctly code. Thanks for your advices. Best, Lanbo ___ Freesurfer mailing list 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.
Re: [Freesurfer] mris_apply_reg
here you go ... https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg On 12/9/16 4:01 PM, Matthew Defenderfer wrote: Hi All, I am trying to mirror labels across hemispheres and found various threads using mris_apply_reg. Unfortunately the version of that command I have does not recognize labels and all of the links in the mailing list seem to be broken. Would it be possible to get a link to the updated command? Thank you. -Matthew Defenderfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list 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] mris_apply_reg
Hi All, I am trying to mirror labels across hemispheres and found various threads using mris_apply_reg. Unfortunately the version of that command I have does not recognize labels and all of the links in the mailing list seem to be broken. Would it be possible to get a link to the updated command? Thank you. -Matthew Defenderfer ___ Freesurfer mailing list 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.
