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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@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

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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 greve@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@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 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

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of James Michael Roe j.m.roe@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@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, use greve@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@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 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

_______________________________________________ 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

External Email - Use Caution

Thanks for the quick reply. Have sent the file to you now

- James

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of James Michael Roe j.m.roe@psykologi.uio.nomailto:j.m.roe@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: 08 November 2018 15:01 To: freesurfer@nmr.mgh.harvard.edumailto: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 greve@nmr.mgh.harvard.edumailto:greve@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: 07 November 2018 19:02 To: freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edumailto:fischl@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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@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

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From:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of James Michael Roej.m.roe@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

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From:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D.DGREVE@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, usegreve@nmr.mgh.harvard.edu and not my email above

On 11/08/2018 08:21 AM, James Michael Roe wrote:

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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

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From:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D.DGREVE@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:

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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

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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischlfischl@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:

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​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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