adding time points to longitudinal base template

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Govindarajan, Koushik Athreya

11 Mar 2014 11 Mar '14

10:08 a.m.

Dear FS experts,

I have a serial study in which I have run cross-sectional and longitudinal analysis on 5 time points. Now, I want to add a 6th time point to my dataset. Do I have to rerun my base template creation step from scratch or is there a way to just add further time points to an existing template?

Thanks Koushik

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Martin Reuter

14 Mar 14 Mar

10:30 a.m.

Hi Koushik,

there is a way to add time points without recreating the base: recon-all -long <tpNsubjid> <longbasesubjid> -addtp -all

This is what the recon-all help says about that: "If a new timepoint needs to be added to a longitudinal run where a base subject has already been created (from prior timepoints), then the -addtp command can be added to the -long command in order to 'fix-up' the longitudinal stream to accept the new timepoint. Note that the base subject is *not* recomputed using the new timepoint. This potentially introduces a bias, and it is recommended to NOT add a time point this way! Instead recreate the base from all time points and run all longitudinals again."

So it's up to you. But given you already have 5 time points in your base and add only 1, you may be fine. The base should be pretty stable with 5 and if the 6th is not too different, it should not matter much. I don't think anyone has ever done a thorough analysis about adding time points.

Best, Martin

On 03/11/2014 10:08 AM, Govindarajan, Koushik Athreya wrote:

...

Dear FS experts,
       I have a serial study in which I have run cross-sectional 
and longitudinal analysis on 5 time points. Now, I want to add a 6^th time point to my dataset. Do I have to rerun my base template creation step from scratch or is there a way to just add further time points to an existing template?

Thanks

Koushik

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

-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu

Govindarajan, Koushik Athreya

11:25 a.m.

New subject: adding time points to longitudinal base template {Disarmed}

Thanks Martin, I will try it out.

From: Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu] Sent: Friday, March 14, 2014 9:31 AM To: Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] adding time points to longitudinal base template

Hi Koushik,

there is a way to add time points without recreating the base: recon-all -long <tpNsubjid> <longbasesubjid> -addtp -all

Best, Martin

On 03/11/2014 10:08 AM, Govindarajan, Koushik Athreya wrote: Dear FS experts,

Thanks Koushik

_______________________________________________

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Martin Reuter, Ph.D.

Assistant in Neuroscience - Massachusetts General Hospital

Instructor in Neurology - Harvard Medical School

MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging

149 Thirteenth Street, Suite 2301

Charlestown, MA 02129

Phone: +1-617-724-5652

Email:

mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu

reuter@mit.edumailto:reuter@mit.edu

Web : http://reuter.mit.edu https://urldefense.proofpoint.com/v1/url?u=http://reuter.mit.edu&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0A&m=DVyhlZm48BQ7pEr20iqqosHWjgQ31wzMoC9FDk9YpEo%3D%0A&s=30e97dd7834b287056c1385ccff33fcd591a190ee3917c4441cadea4d971b918

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.

Govindarajan, Koushik Athreya

19 Mar 19 Mar

11:50 a.m.

New subject: adding time points to longitudinal base template {Disarmed}

Hi Martin,

I tried this method of -addtp to add a new time point but recon-all failed with the message saying my new timepoint was not in the 'base-tps' file of the base template. Should I be doing something else before I run this step?

Thanks Koushik

Hi Koushik,

there is a way to add time points without recreating the base: recon-all -long <tpNsubjid> <longbasesubjid> -addtp -all

Best, Martin

On 03/11/2014 10:08 AM, Govindarajan, Koushik Athreya wrote: Dear FS experts,

Thanks Koushik

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

Martin Reuter, Ph.D.

Assistant in Neuroscience - Massachusetts General Hospital

Instructor in Neurology - Harvard Medical School

MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging

149 Thirteenth Street, Suite 2301

Charlestown, MA 02129

Phone: +1-617-724-5652

Email:

mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu

reuter@mit.edumailto:reuter@mit.edu

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.

Martin Reuter

12:20 p.m.

New subject: adding time points to longitudinal base template {Disarmed}

Hi Koushik,

What version are you using? Not sure when we added this, maybe in 5.2. So you would need 5.3 for it.

If you use 5.3 already, can you send me the exact command and output.

Thanks, Martin

On 03/19/2014 11:50 AM, Govindarajan, Koushik Athreya wrote:

...

Hi Martin,
  I tried this method of --addtp to add a new time point but 
recon-all failed with the message saying my new timepoint was not in the 'base-tps' file of the base template. Should I be doing something else before I run this step?

Thanks

Koushik

*From:*Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu] *Sent:* Friday, March 14, 2014 9:31 AM *To:* Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] adding time points to longitudinal base template

Hi Koushik,

there is a way to add time points without recreating the base: recon-all -long <tpNsubjid> <longbasesubjid> -addtp -all

This is what the recon-all help says about that: "If a new timepoint needs to be added to a longitudinal run where a base subject has already been created (from prior timepoints), then the -addtp command can be added to the -long command in order to 'fix-up' the longitudinal stream to accept the new timepoint. Note that the base subject is *not* recomputed using the new timepoint. This potentially introduces a bias, and it is recommended to NOT add a time point this way! Instead recreate the base from all time points and run all longitudinals again."

So it's up to you. But given you already have 5 time points in your base and add only 1, you may be fine. The base should be pretty stable with 5 and if the 6th is not too different, it should not matter much. I don't think anyone has ever done a thorough analysis about adding time points.

Best, Martin

On 03/11/2014 10:08 AM, Govindarajan, Koushik Athreya wrote:
Dear FS experts,

           I have a serial study in which I have run
cross-sectional and longitudinal analysis on 5 time points. Now, I
want to add a 6^th time point to my dataset. Do I have to rerun my
base template creation step from scratch or is there a way to just
add further time points to an existing template?

Thanks

Koushik




_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>

*MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be*  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://urldefense.proofpoint.com/v1/url?u=https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0A&m=DVyhlZm48BQ7pEr20iqqosHWjgQ31wzMoC9FDk9YpEo%3D%0A&s=48648d97d14c3c96469c77ba99084506ab3a9eb1d6046d5937b5a35a037bce5d>
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129

Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edu mailto:reuter@mit.edu Web :*MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be* http://reuter.mit.edu https://urldefense.proofpoint.com/v1/url?u=http://reuter.mit.edu&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0A&m=DVyhlZm48BQ7pEr20iqqosHWjgQ31wzMoC9FDk9YpEo%3D%0A&s=30e97dd7834b287056c1385ccff33fcd591a190ee3917c4441cadea4d971b918

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.

-- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu

Govindarajan, Koushik Athreya

12:56 p.m.

New subject: adding time points to longitudinal base template {Disarmed} {Disarmed}

Hi Martin,

I use version 5.1. I did try this with version 5.3 also but I end up with the same error:

recon-all -long 23061_ip cr096_base -addtp -all ERROR: 23061_ip is not in /home/koushikg/data/longitudinal/cr096_base/base-tps

Thanks Koushik

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter Sent: Wednesday, March 19, 2014 11:21 AM To: Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] adding time points to longitudinal base template {Disarmed}

Hi Koushik,

What version are you using? Not sure when we added this, maybe in 5.2. So you would need 5.3 for it.

If you use 5.3 already, can you send me the exact command and output.

Thanks, Martin On 03/19/2014 11:50 AM, Govindarajan, Koushik Athreya wrote: Hi Martin,

Thanks Koushik

From: Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu] Sent: Friday, March 14, 2014 9:31 AM To: Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] adding time points to longitudinal base template

Hi Koushik,

there is a way to add time points without recreating the base: recon-all -long <tpNsubjid> <longbasesubjid> -addtp -all

Best, Martin

On 03/11/2014 10:08 AM, Govindarajan, Koushik Athreya wrote: Dear FS experts,

Thanks Koushik

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://urldefense.proofpoint.com/v1/url?u=https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0A&m=DVyhlZm48BQ7pEr20iqqosHWjgQ31wzMoC9FDk9YpEo%3D%0A&s=48648d97d14c3c96469c77ba99084506ab3a9eb1d6046d5937b5a35a037bce5d

Martin Reuter, Ph.D.

Assistant in Neuroscience - Massachusetts General Hospital

Instructor in Neurology - Harvard Medical School

MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging

149 Thirteenth Street, Suite 2301

Charlestown, MA 02129

Phone: +1-617-724-5652

Email:

mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu

reuter@mit.edumailto:reuter@mit.edu

Web : MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be http://reuter.mit.edu https://urldefense.proofpoint.com/v1/url?u=http://reuter.mit.edu&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0A&m=DVyhlZm48BQ7pEr20iqqosHWjgQ31wzMoC9FDk9YpEo%3D%0A&s=30e97dd7834b287056c1385ccff33fcd591a190ee3917c4441cadea4d971b918

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 https://urldefense.proofpoint.com/v1/url?u=http://www.partners.org/complianceline&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0A&m=WIEt0pBhhMz4urFZQWv%2BQ2t5ALMKMVNF1jb1W2E3JAQ%3D%0A&s=f298a877f57b8985c8dafbd26273f7ea1caac406cc250f9e6320494fb0ea0d5b . 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.

Martin Reuter, Ph.D.

Instructor in Neurology

Harvard Medical School

Assistant in Neuroscience

Dept. of Radiology, Massachusetts General Hospital

Dept. of Neurology, Massachusetts General Hospital

Research Affiliate

Computer Science and Artificial Intelligence Lab,

Dept. of Electrical Engineering and Computer Science,

Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging

149 Thirteenth Street, Suite 2301

Charlestown, MA 02129

Phone: +1-617-724-5652

Email:

mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu

reuter@mit.edumailto:reuter@mit.edu

Web : http://reuter.mit.edu https://urldefense.proofpoint.com/v1/url?u=http://reuter.mit.edu&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0A&m=WIEt0pBhhMz4urFZQWv%2BQ2t5ALMKMVNF1jb1W2E3JAQ%3D%0A&s=52d4bd081824057aeb06ab89425dfecbcc5bf7b669acde96875d7eb42a41e223

Martin Reuter

25 Mar 25 Mar

10:54 a.m.

New subject: adding time points to longitudinal base template {Disarmed} {Disarmed}

Hi Koushik,

there seems to be a bug. There's a safety check (that usually makes sense) but when adding a tp, of course it is not yet contained in the base.

Fix it by:

For Version 5.3 change the line 6148 in recon-all from if ( ! $found_tpNid ) then to if ( ! $found_tpNid && ! $DoAddTp ) then

for 5.1 change line 5407 from if ($status) then to if ( $status && ! $DoAddTp ) then

Good luck, Martin

On 03/19/2014 12:56 PM, Govindarajan, Koushik Athreya wrote:

...

Hi Martin,

 I use version 5.1. I did try this with version 5.3 also but I end

up with the same error:

recon-all --long 23061_ip cr096_base --addtp --all

ERROR: 23061_ip is not in /home/koushikg/data/longitudinal/cr096_base/base-tps

Thanks

Koushik

*From:*freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Martin Reuter *Sent:* Wednesday, March 19, 2014 11:21 AM *To:* Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] adding time points to longitudinal base template {Disarmed}

Hi Koushik,

What version are you using? Not sure when we added this, maybe in 5.2. So you would need 5.3 for it.

If you use 5.3 already, can you send me the exact command and output.

Thanks, Martin

On 03/19/2014 11:50 AM, Govindarajan, Koushik Athreya wrote:

Hi Martin,

      I tried this method of --addtp to add a new time point but
recon-all failed with the message saying my new timepoint was not
in the 'base-tps' file of the base template. Should I be doing
something else before I run this step?

Thanks

Koushik

*From:*Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu]
*Sent:* Friday, March 14, 2014 9:31 AM
*To:* Govindarajan, Koushik Athreya;
freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] adding time points to longitudinal
base template

Hi Koushik,

there is a way to add time points without recreating the base:
  recon-all -long <tpNsubjid> <longbasesubjid> -addtp -all

This is what the recon-all help says about that:
"If a new timepoint needs to be added to a longitudinal run where
a base subject
has already been created (from prior timepoints), then the -addtp
command
can be added to the -long command in order to 'fix-up' the
longitudinal
stream to accept the new timepoint. Note that the base subject is
*not*
recomputed using the new timepoint. This potentially introduces a
bias, and it
is recommended to NOT add a time point this way! Instead recreate
the base
from all time points and run all longitudinals again."

So it's up to you. But given you already have 5 time points in
your base and add only 1, you may be fine. The base should be
pretty stable with 5 and if the 6th is not too different, it
should not matter much. I don't think anyone has ever done a
thorough analysis about adding time points.

Best, Martin


On 03/11/2014 10:08 AM, Govindarajan, Koushik Athreya wrote:

    Dear FS experts,

               I have a serial study in which I have run
    cross-sectional and longitudinal analysis on 5 time points.
    Now, I want to add a 6^th time point to my dataset. Do I have
    to rerun my base template creation step from scratch or is
    there a way to just add further time points to an existing
    template?

    Thanks

    Koushik





    _______________________________________________

    Freesurfer mailing list

    Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>

    *MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be*  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://urldefense.proofpoint.com/v1/url?u=https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0A&m=DVyhlZm48BQ7pEr20iqqosHWjgQ31wzMoC9FDk9YpEo%3D%0A&s=48648d97d14c3c96469c77ba99084506ab3a9eb1d6046d5937b5a35a037bce5d>




-- 

Martin Reuter, Ph.D.

Assistant in Neuroscience - Massachusetts General Hospital

Instructor in Neurology   - Harvard Medical School

MGH / HMS / MIT



A.A.Martinos Center for Biomedical Imaging

149 Thirteenth Street, Suite 2301

Charlestown, MA 02129



Phone: +1-617-724-5652

Email:

    mreuter@nmr.mgh.harvard.edu  <mailto:mreuter@nmr.mgh.harvard.edu>

    reuter@mit.edu  <mailto:reuter@mit.edu>

Web  :*MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be*  http://reuter.mit.edu  <https://urldefense.proofpoint.com/v1/url?u=http://reuter.mit.edu&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0A&m=DVyhlZm48BQ7pEr20iqqosHWjgQ31wzMoC9FDk9YpEo%3D%0A&s=30e97dd7834b287056c1385ccff33fcd591a190ee3917c4441cadea4d971b918>  

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
*MailScanner has detected a possible fraud attempt from
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http://www.partners.org/complianceline
<https://urldefense.proofpoint.com/v1/url?u=http://www.partners.org/complianceline&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0A&m=WIEt0pBhhMz4urFZQWv%2BQ2t5ALMKMVNF1jb1W2E3JAQ%3D%0A&s=f298a877f57b8985c8dafbd26273f7ea1caac406cc250f9e6320494fb0ea0d5b>
. If the e-mail was sent to you in error
but does not contain patient information, please contact the
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dispose of the e-mail.

-- Martin Reuter, Ph.D.

Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129

Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edu mailto:reuter@mit.edu Web :*MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be* http://reuter.mit.edu https://urldefense.proofpoint.com/v1/url?u=http://reuter.mit.edu&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0A&m=WIEt0pBhhMz4urFZQWv%2BQ2t5ALMKMVNF1jb1W2E3JAQ%3D%0A&s=52d4bd081824057aeb06ab89425dfecbcc5bf7b669acde96875d7eb42a41e223

Govindarajan, Koushik Athreya

27 Mar 27 Mar

10:19 a.m.

New subject: adding time points to longitudinal base template {Disarmed} {Disarmed} {Disarmed}

Thanks Martin, I tried that on version 5.1 and it worked.

Regards Koushik

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter Sent: Tuesday, March 25, 2014 9:55 AM To: Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] adding time points to longitudinal base template {Disarmed} {Disarmed}

Hi Koushik,

there seems to be a bug. There's a safety check (that usually makes sense) but when adding a tp, of course it is not yet contained in the base.

Fix it by:

For Version 5.3 change the line 6148 in recon-all from if ( ! $found_tpNid ) then to if ( ! $found_tpNid && ! $DoAddTp ) then

for 5.1 change line 5407 from if ($status) then to if ( $status && ! $DoAddTp ) then

Good luck, Martin On 03/19/2014 12:56 PM, Govindarajan, Koushik Athreya wrote: Hi Martin,

I use version 5.1. I did try this with version 5.3 also but I end up with the same error:

recon-all -long 23061_ip cr096_base -addtp -all ERROR: 23061_ip is not in /home/koushikg/data/longitudinal/cr096_base/base-tps

Thanks Koushik

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter Sent: Wednesday, March 19, 2014 11:21 AM To: Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] adding time points to longitudinal base template {Disarmed}

Hi Koushik,

What version are you using? Not sure when we added this, maybe in 5.2. So you would need 5.3 for it.

If you use 5.3 already, can you send me the exact command and output.

Thanks, Martin On 03/19/2014 11:50 AM, Govindarajan, Koushik Athreya wrote: Hi Martin,

Thanks Koushik

Hi Koushik,

there is a way to add time points without recreating the base: recon-all -long <tpNsubjid> <longbasesubjid> -addtp -all

Best, Martin

On 03/11/2014 10:08 AM, Govindarajan, Koushik Athreya wrote: Dear FS experts,

Thanks Koushik

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Instructor in Neurology

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Dept. of Radiology, Massachusetts General Hospital

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Dept. of Electrical Engineering and Computer Science,

Massachusetts Institute of Technology

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Charlestown, MA 02129

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Govindarajan, Koushik Athreya
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