Hi Sara,

yes, should work, just make sure that all cross are 5.1 (and not mixed) to remain consistent. By the way 5.1 can process differently many time points for each subject. Just not subjects with a single time point only. To include those you'd need 5.2

Best, Martin

On 03/06/2013 01:32 PM, Nick Schmansky wrote:

Sarah,

I'm cc'ing martin reuter on this, but yes, you should be able to use your cross-sectionally processed scans from v5.1 in a longitudinal analysis using v5.2.

Nick

On Wed, 2013-03-06 at 05:46 +0000, Sarah Whittle wrote:

...

Hi,

RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all of the possible combinations of longitudinal scans.

e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3

Obviously the new feature in version 5.2 (i.e., being able to run all images together, regardless of whether some time points are missing for some people) would be MUCH better. Is this possible to do using our 5.1 cross-sectionally processed images? Given the time we've put into manual editing, we really wouldn't want to have to run everything again through 5.2.

Thanks,

Sarah

.... Hi Henk-Jan,

to avoid bias between subjects with single time points and others, we run them through the same steps. This way it is possible to include them into the statistical analysis. (For this an artificial base is created with the head in an upright and straight position).

This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single time point to the -base and then run it with -long. Nice and transparent :-).

Anyway, you probably should wait till 5.2. There is several programs that changed for this to work. Also the current recon-all contains many changes not related to this. If you absolutely cannot wait, let me know and I'll take a look at how difficult it is to go back and adjust 5.1.

Best, Martin

On Tue, 2012-12-04 at 17:06 +0000, Westeneng, H.J. wrote:

...

Hi Freesurfer experts,

This week a read the article of Bernal-Rusiel et al. titled “Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models”. In this article you described the submission of single time-point scans to the longitudinal pipeline of Freesurfer. I’m very interested in how to do this. Your help will be appreciated.

Thanks in advance,

Henk-Jan

---

De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.

Denk s.v.p aan het milieu voor u deze e-mail afdrukt.

---

This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197.

Please consider the environment before printing this e-mail.

---

Freesurfer mailing list Freesurfer at 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

Hi Sarah   The linear mixed effects (LME) estimation procedure deals with missing data and variable timing across subjects by specifying the time interval since baseline for each scan. You will have a different number of rows for each subject in your design matrix depending on how many time points they have.   If your data exhibit significant between-subject variability in between-scan time intervals and number of time points, and several subjects with a single time point then you should use our LME matlab toolbox for the statistics.   Best -Jorge

---

De: Sarah Whittle swhittle@unimelb.edu.au Para: Martin Reuter mreuter@nmr.mgh.harvard.edu; Nick Schmansky nicks@nmr.mgh.harvard.edu CC: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Enviado: Miércoles 6 de marzo de 2013 17:17 Asunto: Re: [Freesurfer] Longitudinal analysis of one timepoint

Thanks Martin and Nick,

We have a number of subjects with single time points too, so I think 5.2 is the best way to go.

Is there a way to specify which subjects have data at what time points. For example, if one subject has data at Time 1 and Time 3, and another has data at Time 2 and Time 3, can this info be fed into freesurfer somehow? Or, do you just deal with this during post processing by specifying the years between scans (which would be different for these two cases)?

Also, when creating the longitudinal .dat file, I assume you would have a different number of rows for each subject depending on how many time points they have, and the value you would enter for 'years' would just be years since baseline?

Finally, can you use QDEC with three time points? Or would linear mixed effects models be the way to go?

Thanks,

Sarah ________________________________________ From: Martin Reuter [mreuter@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 5:41 AM To: Nick Schmansky Cc: Sarah Whittle; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sara,

yes, should work, just make sure that all cross are 5.1  (and not mixed) to remain consistent. By the way 5.1 can process differently many time points for each subject. Just not subjects with a single time point only. To include those you'd need 5.2

Best, Martin

On 03/06/2013 01:32 PM, Nick Schmansky wrote:

...

Sarah,

I'm cc'ing martin reuter on this, but yes, you should be able to use your cross-sectionally processed scans from v5.1 in a longitudinal analysis using v5.2.

Nick

On Wed, 2013-03-06 at 05:46 +0000, Sarah Whittle wrote:

...

Hi,

RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all of the possible combinations of longitudinal scans.

e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3

Obviously the new feature in version 5.2 (i.e., being able to run all images together, regardless of whether some time points are missing for some people) would be MUCH better. Is this possible to do using our 5.1 cross-sectionally processed images? Given the time we've put into manual editing, we really wouldn't want to have to run everything again through 5.2.

Thanks,

Sarah

.... Hi Henk-Jan,

to avoid bias between subjects with single time points and others, we run them through the same steps. This way it is possible to include them into the statistical analysis. (For this an artificial base is created with the head in an upright and straight position).

This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single time point to the -base and then run it with -long. Nice and transparent :-).

Anyway, you probably should wait till 5.2. There is several programs that changed for this to work. Also the current recon-all contains many changes not related to this. If you absolutely cannot wait, let me know and I'll take a look at how difficult it is to go back and adjust 5.1.

Best, Martin

On Tue, 2012-12-04 at 17:06 +0000, Westeneng, H.J. wrote:

...

Hi Freesurfer experts,

This week a read the article of Bernal-Rusiel et al. titled “Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models”. In this article you described the submission of single time-point scans to the longitudinal pipeline of Freesurfer. I’m very interested in how to do this. Your help will be appreciated.

Thanks in advance,

Henk-Jan

---

De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.

Denk s.v.p aan het milieu voor u deze e-mail afdrukt.

---

This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197.

Please consider the environment before printing this e-mail.

---

Freesurfer mailing list Freesurfer at 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

-- Dr. Martin Reuter 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/

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

Thanks very much! ________________________________________ From: Martin Reuter [mreuter@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 10:22 AM To: Sarah Whittle Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sarah,

you deal with the time during post-processing (statistical analysis).

Yes, you have differently many rows for each subject. Years could be time from baseline, or time from start of study (e.g. start of drug treatment). It may be the same, but if some subjects are missing the baseline scan in a drug study it may be better to use the start of the drug instead of the first scan.

Mixed effects model is the way to go.

Best, Martin

On 03/06/2013 05:17 PM, Sarah Whittle wrote:

Thanks Martin and Nick,

We have a number of subjects with single time points too, so I think 5.2 is the best way to go.

Is there a way to specify which subjects have data at what time points. For example, if one subject has data at Time 1 and Time 3, and another has data at Time 2 and Time 3, can this info be fed into freesurfer somehow? Or, do you just deal with this during post processing by specifying the years between scans (which would be different for these two cases)?

Also, when creating the longitudinal .dat file, I assume you would have a different number of rows for each subject depending on how many time points they have, and the value you would enter for 'years' would just be years since baseline?

Finally, can you use QDEC with three time points? Or would linear mixed effects models be the way to go?

Thanks,

Sarah ________________________________________ From: Martin Reuter [mreuter@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 5:41 AM To: Nick Schmansky Cc: Sarah Whittle; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sara,

yes, should work, just make sure that all cross are 5.1 (and not mixed) to remain consistent. By the way 5.1 can process differently many time points for each subject. Just not subjects with a single time point only. To include those you'd need 5.2

Best, Martin

On 03/06/2013 01:32 PM, Nick Schmansky wrote:

...

Sarah,

I'm cc'ing martin reuter on this, but yes, you should be able to use your cross-sectionally processed scans from v5.1 in a longitudinal analysis using v5.2.

Nick

On Wed, 2013-03-06 at 05:46 +0000, Sarah Whittle wrote:

...

Hi,

RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all of the possible combinations of longitudinal scans.

e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3

Obviously the new feature in version 5.2 (i.e., being able to run all images together, regardless of whether some time points are missing for some people) would be MUCH better. Is this possible to do using our 5.1 cross-sectionally processed images? Given the time we've put into manual editing, we really wouldn't want to have to run everything again through 5.2.

Thanks,

Sarah

.... Hi Henk-Jan,

to avoid bias between subjects with single time points and others, we run them through the same steps. This way it is possible to include them into the statistical analysis. (For this an artificial base is created with the head in an upright and straight position).

This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single time point to the -base and then run it with -long. Nice and transparent :-).

Anyway, you probably should wait till 5.2. There is several programs that changed for this to work. Also the current recon-all contains many changes not related to this. If you absolutely cannot wait, let me know and I'll take a look at how difficult it is to go back and adjust 5.1.

Best, Martin

On Tue, 2012-12-04 at 17:06 +0000, Westeneng, H.J. wrote:

...

Hi Freesurfer experts,

This week a read the article of Bernal-Rusiel et al. titled “Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models”. In this article you described the submission of single time-point scans to the longitudinal pipeline of Freesurfer. I’m very interested in how to do this. Your help will be appreciated.

Thanks in advance,

Henk-Jan

---

De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.

Denk s.v.p aan het milieu voor u deze e-mail afdrukt.

---

This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197.

Please consider the environment before printing this e-mail.

---

Freesurfer mailing list Freesurfer at 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

-- Dr. Martin Reuter 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

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.

-- Dr. Martin Reuter 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

Hi Sarah,

you should be able to find out how to split strings and loop over entries somewhere online. there is lots of documentations and forums concerned with shell scripting out there.

something like: read each string split it at the ',' take the first as base and loop over the rest

I probably would use python for it.

Best, Martin

On 03/21/2013 06:26 AM, Sarah Whittle wrote:

Hi Martin,

Just following up on the below, we're having trouble deciding the best way to run all of the images through the longitudinal stream.

We have a text file (subjects.txt), specifying the base, and time point ID's for each participant. Base comes first, and follow-up images are the base ID_timepoint (e,g., _1, _2, _3). An example for just a few subjects:

110,110_1,110_2,110_3 2403,2403_1,2403_3 2928,2928_1,2928_2,2928_3 2932,2932_1,2932_2 3026,3026_1 3335,3335_1,3335_2,3335_3 352,352_1,352_2,352_3 5115,5115_2,5115_3

Then we run a script to allocate these files to base, time point 1, time point 2, etc.:

SUBJLIST=`cat subjecs..txt` for SUBJ in $SUBJLIST

do

TEMPID=`echo $SUBJ|awk '{print $1}' FS=","` TP1=`echo $SUBJ|awk '{print $2}' FS=","` TP2=`echo $SUBJ|awk '{print $3}' FS=","` TP3=`echo $SUBJ|awk '{print $4}' FS=","`

-v SUBJ_TEMPID=$TEMPID,SUBJ_TP1=$TP1,SUBJ_TP2=$TP2,SUBJ_TP3=$TP3

done

recon-all -base $SUBJ_TEMPID -tp $SUBJ_TP1 -tp $SUBJ_TP2 -tp $SUBJ_TP3 -all -nuintensitycor-3T

recon-all -long $SUBJ_TP1 $SUBJ_TEMPID -all -nuintensitycor-3T

recon-all -long $SUBJ_TP2 $SUBJ_TEMPID -all -nuintensitycor-3T"

recon-all -long $SUBJ_TP3 $SUBJ_TEMPID -all -nuintensitycor-3T"

This falls over because there's not base + three images in each row of the subject list. I assume we'll have to make some kind of IF THEN statements to run these commands separately or individuals that have had 1, 2 or 3 scans?

Is there a simpler way of doing this though?? I feel like we're making things more complicated than they need to be!

Thanks,

Sarah

---

From: Martin Reuter [mreuter@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 10:22 AM To: Sarah Whittle Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sarah,

you deal with the time during post-processing (statistical analysis).

Yes, you have differently many rows for each subject. Years could be time from baseline, or time from start of study (e.g. start of drug treatment). It may be the same, but if some subjects are missing the baseline scan in a drug study it may be better to use the start of the drug instead of the first scan.

Mixed effects model is the way to go.

Best, Martin

On 03/06/2013 05:17 PM, Sarah Whittle wrote:

...

Thanks Martin and Nick,

We have a number of subjects with single time points too, so I think 5.2 is the best way to go.

Is there a way to specify which subjects have data at what time points. For example, if one subject has data at Time 1 and Time 3, and another has data at Time 2 and Time 3, can this info be fed into freesurfer somehow? Or, do you just deal with this during post processing by specifying the years between scans (which would be different for these two cases)?

Also, when creating the longitudinal .dat file, I assume you would have a different number of rows for each subject depending on how many time points they have, and the value you would enter for 'years' would just be years since baseline?

Finally, can you use QDEC with three time points? Or would linear mixed effects models be the way to go?

Thanks,

Sarah ________________________________________ From: Martin Reuter [mreuter@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 5:41 AM To: Nick Schmansky Cc: Sarah Whittle; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sara,

yes, should work, just make sure that all cross are 5.1 (and not mixed) to remain consistent. By the way 5.1 can process differently many time points for each subject. Just not subjects with a single time point only. To include those you'd need 5.2

Best, Martin

On 03/06/2013 01:32 PM, Nick Schmansky wrote:

...

Sarah,

I'm cc'ing martin reuter on this, but yes, you should be able to use your cross-sectionally processed scans from v5.1 in a longitudinal analysis using v5.2.

Nick

On Wed, 2013-03-06 at 05:46 +0000, Sarah Whittle wrote:

...

Hi,

RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all of the possible combinations of longitudinal scans.

e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3

Obviously the new feature in version 5.2 (i.e., being able to run all images together, regardless of whether some time points are missing for some people) would be MUCH better. Is this possible to do using our 5.1 cross-sectionally processed images? Given the time we've put into manual editing, we really wouldn't want to have to run everything again through 5.2.

Thanks,

Sarah

.... Hi Henk-Jan,

to avoid bias between subjects with single time points and others, we run them through the same steps. This way it is possible to include them into the statistical analysis. (For this an artificial base is created with the head in an upright and straight position).

This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single time point to the -base and then run it with -long. Nice and transparent :-).

Anyway, you probably should wait till 5.2. There is several programs that changed for this to work. Also the current recon-all contains many changes not related to this. If you absolutely cannot wait, let me know and I'll take a look at how difficult it is to go back and adjust 5.1.

Best, Martin

On Tue, 2012-12-04 at 17:06 +0000, Westeneng, H.J. wrote:

...

Hi Freesurfer experts,

This week a read the article of Bernal-Rusiel et al. titled “Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models”. In this article you described the submission of single time-point scans to the longitudinal pipeline of Freesurfer. I’m very interested in how to do this. Your help will be appreciated.

Thanks in advance,

Henk-Jan

---

De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.

Denk s.v.p aan het milieu voor u deze e-mail afdrukt.

---

This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197.

Please consider the environment before printing this e-mail.

---

Freesurfer mailing list Freesurfer at 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

-- Dr. Martin Reuter 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

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.

-- Dr. Martin Reuter 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

Hi,

Given the issues discovered with 5.2, we're now wondering whether we should just go back to 5.1 or wait until 5.3 (under a bit of time pressure).

Can I just clarify the how the capability of 5.2 (and 5.3) to run subjects with single time points in longitudinal analysis (by creating an artificial, upright and straight base image) is better than just using the cross-sectional output from single subject data in longitudinal analysis?

Is it because for linear mixed effects models analysis you need a base template for each time point?

Thanks,

Sarah ________________________________________ From: Sarah Whittle Sent: Friday, 22 March 2013 6:50 AM To: Martin Reuter Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Longitudinal analysis of one timepoint

Ok, thank you. ________________________________________ From: Martin Reuter [mreuter@nmr.mgh.harvard.edu] Sent: Friday, 22 March 2013 12:36 AM To: Sarah Whittle Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sarah,

you should be able to find out how to split strings and loop over entries somewhere online. there is lots of documentations and forums concerned with shell scripting out there.

something like: read each string split it at the ',' take the first as base and loop over the rest

I probably would use python for it.

Best, Martin

On 03/21/2013 06:26 AM, Sarah Whittle wrote:

Hi Martin,

Just following up on the below, we're having trouble deciding the best way to run all of the images through the longitudinal stream.

We have a text file (subjects.txt), specifying the base, and time point ID's for each participant. Base comes first, and follow-up images are the base ID_timepoint (e,g., _1, _2, _3). An example for just a few subjects:

110,110_1,110_2,110_3 2403,2403_1,2403_3 2928,2928_1,2928_2,2928_3 2932,2932_1,2932_2 3026,3026_1 3335,3335_1,3335_2,3335_3 352,352_1,352_2,352_3 5115,5115_2,5115_3

Then we run a script to allocate these files to base, time point 1, time point 2, etc.:

SUBJLIST=`cat subjecs..txt` for SUBJ in $SUBJLIST

do

TEMPID=`echo $SUBJ|awk '{print $1}' FS=","` TP1=`echo $SUBJ|awk '{print $2}' FS=","` TP2=`echo $SUBJ|awk '{print $3}' FS=","` TP3=`echo $SUBJ|awk '{print $4}' FS=","`

-v SUBJ_TEMPID=$TEMPID,SUBJ_TP1=$TP1,SUBJ_TP2=$TP2,SUBJ_TP3=$TP3

done

recon-all -base $SUBJ_TEMPID -tp $SUBJ_TP1 -tp $SUBJ_TP2 -tp $SUBJ_TP3 -all -nuintensitycor-3T

recon-all -long $SUBJ_TP1 $SUBJ_TEMPID -all -nuintensitycor-3T

recon-all -long $SUBJ_TP2 $SUBJ_TEMPID -all -nuintensitycor-3T"

recon-all -long $SUBJ_TP3 $SUBJ_TEMPID -all -nuintensitycor-3T"

This falls over because there's not base + three images in each row of the subject list. I assume we'll have to make some kind of IF THEN statements to run these commands separately or individuals that have had 1, 2 or 3 scans?

Is there a simpler way of doing this though?? I feel like we're making things more complicated than they need to be!

Thanks,

Sarah

---

From: Martin Reuter [mreuter@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 10:22 AM To: Sarah Whittle Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sarah,

you deal with the time during post-processing (statistical analysis).

Yes, you have differently many rows for each subject. Years could be time from baseline, or time from start of study (e.g. start of drug treatment). It may be the same, but if some subjects are missing the baseline scan in a drug study it may be better to use the start of the drug instead of the first scan.

Mixed effects model is the way to go.

Best, Martin

On 03/06/2013 05:17 PM, Sarah Whittle wrote:

...

Thanks Martin and Nick,

We have a number of subjects with single time points too, so I think 5.2 is the best way to go.

Is there a way to specify which subjects have data at what time points. For example, if one subject has data at Time 1 and Time 3, and another has data at Time 2 and Time 3, can this info be fed into freesurfer somehow? Or, do you just deal with this during post processing by specifying the years between scans (which would be different for these two cases)?

Also, when creating the longitudinal .dat file, I assume you would have a different number of rows for each subject depending on how many time points they have, and the value you would enter for 'years' would just be years since baseline?

Finally, can you use QDEC with three time points? Or would linear mixed effects models be the way to go?

Thanks,

Sarah ________________________________________ From: Martin Reuter [mreuter@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 5:41 AM To: Nick Schmansky Cc: Sarah Whittle; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sara,

yes, should work, just make sure that all cross are 5.1 (and not mixed) to remain consistent. By the way 5.1 can process differently many time points for each subject. Just not subjects with a single time point only. To include those you'd need 5.2

Best, Martin

On 03/06/2013 01:32 PM, Nick Schmansky wrote:

...

Sarah,

I'm cc'ing martin reuter on this, but yes, you should be able to use your cross-sectionally processed scans from v5.1 in a longitudinal analysis using v5.2.

Nick

On Wed, 2013-03-06 at 05:46 +0000, Sarah Whittle wrote:

...

Hi,

RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all of the possible combinations of longitudinal scans.

e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3

Obviously the new feature in version 5.2 (i.e., being able to run all images together, regardless of whether some time points are missing for some people) would be MUCH better. Is this possible to do using our 5.1 cross-sectionally processed images? Given the time we've put into manual editing, we really wouldn't want to have to run everything again through 5.2.

Thanks,

Sarah

.... Hi Henk-Jan,

to avoid bias between subjects with single time points and others, we run them through the same steps. This way it is possible to include them into the statistical analysis. (For this an artificial base is created with the head in an upright and straight position).

This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single time point to the -base and then run it with -long. Nice and transparent :-).

Anyway, you probably should wait till 5.2. There is several programs that changed for this to work. Also the current recon-all contains many changes not related to this. If you absolutely cannot wait, let me know and I'll take a look at how difficult it is to go back and adjust 5.1.

Best, Martin

On Tue, 2012-12-04 at 17:06 +0000, Westeneng, H.J. wrote:

...

Hi Freesurfer experts,

This week a read the article of Bernal-Rusiel et al. titled “Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models”. In this article you described the submission of single time-point scans to the longitudinal pipeline of Freesurfer. I’m very interested in how to do this. Your help will be appreciated.

Thanks in advance,

Henk-Jan

---

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Denk s.v.p aan het milieu voor u deze e-mail afdrukt.

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This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197.

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Freesurfer mailing list Freesurfer at 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

-- Dr. Martin Reuter 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

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.

-- Dr. Martin Reuter 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

-- Dr. Martin Reuter 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

Sarah,

Hi, to help you decide, since I dont know what your study entails or the timeline, this is some info:

- bug in 5.2 affects just white and pial surface placement, so thickness and area data will be off. surface registration, and its off-shoot data, like aparc labels and inter-subject surface registration, are unaffected by the bug.

- we're doing everything we can to get the new release out in less than two weeks. but by monday, there should be a beta of each platform (centos6_x86_64 already there) posted here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/

if the extensive testing passes, then the beta becomes the release (although in between we will be updating freeview with new features and a speed increase in scrolling).

Hope this helps, sorry for the interruption!

Nick

Hi Sarah. I cannot comment on 5.1 vs waiting for 5.3.

About the single time point. The reason is not that we need the base. We just want to make sure that that image undergoes the same processing steps as all other images to avoid a processing bias. Mixed effects models allow inclusion of subjects with single time points so it makes sense to include them to gain power. Best Martin

Sarah Whittle swhittle@unimelb.edu.au wrote:

...

Hi,

Given the issues discovered with 5.2, we're now wondering whether we should just go back to 5.1 or wait until 5.3 (under a bit of time pressure).

Can I just clarify the how the capability of 5.2 (and 5.3) to run subjects with single time points in longitudinal analysis (by creating an artificial, upright and straight base image) is better than just using the cross-sectional output from single subject data in longitudinal analysis?

Is it because for linear mixed effects models analysis you need a base template for each time point?

Thanks,

Sarah ________________________________________ From: Sarah Whittle Sent: Friday, 22 March 2013 6:50 AM To: Martin Reuter Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Longitudinal analysis of one timepoint

Ok, thank you. ________________________________________ From: Martin Reuter [mreuter@nmr.mgh.harvard.edu] Sent: Friday, 22 March 2013 12:36 AM To: Sarah Whittle Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sarah,

you should be able to find out how to split strings and loop over entries somewhere online. there is lots of documentations and forums concerned with shell scripting out there.

something like: read each string split it at the ',' take the first as base and loop over the rest

I probably would use python for it.

Best, Martin

On 03/21/2013 06:26 AM, Sarah Whittle wrote:

...

Hi Martin,

Just following up on the below, we're having trouble deciding the

best way to run all of the images through the longitudinal stream.

...

We have a text file (subjects.txt), specifying the base, and time

point ID's for each participant. Base comes first, and follow-up images are the base ID_timepoint (e,g., _1, _2, _3). An example for just a few subjects:

...

110,110_1,110_2,110_3 2403,2403_1,2403_3 2928,2928_1,2928_2,2928_3 2932,2932_1,2932_2 3026,3026_1 3335,3335_1,3335_2,3335_3 352,352_1,352_2,352_3 5115,5115_2,5115_3

Then we run a script to allocate these files to base, time point 1,

time point 2, etc.:

...

SUBJLIST=`cat subjecs..txt` for SUBJ in $SUBJLIST

do

TEMPID=`echo $SUBJ|awk '{print $1}' FS=","` TP1=`echo $SUBJ|awk '{print $2}' FS=","` TP2=`echo $SUBJ|awk '{print $3}' FS=","` TP3=`echo $SUBJ|awk '{print $4}' FS=","`

-v SUBJ_TEMPID=$TEMPID,SUBJ_TP1=$TP1,SUBJ_TP2=$TP2,SUBJ_TP3=$TP3

done

recon-all -base $SUBJ_TEMPID -tp $SUBJ_TP1 -tp $SUBJ_TP2 -tp

$SUBJ_TP3 -all -nuintensitycor-3T

...

recon-all -long $SUBJ_TP1 $SUBJ_TEMPID -all -nuintensitycor-3T

recon-all -long $SUBJ_TP2 $SUBJ_TEMPID -all -nuintensitycor-3T"

recon-all -long $SUBJ_TP3 $SUBJ_TEMPID -all -nuintensitycor-3T"

This falls over because there's not base + three images in each row

of the subject list. I assume we'll have to make some kind of IF THEN statements to run these commands separately or individuals that have had 1, 2 or 3 scans?

...

Is there a simpler way of doing this though?? I feel like we're

making things more complicated than they need to be!

...

Thanks,

Sarah

---

From: Martin Reuter [mreuter@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 10:22 AM To: Sarah Whittle Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sarah,

you deal with the time during post-processing (statistical analysis).

Yes, you have differently many rows for each subject. Years could be time from baseline, or time from start of study (e.g. start of drug treatment). It may be the same, but if some subjects

are

...

missing the baseline scan in a drug study it may be better to use the start of the drug instead of the first scan.

Mixed effects model is the way to go.

Best, Martin

On 03/06/2013 05:17 PM, Sarah Whittle wrote:

...

Thanks Martin and Nick,

We have a number of subjects with single time points too, so I think

5.2 is the best way to go.

...

...

Is there a way to specify which subjects have data at what time

points. For example, if one subject has data at Time 1 and Time 3, and another has data at Time 2 and Time 3, can this info be fed into freesurfer somehow? Or, do you just deal with this during post processing by specifying the years between scans (which would be different for these two cases)?

...

...

Also, when creating the longitudinal .dat file, I assume you would

have a different number of rows for each subject depending on how many time points they have, and the value you would enter for 'years' would just be years since baseline?

...

...

Finally, can you use QDEC with three time points? Or would linear

mixed effects models be the way to go?

...

...

Thanks,

Sarah ________________________________________ From: Martin Reuter [mreuter@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 5:41 AM To: Nick Schmansky Cc: Sarah Whittle; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sara,

yes, should work, just make sure that all cross are 5.1 (and not

mixed)

...

...

to remain consistent. By the way 5.1 can process differently many time points for each subject. Just not subjects with a single time point only. To include those you'd need 5.2

Best, Martin

On 03/06/2013 01:32 PM, Nick Schmansky wrote:

...

Sarah,

I'm cc'ing martin reuter on this, but yes, you should be able to

use

...

...

...

your cross-sectionally processed scans from v5.1 in a longitudinal analysis using v5.2.

Nick

On Wed, 2013-03-06 at 05:46 +0000, Sarah Whittle wrote:

...

Hi,

RE the below post, we have longitudinal data from three time

points,

...

...

...

...

but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including

a

...

...

...

...

lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all

of

...

...

...

...

the possible combinations of longitudinal scans.

e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3

Obviously the new feature in version 5.2 (i.e., being able to run

all

...

...

...

...

images together, regardless of whether some time points are

missing

...

...

...

...

for some people) would be MUCH better. Is this possible to do

using

...

...

...

...

our 5.1 cross-sectionally processed images? Given the time we've

put

...

...

...

...

into manual editing, we really wouldn't want to have to run

everything

...

...

...

...

again through 5.2.

Thanks,

Sarah

.... Hi Henk-Jan,

to avoid bias between subjects with single time points and others,

we

...

...

...

...

run them through the same steps. This way it is possible to

include them

...

...

...

...

into the statistical analysis. (For this an artificial base is

created

...

...

...

...

with the head in an upright and straight position).

This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single

time

...

...

...

...

point to the -base and then run it with -long. Nice and transparent :-).

Anyway, you probably should wait till 5.2. There is several

programs

...

...

...

...

that changed for this to work. Also the current recon-all contains

many

...

...

...

...

changes not related to this. If you absolutely cannot wait, let me

know

...

...

...

...

and I'll take a look at how difficult it is to go back and adjust

5.1.

...

...

...

...

Best, Martin

On Tue, 2012-12-04 at 17:06 +0000, Westeneng, H.J. wrote: > Hi Freesurfer experts, > > > > This week a read the article of Bernal-Rusiel et al. titled > “Statistical analysis of longitudinal neuroimage data with Linear > Mixed Effects models”. In this article you described the

submission of

...

...

...

...

> single time-point scans to the longitudinal pipeline of

Freesurfer.

...

...

...

...

> I’m very interested in how to do this. Your help will be

appreciated.

...

...

...

...

> > > > Thanks in advance, > > > > Henk-Jan > > > >

---

...

...

...

...

> > De informatie opgenomen in dit bericht kan vertrouwelijk zijn en

is

...

...

...

...

> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht > onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken

en de

...

...

...

...

> afzender direct te informeren door het bericht te retourneren.

Het

...

...

...

...

> Universitair Medisch Centrum Utrecht is een publiekrechtelijke > rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en > Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer

van

...

...

...

...

> Koophandel voor Midden-Nederland onder nr. 30244197. > > Denk s.v.p aan het milieu voor u deze e-mail afdrukt. > > >

---

...

...

...

...

> > This message may contain confidential information and is intended > exclusively for the addressee. If you receive this message > unintentionally, please do not use the contents but notify the

sender

...

...

...

...

> immediately by return e-mail. University Medical Center Utrecht

is a

...

...

...

...

> legal person by public law and is registered at the Chamber of > Commerce for Midden-Nederland under no. 30244197. > > Please consider the environment before printing this e-mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer at 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

-- Dr. Martin Reuter 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

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.

-- Dr. Martin Reuter 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

-- Dr. Martin Reuter 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

-- Sent from my Android phone with K-9 Mail. Please excuse my brevity.