Hi Martin,

Thank you for your help.

By re-processing, do you mean running recon-alls all over again?

Could you elaborate on the advantage of creating a new subjectsdir and copying over the orig dirs for each subject?

On a related note, would it be better to run the full recon-all pipeline for each subject? I have been running batches of subjects at each stage (i.e. autorecon1, autorecon2, and finally autorecon3).

Thank you again.

Best Wishes, Elijah

On Wed, Jan 15, 2014 at 9:02 PM, Martin Reuter mreuter@nmr.mgh.harvard.eduwrote:

Hi Elijah,

if you have minimal edits, I'd recommend to reprocess the data from scratch with 5.3 (that is supposed to be the same as using the -clean flag when rerunning 5.3 on top of the old 5.0 data). But I'd recommend to create a new subjectsdir, copy over the subjedid/mri/orig dirs for each subject and rerun from scratch with 5.3 the independent, base and long runs.

Best, Martin

On 01/13/2014 06:18 PM, Elijah Mak wrote:

Greetings Freesurfer Community,

I am running a longitudinal study using Freesurfer v.5.3 to compare rate of cortical thinning between 2 groups of subjects. I hope I can seek some expert advice on the following situation:

All data (both the baseline and follow-up) has been processed independently using recon-all. This has been done on Freesurfer 5.0.

Since then, I have upgraded to Freesurfer v5.3 to utilize the linear mixed effect capability.

For the construction of base and longs, I understand that it is important to add -clean flag to my recon-all strings to overwrite brainmask.mgz etc. When must this be done?

I am still new to Freesurer, and I'd greatly appreciate any advice regarding workflow.

Many Thanks,

Elijah

--

Elijah Mak, B.A.

Doctoral Candidate *|* Psychiatry

University of Cambridge *| *Department of Psychiatry

Trinity College, Cambridge, CB2 1TQ

---

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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

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.

Hi Martin,

We corresponded about the longitudinal pipeline earlier. Your help has been much appreciated. I am now at the stage where I am ready to perform QDEC analyses using the 2-stage method.

In my Subject DIR, I have all the longs (Tp1 and 2) and their corresponding bases. However, when i run the following command

long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR

It says that fsaverage is missing.

Can I simply copy the fsverage folder from the default Freesurfer "subjects" folder?

Many thanks! Best Regards, Elijah

On Wed, Jan 15, 2014 at 10:15 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:

Hi Elijah,

On 01/15/2014 04:10 PM, Elijah Mak wrote:

Hi Martin,

Thank you for your help.

By re-processing, do you mean running recon-alls all over again?

Yes. 5.0 is old and it is better to run everything with 5.3 from beginning to end. If you have a lot of data or a lot of edits, you can try running -base and -long in 5.3 and keep the independent (cross sectional) stuff in 5.0, but I don't recommend mixing versions.

Could you elaborate on the advantage of creating a new subjectsdir and copying over the orig dirs for each subject?

This way you keep a backup copy of your old 5.0 processed data (to lookup edits etc). If you have a script that calls recon-all with the -i flag for inputs, you don't need to copy the mri/orig dirs (it will grab the data from the dicoms again). Copying the orig dirs and dropping -i will skip that step.

On a related note, would it be better to run the full recon-all pipeline for each subject? I have been running batches of subjects at each stage (i.e. autorecon1, autorecon2, and finally autorecon3).

Yes, full pipeline (-all) on all subjects is what I usually do. You can run individual steps and check intermediate results if you like, but I usually run everything and check everything at the end.

Best, Martin

Thank you again.

Best Wishes, Elijah

On Wed, Jan 15, 2014 at 9:02 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:

...

Hi Elijah,

if you have minimal edits, I'd recommend to reprocess the data from scratch with 5.3 (that is supposed to be the same as using the -clean flag when rerunning 5.3 on top of the old 5.0 data). But I'd recommend to create a new subjectsdir, copy over the subjedid/mri/orig dirs for each subject and rerun from scratch with 5.3 the independent, base and long runs.

Best, Martin

On 01/13/2014 06:18 PM, Elijah Mak wrote:

Greetings Freesurfer Community,

I am running a longitudinal study using Freesurfer v.5.3 to compare rate of cortical thinning between 2 groups of subjects. I hope I can seek some expert advice on the following situation:

All data (both the baseline and follow-up) has been processed independently using recon-all. This has been done on Freesurfer 5.0.

Since then, I have upgraded to Freesurfer v5.3 to utilize the linear mixed effect capability.

For the construction of base and longs, I understand that it is important to add -clean flag to my recon-all strings to overwrite brainmask.mgz etc. When must this be done?

I am still new to Freesurer, and I'd greatly appreciate any advice regarding workflow.

Many Thanks,

Elijah

--

Elijah Mak, B.A.

Doctoral Candidate | Psychiatry

University of Cambridge | Department of Psychiatry

Trinity College, Cambridge, CB2 1TQ

---

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

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.

--

Elijah Mak, B.A.

Doctoral Candidate | Psychiatry

University of Cambridge | Department of Psychiatry

Trinity College, Cambridge, CB2 1TQ

-- 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