Hi Elijah,
Just create a link ln -s pathtofsaverage ./
Usually this is done during recon-all
Sent via my smartphone, please excuse brevity.
-------- Original message -------- From: Elijah Mak fkm24@medschl.cam.ac.uk Date:06/04/2014 7:17 AM (GMT-05:00) To: Martin Reuter mreuter@nmr.mgh.harvard.edu,freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed scans
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
Hi Martin,
Many thanks for your help!
How is fsaverage created?
I ran all my recon-alls (cross, base, and longs) in a single $Subject_DIR folder. Then , I moved the longs and bases to another folder for organizational purposes, which explains why the fsaverage is missing.
Is the fsverage study-specific? Or can I point the path of the fsverage to the same fsaverage that came with the original installation of Freesurfer?
Many thanks again.
Best Regards, Elijah
On Wed, Jun 4, 2014 at 3:17 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:
Hi Elijah,
Just create a link ln -s pathtofsaverage ./
Usually this is done during recon-all
Sent via my smartphone, please excuse brevity.
-------- Original message -------- From: Elijah Mak Date:06/04/2014 7:17 AM (GMT-05:00) To: Martin Reuter ,freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed scans
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
-- Elijah Mak, Gates Scholar
PhD Candidate | Psychiatry
University of Cambridge | Department of Psychiatry
Trinity College, Cambridge, CB2 1TQ
freesurfer@nmr.mgh.harvard.edu
-
Elijah Mak -
Martin Reuter