The one that comes with Freesurfer. It's always the same. Best Martin
Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Elijah Mak <[email protected]> Date:06/04/2014 10:54 AM (GMT-05:00) To: Martin Reuter <[email protected]> Cc: [email protected] Subject: Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed scans 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 <[email protected]> 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 ,[email protected] > 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 > <[email protected]> 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 >> <[email protected]> >> 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 >>> [email protected] >>> 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: >>> [email protected] >>> [email protected] >>> 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: >> [email protected] >> [email protected] >> Web : http://reuter.mit.edu > > > > -- > Elijah Mak, Gates Scholar > > PhD Candidate | Psychiatry > > University of Cambridge | Department of Psychiatry > > Trinity College, Cambridge, CB2 1TQ > > -- Elijah Mak, Gates Scholar PhD Candidate | Psychiatry University of Cambridge | Department of Psychiatry Trinity College, Cambridge, CB2 1TQ
_______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
