Freesurfer

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17 participants
30099 discussions

pial layers
by Borzello, Mia 04 Jun '14

04 Jun '14

Hi Freesurfers, I ran mris_compute_lgi to make the pial layers but they've error- I've included a screenshot. It says it can't find that directory, but I'm pretty sure that directly exists. Thanks so much for your help, Mia

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Advice - best method, longitudinal vs. cross-sectional
by Alexandru Hanganu 04 Jun '14

04 Jun '14

Hello Everyone, could someone please give us an advice about which method you consider is the best for our study ? we have two groups with MRI at Time 1. Each group received medication. After this we performed another MRI at Time 2 after 2 weeks. The best method for this study is a longitudinal one or a cross-sectional GLM ? We consider that the distance between the time points is too small, and the longitudinal method is not the best choice. Hence,this study should be treated as a cross-sectional one. In this case we think about performing a simple GLM with the contrasts: 0.5 0.5 0.5 0.5 or 1 -1 -1 1 for the groups: 1) grp 1 time 1 2) grp 1 time 2 3) grp 2 time 1 4) grp 2 time 2 we are searching to see whether medication had any impact on the cortical morphology in each group and between the groups. Thank you ! Best regards, Alex.

2 2

Fwd: Re: surface upside down, wrong hemis, nouveau error
by Jana Klimova 04 Jun '14

04 Jun '14

Hello, I have got the same problem when I load a surface in tksurfer, though I am not getting the error message about nouveau. I wonder whether Iain (or anyone) has managed to solve the problem and how? Thanks a lot in advance for any help. Best regards, Jana

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Re: [Freesurfer] FSFAST
by Douglas N Greve 04 Jun '14

04 Jun '14

Hi Walid, please remember to send email to the list and not to us personally. Thanks! It is possible to use motion as a nuisance regressor. I don't like to do so because you sometimes get some motion that is correlated with the task. This can greatly change the results. Adding the MC nuisance variable often does not help much with the residual motion signal. So it tends to hurt and not help much so I don't recommend it. doug On 06/04/2014 06:25 AM, Walid Yassin wrote: > Dear Douglas, > > I have a question about FSFAST, is it possible to tell me why is it not ok to use motion as nuisance regressor? > > Thank you in advance, > > Best, > Walid > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Orthogonalising covariates
by Saloni Sharma 04 Jun '14

04 Jun '14

Dear Freesurfers, does qdec allows you to orthogonalise one covariate relative to the other? Regards, Saloni

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Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed scans
by Martin Reuter 04 Jun '14

04 Jun '14

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(a)medschl.cam.ac.uk> Date:06/04/2014 7:17 AM (GMT-05:00) To: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu>,freesurfer(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu >> reuter(a)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(a)nmr.mgh.harvard.edu > reuter(a)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

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free-surfer longitudinal Qdec table
by Anna Jonsson 04 Jun '14

04 Jun '14

Hi, I would like to make my freesurfer longitudinal qdec table for the to use in the lme matlab tools. However, does the fsid need to refer to the longitidunally derived subject; eg XXX.long, or the cross-sectionally derived subject, eg XXX. Im not sure based on the specification online. Kind Regards Anna

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v.5.3 Longitudinal Analysis on v.5.0 processed scans
by Elijah Mak 04 Jun '14

04 Jun '14

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

2 4

mri_convert ERROR: could not determine file
by Marko Dakovic 04 Jun '14

04 Jun '14

Hi there, I have the same problem as Morgan. During execution of reg-feat2anat the error message appears mri_convert ERROR: could not determine file /usr/local/freesurfer/subjects....If I understood well the solution is in updated version of reg-feat However, I cannot find the updated reg-feat2anat in ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat> Would you be so kind to upload the file again. Thanks in advance, Best regards, Marko Dakovic, PhD Center for Magnetic Resonance Clinical Center of Serbia Pasterova 2 Belgrade 11000 Serbia

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Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional
by Martin Reuter 03 Jun '14

03 Jun '14

Hi Alex, The time distance does not matter. It's best to use a longitudinal method (both for the image processing, to reduce noise, and for the statistics, to gain power). Your design seems to be missing a control group (unless one off your groups is placebo). In your design you can compare changes across the two groups. But if you look at a single group and detect longitudinal change you will not know if it is the drug or something else that caused it. Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Alexandru Hanganu <al.hanganu(a)yahoo.ca> Date:06/03/2014 6:15 PM (GMT-05:00) To: FS Mailing List <Freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional Hello Everyone, could someone please give us an advice about which method you consider is the best for our study ? we have two groups with MRI at Time 1. Each group received medication. After this we performed another MRI at Time 2 after 2 weeks. The best method for this study is a longitudinal one or a cross-sectional GLM ? We consider that the distance between the time points is too small, and the longitudinal method is not the best choice. Hence, this study should be treated as a cross-sectional one. In this case we think about performing a simple GLM with the contrasts: 0.5 0.5 0.5 0.5 or 1 -1 -1 1 for the groups: 1) grp 1 time 1 2) grp 1 time 2 3) grp 2 time 1 4) grp 2 time 2 we are searching to see whether medication had any impact on the cortical morphology in each group and between the groups. Thank you ! Best regards, Alex.

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