[Freesurfer] How to use qdec to compare actual to expected thickness changes?

Dear FreeSurfers, we have MR scans from a group of healthy subjects (about 40, equal number of males and females, age range 25 to 65 years), who were scanned at two time points (about four months separation). In between they experienced exposure to a condition that might or might not influenc

Re: [Freesurfer] subcortical atlases

I understand. Thank you Bruce, for you good work. Joshua - Joshua Lee Doctoral Candidate Department of Psychology & Center for Mind and Brain University of California, Davis 530.747.3805 On Wed, Jun 4, 2014 at 5:53 PM, Bruce Fischl wrote: > Hi Josh > > sorry, it was impossible to get IRB appro

Re: [Freesurfer] subcortical atlases

Hi Josh sorry, it was impossible to get IRB approval for such a thing given that the data was collected a long time ago by various people. sorry Bruce On Wed, 4 Jun 2014, Joshua Lee wrote: > Hello Freesurfer Gurus, > > I was wondering whether the original individual subject atlases used to

Re: [Freesurfer] FW: Queries about semi-inflated surface for overlay

Hi Zixuan didn't I answer this? If you run mris_inflate -w 1 -scale 1 lh.white lh.white_inflated it will save snapshots at every iteration and you can pick how inflated you want it. cheers Bruce On Wed, 4 Jun 2014, Zixuan Yang wrote: Dear FreeSurfer experts,   Really sorry for send my

[Freesurfer] subcortical atlases

Hello Freesurfer Gurus, I was wondering whether the original individual subject atlases used to construct the probabilistic atlases for subcortical segmentation have been made available for download? Thanks! josh - ___ Freesurfer mailing list Freesurfer@

[Freesurfer] FW: Queries about semi-inflated surface for overlay

Dear FreeSurfer experts, Really sorry for send my queries again (please see below). Could you please kindly offer us some advices in dealing with semi-inflated surface? Many thanks in advance and kind regards, Zixuan From: Zixuan Yang Sent: Monday, 2 June 2014 6:10 PM To: 'freesurfer@nmr.mgh.ha

[Freesurfer] visualize group analysis results of qdec

Hello FreeSufers, I ran several analyses in qdec, and now have problem visualize previous analyses results...which sounds dumb... Please let me know if you have any ideas. I used fsaverage. I found this page http://freesurfer.net/fswiki/FsTutorial/Visualization using tksurfer, but it needs to do

Re: [Freesurfer] pial layers

Hi Mia, If you don't use recon-all, your log will not be saved in recon.log. You can redirect the output in a text file instead, i.e mris_compute_lgi --i lh.pial --close_sphere_size 30 --smooth_iters 6 > mylog.txt Best, Marie On Jun 4, 2014, at 8:22 PM, "Borzello, Mia" mailto:mborze...@par

Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional

Thank you very much for your answer Bruce ! have a nice evening, Alex. Le 3 juin 14 7:6, Bruce Fischl a écrit : > Hi Alex > > I would think that longitudinal analysis is still the way to go as we try > to improve both reliability and sensitivity using the fact that we have > multiple scans/subj

[Freesurfer] Unpacking Problem

Hello,I’m trying to unpack and run recon-all on a set of MEMPRAGE images we’ve obtained in Lunder 6 scanner (Siemens Skyra), but recon-all is giving me errors. I’ve attached for the scan.info file (outputted by unpacksdcmdir), the unpack.config file that I used to unpack the MEMPRAGE images, and th

Re: [Freesurfer] pial layers

Hi Mia, I'm not sure to understand what you mean with pial layers. Recon-all -lgi computes the local gyrification index. Can you please send the full command and full log of the error that you get? Best, Marie On 4 juin 2014, at 19:47, "Borzello, Mia" mailto:mborze...@partners.org>> wrote:

[Freesurfer] pial layers

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 ___ Freesurfer mailing list

Re: [Freesurfer] Longitudinal design

Hi Martin, I reran everything from scratch and this time the recons ended without error. Few more questions: 1) Is the brainmask.mgz vs wm.mgz problem that I described in my previous email (surfaces only starting to show rather late at the posterior end of some subjects) something that I need to

[Freesurfer] Fwd: Re: surface upside down, wrong hemis, nouveau error

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

Re: [Freesurfer] FSFAST

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

Re: [Freesurfer] A question about mri_glmfit-sim --3spaces

The first and third are the same. Don't use the 2nd doug On 06/04/2014 06:12 AM, 王晗 wrote: > Hi,all: > I was using mri_glmfit-sim for multiple correction,but I'm wondering > if --3paces could influence the correction result. > From the website I saw the explanation below: > mri_glmfit-sim --glmd

Re: [Freesurfer] 3dvolreg Error for preproc-sess

Do the other programs in AFNI work on that computer? If 3dvolreg works, then copy that to 3dvolreg.afni in $FREESURFER_HOME/bin doug On 06/03/2014 12:01 PM, Nitenson, Adam wrote: > Hi all, > > I'm running version 5.2 off-site, and I keep running up against an > error for preproc-sess. From my

Re: [Freesurfer] free-surfer longitudinal Qdec table

Hi Anna, Fsid is the cross sectionall name without the .long. Best martin Sent via my smartphone, please excuse brevity. Original message From: Anna Jonsson Date:06/04/2014 7:22 AM (GMT-05:00) To: Freesurfer support list Subject: [Freesurfer] free-surfer longitudinal Qde

Re: [Freesurfer] selxavg3-sess error in ==> fast_selxavg3 at 434

This is a strange error that I cannot figure out from the terminal output. What version of FS are you using? Here's something you can try: Run selxavg3-sess with --monly sxa3.m This will return right away having created sxa3.m Start matlab and run sxa3. It will stop at the error below. Then ty

Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed scans

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 Date:06/04/2014 10:54 AM (GMT-05:00) To: Martin Reuter Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] v.

Re: [Freesurfer] Orthogonalising covariates

No it does not. None of our tools do. If you want to do that, you'll have to do it yourself and pass the result to mri_glfmit doug On 06/01/2014 02:23 PM, Saloni Sharma wrote: > Dear Freesurfers, > > does qdec allows you to orthogonalise one covariate relative to the other? > > Regards, > Saloni >

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-

[Freesurfer] trac-all -stat option

Hello, I am trying to examine FA along the trajectory of the white matter tract, as described in the wiki: http://freesurfer.net/fswiki/FsTutorial/TraculaStatistics (half way down the page). I am using the FreeSurfer version 3.0. The wiki says: The pathstats.byvoxel.txt files will generally not

Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed scans

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:

[Freesurfer] free-surfer longitudinal Qdec table

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 Reg

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

[Freesurfer] mri_convert ERROR: could not determine file

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/subjectsIf I understood well the solution is in updated version of reg-feat However, I cannot find the updated reg-fea

[Freesurfer] A question about mri_glmfit-sim --3spaces

Hi,all: I was using mri_glmfit-sim for multiple correction,but I'm wondering if --3paces could influence the correction result. From the website I saw the explanation below: mri_glmfit-sim --glmdir my-glm.wls --cache 3 pos --cwpvalthresh .0166 Using a cluster-wis