Freesurfer

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30099 discussions

Base Misalignment during Longitudinal Image Processing
by XUAN AMELIA TRAN 03 Jul '14

03 Jul '14

Hi there, I used inputs from two time points that have been processed with Freesurfer 5.0.0 cross-sectional pipeline. I used the following command to create the base template (using Freesurfer 5.0.0): recon-all -base <templateid> -tp <tp1id> -tp <tp2id> -all The job log said the run was successful. However when inspected with freeview, the norm.mgz for base output shows misalignment (see image attached). Does anyone know how to fix this problem? Thank you! Xuan

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Voxels included in wm.mgz but not in white matter surface
by james pardon 03 Jul '14

03 Jul '14

Hi, I'm working on some subjects with gray matter lesions, where usually these lesions happen at the boundary of GM and WM (mostly patients with MS). The problem is that Freesurfer can not follow the cortex past this areas. I have tried to use control points, white matter edits and even editing the problematic regions on orig.mgz volume with neighboring voxels and re running recon-all. My results have improved substantially, however I still have a problem where after white matter edit, and adding some new voxels to wm.mgz, the wm surface (and overlying pial surface) does not respect the wm.mgz. In the attached screenshot for example, I can see some areas that are part of wm.mgz (in red) but not included in WM surface. I was wondering whether anyone can give a hint on what recon-all steps I might need to re-run? Thanks James

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talairach fixes
by Elissa McIntosh 03 Jul '14

03 Jul '14

Hello freesurfer experts, I have two questions. First, I've come across some of my subjects who have crooked alignment on the horizontal view, but have seemingly good talairach results. Does it matter that the alignment is crooked as long as talairach is good? My second question is how off does a talairach have to be to merit a manual fix? I've attached an image of someone whose talairach is slightly off making the green line go outside the brain more than it usually does. But I don't know if I'll do more harm by adjusting it slightly. On a related note, does it matter that the green line seems to go outside the brain in the moveable image? Where the green line extends beyond I've had to make manual edits in most of my subjects. Thank you!

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aseg.mgz and brainmask.mgz misalignment
by Mark Plantz 03 Jul '14

03 Jul '14

Hello freesurfers, I recently ran recon-all on a subject and noticed that aseg.auto_noCCseg.mgz and brainmask.mgz are not aligned properly. Not only is the overlap incorrect, but it appears that the slice #'s do not correlate with eachother. For instance, slice 120 of aseg.auto is not the same region as slice 120 of brainmask.mgz. I attached a screenshot to help illustrate the problem. Any ideas how to fix this problem manually? Thank you! - MP

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-normalization all black
by Teo Gelles 03 Jul '14

03 Jul '14

Hi Everyone, I would like to normalize some images. But even when I test the -normalize option with recon-all -s burt/ -normalization which from what I can see changes /burt/mri/nu.mgz (which came with the freesurfer download) to /burt/mri/T1.mgz, T1.mgz is entirely black. Is there a way to fix this issue? Thanks. Teo

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freeview error
by Cooke, Gillian 03 Jul '14

03 Jul '14

Hi All, I was hoping that someone might be able to help me. When I load a surface into freeview (e.g. /Applications/freesurfer/subjects/fsaverage/surf/lh.inflated), I get an error in my terminal: Did not find any volume geometry information in the surface When I go on to load in my multiple comparisons corrected image the entire surface turns yellow. Any suggestions for a fix? Many thanks, Gill _____________________ Gillian Cooke, Ph.D. Postdoctoral Research Associate Lifelong Brain & Cognition Lab Beckman Institute University of Illinois, Urbana

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mkcontrast manual weighting?
by DeCross, Stephanie N. 03 Jul '14

03 Jul '14

Hi, I’m making contrasts, and my 6 conditions are as follows: #1 female approach #2 male approach #3 female withdraw #4 male withdraw #5 car approach #6 car withdraw If I want to create the contrast all-approaching-things minus fixation, I’m dealing with #1 female approach, #2 male approach, and #5 car approach. When I’m making the contrasts with mkcontrast, if I do (-a 1 -a 2 -a 5) that’s not what I want, because Matlab then weights each of them as .333. What I really want is for the car’s weight to equal the combined face’s weight to account for the 2 types of genders but only 1 type of car. Would it be correct to manually weight it as: ( .25 .25 0 0 .5 0)? I’m pretty sure that’s correct, but I just wanted to double check. Thanks, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078

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MINC_BIN_DIR
by Paras Patel 03 Jul '14

03 Jul '14

HI, I am trying to use recon-all for brain analysis work. I have managed to get 4 of them done, but after being away for a couple of days I not get this error: firstly: MINC_BIN_DIR not defined nu_correct also shows to be missing therefore the analysis does not work. I have searched through the help pages and tried the source /usr/local/freesurfer/SetUpFreeSurfer.csh but i get an error with that also. line 42: syntax error : unexpected end of file Also one of the help pages suggested accessing the BIN folder in freesurfer but I do not have this folder either. Any help would be appreciated, Thanks, Paras

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Re: [Freesurfer] Longitudinal pipeline + LME question
by Martin Reuter 03 Jul '14

03 Jul '14

Hi Brianna, I recommend to run all scans of a patient with one single subject template (base). Then , if you are interested if atrophy rates change after intervention, you could use a piecewise linear model, with a node at the surgery. You can then compare your change in slopes with the change in the control group (without intervention). If you are interested not in atrophy rates, but only if volume or thickness changes, the model would be different, but you still need a controll group to test if what you find is different from control group behaviour. Best martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Brianna Damadian <bdamadia(a)buffalo.edu> Date:07/03/2014 1:57 AM (GMT+01:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal pipeline + LME question Hi Martin, Thanks for the response. What we are trying to do is look at changes within the same subject after a certain date (date of a surgical procedure). Would it make more sense to run all scans before and after this date in the same longitudinal pipeline and then look for differences or to run all pre-intervention scans with a separate longitudinal template from the post-intervention scans and then look for differences between the "pre" group as a whole and the "post" group as a whole? We are looking for the method that will give us the least variability due to processing differences. Any input you have would be great. Thanks! > On Jul 2, 2014, at 5:31 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: > > Hi Brianna, > > Yes, that is the best option in my opinion. You should include field strength as a covariate, and maybe other acquisition parameters. > > Best Martin > > > Sent via my smartphone, please excuse brevity. > > -------- Original message -------- > From: Brianna Damadian > Date:07/02/2014 10:04 PM (GMT+01:00) > To: Freesurfer(a)nmr.mgh.harvard.edu > Subject: [Freesurfer] Longitudinal pipeline + LME question > > Hello experts, > > We are setting out to look at a sample of 10 (subset of eventual larger sample) who have at least 2 sets of MRI. Some have many more than 2. However, some of the scans were done on different scanners (a few on 1.5T versus most on 3T) and with slightly different parameters (namely, different TR) - not exactly ideal. > > We are looking for changes in total ventricular volume as well as total gray matter and white matter (among others). I am new to this software, but from what I have read in the literature the best approach would be to use the longitudinal pipeline in FreeSurfer and then use the Linear Mixed Effect model (LME) for statistical analysis. In your opinion, is this the correct approach based on our sample/goals? > > Thank you. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > 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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Longitudinal pipeline + LME question
by Martin Reuter 02 Jul '14

02 Jul '14

Hi Brianna, Yes, that is the best option in my opinion. You should include field strength as a covariate, and maybe other acquisition parameters. Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Brianna Damadian <bdamadia(a)buffalo.edu> Date:07/02/2014 10:04 PM (GMT+01:00) To: Freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal pipeline + LME question Hello experts, We are setting out to look at a sample of 10 (subset of eventual larger sample) who have at least 2 sets of MRI. Some have many more than 2. However, some of the scans were done on different scanners (a few on 1.5T versus most on 3T) and with slightly different parameters (namely, different TR) - not exactly ideal. We are looking for changes in total ventricular volume as well as total gray matter and white matter (among others). I am new to this software, but from what I have read in the literature the best approach would be to use the longitudinal pipeline in FreeSurfer and then use the Linear Mixed Effect model (LME) for statistical analysis. In your opinion, is this the correct approach based on our sample/goals? Thank you.

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