Freesurfer March 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
247 discussions

brain.finalsurfs.mgz editing
by Khadka, Sankalpa 02 May '14

02 May '14

Dear freesurfer community, My question is directed to those who have experience with editing brain.finalsurfs.mgz. According to the tutorials, after making edits on brainmask.finalsurfs.mgz (which is normally done when the pial surface is not accurate), we can run, recon-all -autorecon-pial -subjid subj" However, I found an anomaly when I looked at the steps that -autorecon-pial flag goes through. The very first step of autorecon-pial flag is "mri_mask" command. This takes brain.mgz and brainmask.mgz as inputs and gives brain.finalsurfs.mgz as output. Now, if we have made edits on brain.finalsurfs.mgz, it will be overwritten by the new one and hence our edits won't take an effect. I ran few experiments too. First, I made edits on brain.finalsurfs.mgz and ran recon-all with autorecon-pial flag. I ended up with a new brain.finalsurfs.mgz and my edits did not make any changes. Second, I made edits on brain.finalsurfs.mgz and ran with white, smooth2, inflate2, autorecon3 flag (basically starting from mri_make_surfaces command). On doing so, the edits made desirable changes and brain.finalsurfs.mgz remained intact. Third, I made changes on brainmask.mgz and brain.mgz (inputs for mri_mask). It also works as expected. Finally, I also followed the recommended steps from the tutorial by creating brainmask.finalsurfs.manedit.mgz, however, the edits from "manedit" were not carried on to brainmask.finalsurfs.mgz Could anyone please shed some light on this? What would be the best strategy to follow? Thank you, Sankalpa

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Monte Carlo simulation - Longitudinal Pipeline
by Pedro Rosa 26 Apr '14

26 Apr '14

Dear list, I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline in a structural MRI dataset and I would like to use Monte Carlo as the method for correction for multiple comparisons. However, the longitudinal LME tutorial includes only FDR correction (lme_mass_FDR2). Is it possible to use Monte Carlo correction for longitudinal data? Can I input the outputs from MatLab (fstats = lme_mass_F(?h,CM): stats.F / pval / sgn / df) into mri_glmfit and then run Monte Carlo? If not, do you have any other suggestions of how I use Monte Carlo in longitudinal analyses? Thanks in advance, -- Pedro Rosa

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V1 label
by krista kelly 24 Apr '14

24 Apr '14

Hello, I am looking at cortical thickness and surface area using Freesurfer. I have transferred label V1 from freesurfer onto the brains of my participants and when I view them on the inflated brains in tksurfer , I notice that there are holes in the label. Is this an issue when calculating mean cortical thickness and total surface area estimations? Should I fill these in somehow? I've attached a picture to show as an example. Please let me know if the picture cannot be viewed. Thanks! Krista

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Re: [Freesurfer] mri_convert Siemens .IMA error
by Douglas N Greve 22 Apr '14

22 Apr '14

Hi Paul, I was finally able to track down the bug. You can get a new version from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mri_conver… copy it to $FREESURFER_HOME/bin/mri_convert doug On 12/08/2013 06:28 PM, prasser wrote: > Hi Doug, > > Sorry for the delay. Please find 1.IMA attached. > > Thanks, > Paul > > > ---- On Fri, 06 Dec 2013 13:15:29 -0800 *Douglas N Greve > <greve(a)nmr.mgh.harvard.edu>* wrote ---- > > > Can you upload a single dicom file to me? One should be enough > > On 12/06/2013 04:02 PM, Paul Rasser wrote: > >> > >> We are using Freesurfer5.3 on os x 10.8. > >> > > > > > > On 6 Dec 2013, at 2:19 pm, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > >> > >> This may be a known problem. What version of FS are you using and > >> what is your platform? > >> doug > >> > >> > >> > >> > >> On 12/5/13 3:26 PM, prasser wrote: > >>> Thanks, but the orientation shift appears as a skew. Also, we > don't > >>> have any fiducial markers for this group of scans so it would > be a > >>> little tricky to confirm the correct application of > >>> -out_orientation. I would rather let mri_convert handle this from > >>> the .IMAs. > >>> > >>> Is there any additional information I can provide from from > the .IMA > >>> header etc that could shed some light on why mri_convert is > behaving > >>> in this way? > >>> > >>> Thanks, > >>> Paul > >>> > >>> > >>> > >>> ---- On Wed, 04 Dec 2013 22:11:27 -0800 *Mark Plantz > >>> <markplantz2016(a)u.northwestern.edu > <mailto:markplantz2016@u.northwestern.edu>>* wrote ---- > >>> > >>> Not sure if this helps, but you can alter the output orientation > >>> using the flag "--out_orientation" followed by LIA (for > >>> example). Maybe the input file needs to be in a specific > >>> orientation before it can be converted properly. > >>> > >>> > >>> On Wed, Dec 4, 2013 at 9:56 PM, prasser <prasser(a)zoho.com > <mailto:prasser@zoho.com> > >>> <mailto:prasser@zoho.com>> wrote: > >>> > >>> Hi, > >>> > >>> I'm currently having problems converting .IMA files > >>> collected from a Siemens Skyra to .mgz format using > >>> mri_convert from Freesurfer5.3 on os x. > >>> > >>> Using: > >>> > >>> mri_convert -it siemens -ot mgz 1.IMA test.mgz > >>> > >>> I get the error message: > >>> > >>> does not contain a Siemens ASCII header has this file been > >>> anonymised? > >>> > >>> ERROR: cannot unpack mosiacs without ASCII header > >>> > >>> The .IMA files have been taken straight from the scanner > >>> console. > >>> > >>> If I try: > >>> > >>> mri_convert -it dicom -ot mgz 1.IMA test.mgz > >>> > >>> this creates the .mgz, however there is an orientation shift > >>> and a vertical stripe artefact appears in the sagittal view > >>> (please see attached) when compared to the original .IMA. > >>> > >>> Any suggestions on how to convert the Siemens .IMA files > >>> correctly? > >>> > >>> Thanks, > >>> > >>> Paul > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> <mailto:Freesurfer@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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> <mailto:Freesurfer@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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@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. > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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/ > > -- 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/

2 1

Large areas of white matter ignored, even with control points
by Andrea Grant 10 Apr '14

10 Apr '14

Hello, I'm working with T1 weighted scans obtained at 7T and have a problem with a subject. I preprocess the images to deal with the B1 inhomogeneity (normalize to PD and mask noisy pixels), and have successfully segmented about 20 scans. I often need to use control points, but they normally work just as I expect. However, I have one subject where large areas of the brain are completely excluded from the segmentation (basically the entire occipital lobe). I added control points and re-ran, to no effect. I'm attaching a screenshot of the brainmask with surfaces, my control points, and the white matter mask. Clearly, the skull stripping wasn't very successful (I adjusted the watershed threshold manually, but at one value I got the current result and at a single integer lower I lost half the brain). I have successfully segmented other subjects with equally poor skull strips, though, so I don't believe this has any bearing on the current issue. Is editing the white matter mask the only way to fix this? If so, do I need to carefully fill in on every slice, or can I just brush in here and there to sort of "goose" the white matter into that region? I can do the slice by slice fix, but if there's a way to avoid the several hours it will take me, I would love to know! Thanks, Andrea ----- Andrea Grant Visual Neuroimaging Technologist Center for Magnetic Resonance Research, University of Minnesota 2021 6th St. SE, Minneapolis, MN 55455, 612-626-4948 gran0260(a)umn.edu umn.edu/~gran0260 <http://umn.edu/%7Egran0260>

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Export freesurfer data
by ye tian 08 Apr '14

08 Apr '14

Dear Freesurfers, I would like to do some customized model fitting for cortical thickness. Is there a way to export freesurfer data into R or simply as a text? Thank you very much! Sincerely, Ye

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Longitudinal Analysis Questions
by pfotiad＠nmr.mgh.harvard.edu 08 Apr '14

08 Apr '14

Hi FS community, I am using FS 5.3 to do a longitudinal analysis on some data of mine. I have manually edited some of the reconstructed scans (i.e. addition of control points and white voxels) where the reconstruction was not as precise: 1) Is the base template created from the recon-all -base command in the wiki preserving those edits or do I need to reapply them in the base template? I know that this has been answered for previous versions of FS but I was wondering whether anything has changed in more recent versions. 2) Is it ok to run the longitudinal analysis described in the wiki when my subjects have an unequal number of timepoints (i.e. one person has 3 different timepoints, whereas another one has five) or should they all have the same number of timepoints? Thanks in advance! Best, Panos

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Re: [Freesurfer] SNR on DTI data
by Anastasia Yendiki 07 Apr '14

07 Apr '14

Signal-to-noise ratio = mean / standard deviation On Tue, 18 Mar 2014, Yuko Yotsumoto wrote: > Anastasia, > > Thank you so much for your reply. > > So I should calculate the mean and s.d. of the values of the low-b within the white matter region for each subject, and compare those numbers between groups. > Is it correct to say that the higher mean values indicate larger SNR? > > Yuko > > On Mar 18, 2014, at 12:53 AM, Anastasia Yendiki wrote: > >> >> Hi Yuko - You can use the low-b images and compute the SNR of those images inside a mask of the white matter. Because dt_recon computes a registration from the diffusion to the structural data, you can use that registration to map the white matter label from the freesurfer segmentation (aseg) to the diffusion data. Then calculate the mean and standard deviation of the values of the low-b images inside that white matter mask. >> >> Hope this helps, >> a.y >> >> On Mon, 17 Mar 2014, Yuko Yotsumoto wrote: >> >>> Hello Freesurfers, >>> I have DTI data for two groups of subjects, and were asked SNR for each >>> group. >>> I did ROI analysis on FA values, therefore, I do not have the averaged DTI >>> data. >>> I am wondering if there is any way to compute SNR from dt_recon output. It >>> doesn't have to be the ROI specific SNR values, I just need SNR for the >>> whole DTI data for each group. >>> Any suggestions will be appreciated! >>> Yuko Yotsumoto >>> --- >>> ------------------------------------------------------------- >>> Yuko Yotsumoto, Ph. D. >>> Associate Professor >>> The University of Tokyo, Department of Life Sciences >>> Bldg #2, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 Japan >>> phone : (+81)-3-5454-4332 >>> E-mail: cyuko(a)mail.ecc.u-tokyo.ac.jp >> _______________________________________________ >> 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. > > > >

2 2

ROI analyses
by Emily Boeke 07 Apr '14

07 Apr '14

Hi Freesurfers, I have some questions about ROI analyses. 1. I use the mni305 and fsaverage flags during preprocessing. Does this mean that when I run funcroi-config, funcroi-sess, etc, the analysis is being done for each subject in mni305 space, as opposed to native space? Meaning, If I specify -seg aseg.mgz 18 in funcroi-config, the analysis will not be done using the left amygdala from that individual's aseg, but instead will be done in mni305 space with the fsaverage left amygdala ROI? 2. I sometimes want to use labels I've created on fsaverage from averaged group activation to do ROI analyses. If the ROI is in the volume, I convert the label to a mask and run: mri_segstats --i cespct.nii.gz --seg mymask.mgz --id 1 --avgwf ces.mymask.dat In the appropriate contrast folder. What should I do if I want to do the same thing, but with a surface label (in a lh or rh surface analysis, not an mni305 analysis)? Thanks! Emily

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CWP values
by Francesco Puccettone 04 Apr '14

04 Apr '14

Hello, I see that after having qdec apply MonteCarlo correction to a certain contrast, the CWP cluster-wise probability is displayed. Those values, however, are not displayed when the "Find clusters and go to max" button is used, either before or after correction. WHy is that, when it seems that the CWP statistic makes sense for all 3 "stages" (max-vertex pre-correction, mean-cluster post-correction, max-vertex post-correction)? Thank you! --Francesco

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Freesurfer March 2014