Freesurfer February 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
236 discussions

Freesurfer problem on Amazon EC2
by Tawfik Moher Alsady 26 Feb '13

26 Feb '13

Dear Freesurfers, I tried to install freesurfer on amazon EC2 as instructed on the wiki page. Everything went well except that mri_* tools like mri_convert doesn't work. When calling it, it returns nothing.\ I also tried to make another Centos instance and install freesurfer manuall, but the same problem existed. I am trying to use it via ssh (ssh to the server and then enter the freesurfer commands). Any suggestions? And is it fast enough to use FS on Amazon micro instance? On my PC freesurfer takes around 35-40 hours for the whole process. Grazie, Tawfik -- Sent with Sparrow (http://www.sparrowmailapp.com/?sig)

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Tkregister2 / Tksurfer / Tkmedit Won't Open
by Daniel Cole 26 Feb '13

26 Feb '13

Hello freesurfers, I just ran registration of my functional images and am trying to visualize the registration for assessment. However, when I use the commands "tkregister-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -fsd bold -funcstem f" or "tkregister2 --targ T1.mgz --fstarg --s $SUBJECTID --surf --mov $FUNCTIONAL_MRI --reg $REG_DAT --plane sag --movbright $MYBRIGHTNESS" the command gets stuck on "Opening window SUBJECT01". I've also tried just opening tksurfer and tkmedit but the terminal produces no output/windows opening and simply freezes. Any ideas to why this could be occurring? I've let it sit at this stage for multiple hours without anything popping up and without any errors. Thanks! Daniel -- Daniel Cole University of Rochester Brain and Cognitive Sciences dcole10(a)u.rochester.edu

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Re: [Freesurfer] Mac mountain lion installation problem
by Nick Schmansky 26 Feb '13

26 Feb '13

Paula, That seems plenty adequate to run recon-all, so four days to process bert seems odd. Are your energy settings set to goto sleep? The adapter setting should be set to 'never' sleep. Nick > Hi Nick, > > These are my system's specifications: > Processor 2 x 2,4 GHz 6-Core Intel Xeon > Memory 12 GB 1333 MHz DDR3 ECC > Software OS X 10.8.2 (12C60) > > > > Paula > > > Paula Vieweg > Aging & Cognition Research Group > German Center for Neurodegenerative Diseases (DZNE) > Building 15, Room 309a > Leipziger Str. 44 > 39120 Magdeburg > GERMANY > > phone: +49-391-67-24520 > email: paula.vieweg(a)dzne.de > > > > > > Am 25.02.13 19:30 schrieb "Nick Schmansky" unter > <nicks(a)nmr.mgh.harvard.edu>: > >>Paula, >> >>what is the processor type and speed? how much memory do you have on >>your system? >> >>Nick >> >>On Mon, 2013-02-25 at 11:50 +0100, Vieweg, Paula /DZNE wrote: >>> Hi, >>> >>> >>> I have installed Freesurfer (Leopard version) on Mac Mountain Lion and >>> tried to use it for a full segmentation (recon-all -all). >>> On my own files I get a problem with Talairach, the program aborts and >>> I get the recommendation to try it with -notalcheck. >>> I have done this and Freesurfer has since then taken 6 days to run one >>> brain. I have started the example script with Bert and it has run 4 >>> days. I have aborted all the processes now and am asking for help. >>> All other steps in the Testing protocol with Bert seem to work apart >>> from the recon-all -all. >>> I am using 7T data (but with just 1mm isotropic resolution), which is >>> where I thought the problem came from. >>> Since the example script also does not run (that is, does not finish), >>> it seems to be a problem with the installation and possibly my Mac >>> version. >>> Do you have any suggestion how to solve this? >>> >>> >>> Best, >>> Paula >>> >>> >>> Paula Vieweg >>> Aging & Cognition Research Group >>> German Center for Neurodegenerative Diseases (DZNE) >>> Building 15, Room 309a >>> Leipziger Str. 44 >>> 39120 Magdeburg >>> GERMANY >>> >>> >>> phone: +49-391-67-24520 >>> email: paula.vieweg(a)dzne.de >>> _______________________________________________ >>> 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. > > > >

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aseg.mgz display only left hemisphere
by Azeez Adebimpe 26 Feb '13

26 Feb '13

Hi freesurfer experts, The output of the segmentation, aseg.mgz only display right hemisphere. I used option -all in the segmentation. How can I make the both hemispheres visible or is there any specific option to choose for segmentation to make both hemispheres visible? Thank you/ Azeez Adebimpe

2 1

blend own template into FS pipeline
by Schumman Resonance 26 Feb '13

26 Feb '13

Hi FreeSurfer experts, We are dealing with a sample of children MRI and we want to introduce our own templates into the pipeline instead of the MNI/tailarach. Any advice or guidance you can provide on how to go about doing this would be much appreciate it. Thanks, Kev

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Re: [Freesurfer] Registration & segmentation with FSL - obtaining correlation matrix..
by Douglas N Greve 25 Feb '13

25 Feb '13

First check the value of the BBR cost function. If it is over .8, then something is wrong. To check whether it is an LR flip, you can flip the volume LR and re-run the registration to see if it gets better. doug On 02/25/2013 11:19 AM, Sudhin A. Shah wrote: > Hi Doug, > > When I initially pulled out the correlation values (using the matlab code below) after the automated registration process: regfeat2anat & aseg2feat, some ROIS reported NaNs. > > When I manually checked the registration and adjusted it using tkregister2, I found myself stretching/scaling to make it fit. Consequently I do not have NaNs BUT I am now realising that I should'nt have to scale. > > 1) How can I check if left-right reversals have happened - its not obvious by eye > 2) I am going to re-run the automated registration and I can send you a pic and the cost function.. > > Thanks, > S > > ________________________________________ > From: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Monday, February 25, 2013 10:44 AM > To: Bruce Fischl > Cc: Sudhin A. Shah > Subject: Re: [Freesurfer] Registration & segmentation with FSL - obtaining correlation matrix.. > > Hi Sudhin, I'm not sure what the problem is. NaNs in the data? > Stretching the registration? You should not need to stretch the reg.Are > you 100% positive that the func and anat come from the same subject and > there have been on left-right reversals? What is the final value of the > cost function? > doug > > On 02/25/2013 10:06 AM, Bruce Fischl wrote: >> Hi Sudhin >> >> Doug would have some. You definitely shouldn't have to stretch/scale >> to get it to fit. If you do, something critical is wrong. Also, please >> cc the list so that the right person (Doug in this case!) can answer. >> >> cheers >> Bruce >> >> >> On Mon, 25 Feb 2013, Sudhin A. Shah wrote: >> >>> Hi Bruce, >>> >>> They were a result of the registration (between structural and >>> functional) being 'off'. When I manually correct this using >>> tkregister2, they were fine. However, I found that I had to stretch >>> (scale) to get them to fit so (i started a new thread regarding this) >>> are there image examples on what this should look like so I can use >>> as a guide? >>> >>> Thanks, >>> S >>> >>> >>> On Feb 25, 2013, at 9:27 AM, Bruce Fischl wrote: >>> >>>> Hi Sudhin >>>> >>>> are you sure that the NaNs don't exist before registration and >>>> extraction? Cany you check? I don't see why anything we would have >>>> done would introduce them. >>>> >>>> cheers >>>> Bruce >>>> On Fri, 22 Feb 2013, Sudhin A. Shah wrote: >>>> >>>>> Hello >>>>> I have run free surfer and co-registered with the rsfMRI via FSL >>>>> (reg-feat2anat & aseg2feat) >>>>> When I extract the values (as per the matlab code below), I see >>>>> NaNs in certain regions. Of the 19 datasets that I have analyzed I >>>>> have >>>>> see NaNs for the following labels >>>>> 1006 1033 2006 2013 2033 >>>>> Is this a known problem? Is there a solution? >>>>> Thanks, >>>>> S >>>>> On Jan 31, 2013, at 3:41 PM, Douglas N Greve wrote: >>>>> >>>>> Sorry, I don't think we have such a program. You could do it >>>>> in matlab >>>>> fairly easily, eg, >>>>> >>>>> f = MRIread('filtered_func_data'); >>>>> fmat = fast_vol2mat(f); >>>>> a = MRIread('aparc+aseg'); >>>>> seglist = unique(a.vol(:)); >>>>> seglist = seglist(2:end); % remove segid=0 (unkown) >>>>> clear roimean >>>>> for nthseg = 1:length(seglist) >>>>> ind = find(a.vol == seglist(nthseg)); >>>>> roimean(:,nthseg) = mean(fmat(:,ind),2); >>>>> end >>>>> >>>>> m = roimean'*roimean; >>>>> >>>>> On 01/31/2013 01:29 PM, Sudhin A. Shah wrote: >>>>> >>>>> Hello, >>>>> >>>>> This worked perfectly 2 years ago :), but now I am >>>>> having some trouble. >>>>> >>>>> I run reg-feat2anat & aseg2feat with no problem. >>>>> >>>>> I now need a correlation matrix of every ROI (created by >>>>> freesurfer) >>>>> >>>>> against every other ROI. For this I used @ROI_Corr_Mat >>>>> >>>>> (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) >>>>> >>>>> >>>>> Again - this worked fine in the past. >>>>> >>>>> Now I get an error (working with AFNI to see if it can >>>>> be fixed). >>>>> >>>>> Question: Is there any alternative to getting this >>>>> correlation matrix? >>>>> >>>>> i.e every ROI against every other ROI? >>>>> >>>>> Thanks, >>>>> >>>>> S >>>>> >>>>> _______________________________________________ >>>>> >>>>> Freesurfer mailing list >>>>> >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> -- >>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> Outgoing: >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> 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 >>>>> 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 > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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TRACULA trac-all -path giving 'Segmentation error (core dumped) error'
by Susan Kuo 25 Feb '13

25 Feb '13

Hi FreeSurfer Community, I am trying to run TRACULA's last step, 'trac-all -path -c <path-to-dmrirc-config-script>', and am receiving the error: Segmentation fault(core dumped) Moreover, when I look to standard output (terminal), I noticed that the initial 'dmri_paths' command is incomplete. The terminal shows that the command includes the '--init' switch and several arguments (e.g. '<subject ID>/dlabel/diff/rh.atr_PP_avg33_mni_flt_cpts_5.txt'), the last of which is terminated mid-pathname. Can anyone suggest a reason why this would be the case? Thank you, Susie Kuo

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High resolution fMRI and resolution of anatomical scans
by SHAHIN NASR 25 Feb '13

25 Feb '13

Hi, We are planning to collect high resolution *functional* MRI for a group of subjects with voxel size smaller than 1 mm. For these subjects, we already have reconstructed *anatomical *scans with 1 mm voxel size. The question is, do we need to re-collect *anatomical* scans for these subjects with smaller voxel size (e.g. 0.5 x 0.5 x 0.5) or we can still use the old anatomical data for co-registration with freesurfer. P.S.: We usually analyze our subjects in native space but technically we can do this in fsaverage space. So, we only need this co-registration for pre-processing and mapping fMRI data to fsaverage space. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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creating figures using f-score color scale
by Maria Jalbrzikowski 25 Feb '13

25 Feb '13

Dear Freesurfer experts, I was wondering if you could help me in figuring out how to create a figure in tksurfer. A recent publication in PLoS One on William's Syndrome showed a figure with a color scale for the F-scores and reflected the F-values through colors that they obtained in ROI analyses. Does anyone have any suggestions for how they created this figure? I wrote the authors of the manuscript, but have not yet heard back. I would like to make a similar figure for some analyses I've recently run. I've attached a picture of the figure and the title of the article is Regional Brain Differences in Cortical Thickness, Surface Area and Subcortical Volume in Individuals with Williams Syndrome by Shashwath A. Meda, Jennifer R. Pryweller, Tricia A. Thornton-Wells Thank you for your help! Best, Maria Jalbrzikowski -- Maria Jalbrzikowski, M.A. University of California, Los Angeles

3 2

Mac mountain lion installation problem
by Vieweg, Paula /DZNE 25 Feb '13

25 Feb '13

Hi, I have installed Freesurfer (Leopard version) on Mac Mountain Lion and tried to use it for a full segmentation (recon-all -all). On my own files I get a problem with Talairach, the program aborts and I get the recommendation to try it with -notal–check. I have done this and Freesurfer has since then taken 6 days to run one brain. I have started the example script with Bert and it has run 4 days. I have aborted all the processes now and am asking for help. All other steps in the Testing protocol with Bert seem to work apart from the recon-all -all. I am using 7T data (but with just 1mm isotropic resolution), which is where I thought the problem came from. Since the example script also does not run (that is, does not finish), it seems to be a problem with the installation and possibly my Mac version. Do you have any suggestion how to solve this? Best, Paula Paula Vieweg Aging & Cognition Research Group German Center for Neurodegenerative Diseases (DZNE) Building 15, Room 309a Leipziger Str. 44 39120 Magdeburg GERMANY phone: +49-391-67-24520 email: paula.vieweg(a)dzne.de<mailto:paula.vieweg@dzne.de>

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Freesurfer February 2013