Freesurfer September 2011

freesurfer@nmr.mgh.harvard.edu

119 participants
181 discussions

Re: [Freesurfer] integrating FSL and Freesurfer
by noam Schneck 09 Oct '12

09 Oct '12

Hi Doug Here are more detailed versions of my first two questions. 1) I used tkmedit to look at the mean_func produced by a gfeat analysis of one subject's three functional runs overlayed onto the anatomical image produced by recon-all on that same subject(bert/mri/orig.mgz). The registration matrix I used was the anat2std.dat that was produced by running reg-feat2anat on all three of the feat analyses from the individual runs. When I did this I saw that the mean_func image was outside the boundaries of the anatomical image. Correspondingly, when I overlayed the zstat.nii.gz from the gfeat analysis onto the anatomical image I had activation outside of the anatomical image brain. 2) Originally, I ran BBR on a subject that I had run Recon-all for. I used BBR to register the example_func.nii.gz to the bert/mri/orig.mgz. I had BBR output an fsl.mat. I then used ApplyXFM in fsl to apply BBR's fsl.mat to register the example_func.nii.gz onto a T1 image that had been created by converting bert/mri/brainmask.mgz into niftii with mri_convert. I tried it again, this time converting the orig.mgz to niftii. In both cases the example_func in T1 space image produced by ApplyXFM is rotated about 90 degrees and also inverted. This is viewed in fslview, The corresponding T1 images created by mri_convert are not. What can I do to allow me to use BBR's fsl.mat within ApplyXFM?

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Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
by Xue, Feng 19 May '12

19 May '12

Sorry, I didn't notice that the reply address was not the list, I've done re-post it. Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings. It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script. On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > can you post this to the list? There are others better qualified to say > what's going on. But if everything finished ok is there really a problem? > Maybe this is just a warning? > On Sun, 14 Mar 2010, Xue, Feng wrote: > >> Hi Bruce, >> >> Thanks for your reply. The recon-all.log said it finished without >> error. please find the whole scripts root in the attachment. >> I'm also running a raw testing with one subject and without SGEяяMaybe >> I can report the result the day after tomorrow. >> >> BTW, I found in my 64bit Debian nodes, I repeated got the error as below >> (standard_in) 2: Error: comparison in expression >> but in 32bit, I met both. >> >> for the GMail security restriction, I changed recon-all.cmd in the >> attachment to recon-all.cmds. >> >> On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>> what does the recon-all.log say? Did the recon finish correctly? Does >>> this >>> happen if you just run it on the command line? >>> Bruce >>> >>> On Sat, 13 Mar 2010, Xue, Feng wrote: >>> >>>> Dear Bruce & FS experts, >>>> >>>> Please forgive my re-post, for I havn't got any response from last post. >>>> I do appreciate if anyone could give me a hint or suggestion. >>>> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>> >>>> We are running freesurfer with Sun GridEngine. Currently, we >>>> repeatedly got this error in SGE's job error log file on some data >>>> when doing recon_all: >>>> >>>> $ cat recon_xf.e437 >>>> (standard_in) 2: Error: comparison in expression >>>> $ cat recon_xf.e431 >>>> (standard_in) 2: comparison in expression >>>> >>>> I also checked the recon-all-status.log file, but not error was found. >>>> >>>> Has anyone met this problem? Is it critical? >>>> Thanks in advance. >>>> >>>> -- >>>> Best Regards >>>> >>>> Xue, Feng Phd. candidate >>>> Major in Developmental Cognitive Neuroscience >>>> >>>> National Key Laboratory of Cognitive Neuroscience and Learning >>>> Beijing Normal University >>>> Beijing, China. 100875 >>>> Tel: +86-13810154455 >>>> web: http://psychbrain.bnu.edu.cn >>>> ============================================== >>>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University >>>> telnet://bbs.mdjs.org >>>> http://bbs.mdjs.org >>>> _______________________________________________ >>>> 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. >>> >>> >> >> >> > -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org

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Re: [Freesurfer] Freesurfer Digest, Vol 75, Issue 15
by Sebastian Moeller 19 Jan '12

19 Jan '12

Hi Fred, yu probably checked the following already, but on the off chance you have not... Maybe you have set X11 to 256 color mode? Start X11.app (from /Applications/Utilities) go to the X11 menu, select Preferences..., switch to the tab called output and see what is selected for Colors. If it is set to 256 Colors you have your root cause, just switch to something higher and all should be fine. best Sebastian On May 9, 2010, at 9:00 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. tksurfer/tkmedit display color fix in OSX 10.6? (Fred Dick) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 9 May 2010 15:34:35 +0100 > From: Fred Dick <fdick(a)crl.ucsd.edu> > Subject: [Freesurfer] tksurfer/tkmedit display color fix in OSX 10.6? > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <873B33F2-3339-4871-9395-1EFEEC1EFAAB(a)crl.ucsd.edu> > Content-Type: text/plain; charset="us-ascii" > > Dear all > > This is a pretty minor issue (except for figure making) - but has anyone experienced and then fixed a display problem in tksurfer/tkmedit in OSX 10.6 (possibly also 10.5) where graphics seem to be drawn only with 256 colors, thereby giving images a kind of contour-plot look? (See attached image below). [Running 10.6.3, i686-apple-darwin10-gcc-4.2.1, tksurfer 1.309 (yes, older), tkmedit v 1.330] > > I looked around the mail archives but didn't see anyone else commenting on this, but do know someone else having the same issue, so would be happy for any suggestions. > > Thanks, > Fred > > >

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downsampling 4D volume
by ythomas 10 Jan '12

10 Jan '12

Hi, I am trying to downsample a 4D volume using mri_convert. However, it seems to be killing the 4 dimension. For example, if I do mri_convert -voxsize 4 4 4 tmp.mgz tmp444.mgz The original volume which is 256 x 256 x 256 x 120 becomes 64 x 64 x 64. Thanks, Thomas

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TRACULA: how to implement DTI repeat sequence?
by Ansgar Furst 28 Oct '11

28 Oct '11

Dear Anastasia and Team FreeSurfer, First of all thanks so much for developing TRACULA. I think it has a lot of potential! Here is my question: I'm trying to modify "dmrirc_single_subject" file in order to reflect our local sequence and wondered how you are dealing with DTI repeat sequences for the same subject. We acquire 5 B0s and 30 directional scans twice in a row. So our *Diffusion bvalue Table would look like this: ================================================================== * 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 Now I wonder how I would modify the below default settings from the tutorial data to reflect this: ===================================================================== set subjlist = (Diff001) set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) set dcmroot = /usr/local/freesurfer/TUTORIAL_DATA/diffusion_tutorial/ set dcmlist = (Diff001/orig/6-1.dcm) ===================================================================== Oh also, I noticed that in the wiki you have the following settings: ======================================================================= set trainfile = $TUTORIAL_DATA/diffusion_tutorial/subj,train,difftutorial23.txt =============================================================================================== In the latest version of the freesurfer distribution I counted 33 subjects for the training algorithm and therefore use: "subj,train,difftutorial33.txt" pointing to /usr/local/freesurfer/trctrain/trc001 /usr/local/freesurfer/trctrain/trc002 /usr/local/freesurfer/trctrain/trc003 /usr/local/freesurfer/trctrain/trc004 /usr/local/freesurfer/trctrain/trc005 /usr/local/freesurfer/trctrain/trc006 /usr/local/freesurfer/trctrain/trc007 /usr/local/freesurfer/trctrain/trc008 /usr/local/freesurfer/trctrain/trc009 /usr/local/freesurfer/trctrain/trc010 /usr/local/freesurfer/trctrain/trc011 /usr/local/freesurfer/trctrain/trc012 /usr/local/freesurfer/trctrain/trc013 /usr/local/freesurfer/trctrain/trc014 /usr/local/freesurfer/trctrain/trc015 /usr/local/freesurfer/trctrain/trc016 /usr/local/freesurfer/trctrain/trc017 /usr/local/freesurfer/trctrain/trc018 /usr/local/freesurfer/trctrain/trc019 /usr/local/freesurfer/trctrain/trc020 /usr/local/freesurfer/trctrain/trc021 /usr/local/freesurfer/trctrain/trc022 /usr/local/freesurfer/trctrain/trc023 /usr/local/freesurfer/trctrain/trc024 /usr/local/freesurfer/trctrain/trc025 /usr/local/freesurfer/trctrain/trc026 /usr/local/freesurfer/trctrain/trc027 /usr/local/freesurfer/trctrain/trc028 /usr/local/freesurfer/trctrain/trc029 /usr/local/freesurfer/trctrain/trc030 /usr/local/freesurfer/trctrain/trc031 /usr/local/freesurfer/trctrain/trc032 /usr/local/freesurfer/trctrain/trc033 Does that make sense? Thanks so much for your help! Ansgar

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Re: [Freesurfer] Talairach transformation
by Maria Felber 11 Oct '11

11 Oct '11

Dear all, indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria ----- Original Message ----- From: "Avi Snyder" <avi(a)npg.wustl.edu> To: "Sita Kakunoori" <sita(a)nmr.mgh.harvard.edu>, felber(a)cbs.mpg.de, "Avi Snyder" <avi(a)npg.wustl.edu> Cc: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation Hi Sita, Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from those of the target. This condition can easily occur if the target is based on 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images tend to be relatively bright in the center of the head.) Gd++ contrasted MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible. Avi ----------------------------------------------- On 9/13/11 2:26 PM, "Sita Kakunoori" <sita(a)nmr.mgh.harvard.edu> wrote: > >I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this >e-mail. >Hi Dr.Snyder, Not sure if you remember but we saw something similar in a >dataset here at the center where the talairach was much smaller than the >orig.mgz volume and you created a new talairach template to be used with >that dataset. I just wondered if this issue is similar to that. > >Thanks much, >Sita. >---------- Forwarded message ---------- >Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) >From: Maria Felber <felber(a)cbs.mpg.de> >To: freesurfer(a)nmr.mgh.harvard.edu >Subject: [Freesurfer] Talairach transformation > >Hi Bruce, > >so we are back at the beginning. After I ran recon-all -all, I did >exactly that and checked the xform using tkregister2. And here I always >see that my talairach volume (the transform) is always smaller, which can >be very well seen as the orig surfaces of the subjects are always a >little outside the brain and reach well into the skull areas. Of course I >can make the adjustments as descriped in the short instructions. But this >also means I ran the recon-all precess anew for another 30 h per subject. >And that is the reason, why I asked if this is normal that the tailarach >transform is a) always smaller than the original brain, and b) if I can >make any adjustments to prevent that from happening and thus saving >another 30h per subject. >In short: How acurate hat the talairach.xfm has to be and is it possible >to change some parameters to make this transformation a little more >accurate while running the recon-all process only once? >Best, >Maria > > >----- Original Message ----- >From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> >To: "Maria Felber" <felber(a)cbs.mpg.de> >Cc: freesurfer(a)nmr.mgh.harvard.edu >Sent: Tuesday, September 13, 2011 4:07:55 PM >Subject: Re: [Freesurfer] Talairach transformation > >Hi Maria > >you can use tkregister2 to check the accuracy of the talairach.xfm >transform ("xform" for short), and correct it if you want. > >cheers >Bruce >On Tue, 13 Sep 2011, Maria Felber wrote: > >> Hi Bruce, >> >> thanks for the first response. I tried to find some information on the >>webpage about xform, but failed. So what is xform standing for and >>where/how can I check it? >> As in the later processing stages I want to do localization and >DCM-Modeling with my data, I guess the correct talairach coords are kind >of >important for later comparisons. >> Thanks again, >> Maria >> >> ----- Original Message ----- >> From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> >> To: "Maria Felber" <felber(a)cbs.mpg.de> >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Sent: Friday, September 9, 2011 2:13:05 PM >> Subject: Re: [Freesurfer] Talairach transformation >> >> Hi Maria >> >> as long as the tal xform is reasonable I wouldn't worry about it, unless >> for some reason you care a lot about the accuracy of the talairach >>coords. >> >> cheers >> Bruce >> >> p.s. not sure why it would be smaller >> >> On Fri, 9 Sep 2011, Maria Felber wrote: >> >>> Dear all, >>> >>> sorry, if that question came up before in the mailing list and I >>>simple have been unable to find the thread. >>> >>> Following the wiki reconstruction workflow, I ran yesterday the >>>recon-all -all process. The process finished without errors. So the >>>next step was to check the talairach transform. >>> Now, according to the FsTutorial/Talairach I have to make some >>>adjustments and then run the whole process again. That is all nice and >>>good. >>> >>> However, why is it, that the talairach volume is always, no matter >>>which subject I look at, is always significantly smaller than the >>>target volume? Is that normal? Has it to be fixed? Or is that just >>>normal? Attached find one example. >>> As I am using freesurfer for the first time, I am really unsure about >>>that. >>> >>> Thanks for the help, >>> Maria >>> >>> >> >> >> 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. >> >> >> > >-- >Maria J. Felber, PhD Student >Max Planck Institute for Human Cognitive and Brain Sciences >Stephanstraße 1A >04103 Leipzig, Germany >Phone: +49 341 9940-2465/2522 > >-- >Maria J. Felber, PhD Student >Max Planck Institute for Human Cognitive and Brain Sciences >Stephanstraße 1A >04103 Leipzig, Germany >Phone: +49 341 9940-2465/2522 > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522

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Tracula Memory Requirements
by Moiyadi, Ammar 11 Oct '11

11 Oct '11

Hi Freesurfers, I've been getting a memory allocation error (below) when running trac prep and trac paths on my computer with 6 gb ram. Since I was able to run these steps on a computer with 16 gb, I want to know, what is the minimum memory requirement for running tracula? Is the memory allocation error resulting from a lack of memory or is there something else going on that I am not aware of? Error: Loading BEDPOST parameter samples from /usr/local/freesurfer5.1/subjects/1052/dmri.bedpostX MRIalloc(256, 256, 50): could not allocate 262144 bytes for 431th slice Thanks always, Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490

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retinotopy description
by Michelle Umali 10 Oct '11

10 Oct '11

Hi Freesurfers. Is there text describing the retinotopy analysis in Freesurfer mathematically? Thanks. Michelle

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qdec and maximum p-value
by Nikolas Borrel-Jensen 05 Oct '11

05 Oct '11

Hi all. I'm using Qdec to compare two groups of patients, and I'm wondering why the vertex with the highest p-value in the clusters changes when the threshold is changed? When lowering the threshold, the significant area should increase, but intuitively, the vertex corresponding to the area with the maximum p-value should remain the same inside the cluster? I'm using the Monte Carlo z-simulation method to remove false positive. Regards, Nikolas

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bug in surface-based area and volume
by Douglas N Greve 05 Oct '11

05 Oct '11

Hi Y'all, I recently found a bug in the way that FS converts surface-based area (eg, lh.area) and volume (eg, lh.volume) into standard space. I'm testing a fix now, but you should not use area or volume measures until I've posted the fix and you re-run either mris_preproc or qcache. The files themselves are fine, it is the way they are transfered to standard space that is the problem. You will not need to re-analyze any of your individual subject data. The volumes of the subcortical structures are unaffected by this problem. Global measures of cortical volume are also unaffected. I'll get back soon (next week) with the fix. Sorry for the inconvenience. doug -- 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

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Freesurfer September 2011