Freesurfer October 2011

freesurfer@nmr.mgh.harvard.edu

95 participants
160 discussions

Re: [Freesurfer] WM hypointensities and corpus callosum mislabeling
by Warren Winter 12 Oct '11

12 Oct '11

Let me try this again. Here's one that mislabeled parts of the CC as left cerebral white matter at the center slice: Another one mislabels nearly the entire CC at the center slice: Here you can see the light purple blotches above the caudate (light blue); those are labeled as white matter hypointensities: And again here: The overall quality is not great, but we're trying to make the best of what we have. Any advice on correcting these common problems in our dataset (apart from manually doctoring them) would be greatly appreciated! Warren On Oct 11, 2011, at 6:44 PM, Warren Winter wrote: > Here's one that mislabeled parts of the CC as left cerebral white matter at the center slice: > > <Screen shot 2011-10-11 at 6.31.19 PM.png> > Another one mislabels nearly the entire CC at the center slice: > > <Screen shot 2011-10-11 at 6.21.35 PM.png> > > You can see the light purple blotches above the caudate (light blue); those are labeled as white matter hypointensities. > > <Screen shot 2011-10-11 at 6.31.05 PM.png> > > And again here: > > <Screen shot 2011-10-11 at 6.20.18 PM.png> > > The overall quality is not great, but we're trying to make the best of what we have. Any advice on correcting these common problems in our dataset (apart from manually doctoring them) would be greatly appreciated! > > Warren > > On Oct 10, 2011, at 7:59 PM, Bruce Fischl wrote: > >> Hi Warren >> >> can you send us some images to show us what you mean? Or upload an >> example dataset for us to look at? >> >> cheers >> Bruce >> On Mon, 10 Oct 2011, Warren Winter wrote: >> >>> Hello, >>> In a number of our subjects I've been finding white matter hypointensities around the anterior edge of the caudate, as well as mislabelings of the corpus callosum as cerebral >>> white matter (at and/or around slice 128, sagittal). Has anyone else encountered these problems, and are there fixes that don't involve manually doctoring the mislabelings >>> (such as setting a particular flag for recon)? >>> >>> I am quite new to FS so please forgive any rudimentary misunderstandings. >>> >>> Thank you! >>> >>> Warren >>> >>> -- >>> Warren Winter >>> Lab Coordinator >>> Children's Hospital Boston >>> Division of Developmental Medicine >>> 1 Autumn Street, AU 650 >>> Boston, MA 02215 >>> 857-218-5224 >>> >>> >>> >> >> >> 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. > > -- Warren Winter Research Coordinator Children's Hospital Boston Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224

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graph of region neighborhood
by Satrajit Ghosh 12 Oct '11

12 Oct '11

hi folks, do you happen to have any tool/script that produces a graph of aparc region neighborhood? with perhaps the edge weight being the length of shared boundary. cheers, satra

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.img unsupported data type ?
by m.vlutters 11 Oct '11

11 Oct '11

Dear FreeSurfers, First of all, I am completely new to FS so forgive me if I missed something simple. I am currently running freesurfer v5.1.0, using the .vdi file with VirtualBox. (Host = windows 7). I tested the program by running the autorecon1 on subject "bert" and everything seems to work fine so far. Now I have a .img file (which I can view using SPM8), and I would like to convert it to a .mgz file using freesurfer's mri_convert. I tried the following: mri_convert /home/virtualuser/freesurfer/subjects/MySubj/NS-3D.img /home/virtualuser/freesurfer/subjects/MySubj/001 -ot mgz which gives me: $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/MySubj/NS-3D.img... ReadAnalyzeHeader: unsupported data type 0 If I specify the input type as well (-it spm) I get: $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/MySubj/NS-3D.img... ERROR: CountAnalyzeFiles: file with.img extension specified with zero pad variable. I tried it with other .img files I have as well and I get similar errors. (Sometimes with a different number behind 'unsupported data type', like -12080) What am I doing wrong? Does it have something to do with this zero pad variable? I don't expect the .img files to be wrong. They are generated by SPM8. Thanks in advance for any replies! Mark V

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Re: [Freesurfer] WM hypointensities and corpus callosum mislabeling
by Bruce Fischl 11 Oct '11

11 Oct '11

Hmmm, can you upload a couple of examples? On Oct 11, 2011, at 6:44 PM, Warren Winter <Warren.Winter(a)childrens.harvard.edu> wrote: > Here's one that mislabeled parts of the CC as left cerebral white matter at the center slice: > > <Screen shot 2011-10-11 at 6.31.19 PM.png> > Another one mislabels nearly the entire CC at the center slice: > > <Screen shot 2011-10-11 at 6.21.35 PM.png> > > You can see the light purple blotches above the caudate (light blue); those are labeled as white matter hypointensities. > > <Screen shot 2011-10-11 at 6.31.05 PM.png> > > And again here: > > <Screen shot 2011-10-11 at 6.20.18 PM.png> > > The overall quality is not great, but we're trying to make the best of what we have. Any advice on correcting these common problems in our dataset (apart from manually doctoring them) would be greatly appreciated! > > Warren > > On Oct 10, 2011, at 7:59 PM, Bruce Fischl wrote: > >> Hi Warren >> >> can you send us some images to show us what you mean? Or upload an >> example dataset for us to look at? >> >> cheers >> Bruce >> On Mon, 10 Oct 2011, Warren Winter wrote: >> >>> Hello, >>> In a number of our subjects I've been finding white matter hypointensities around the anterior edge of the caudate, as well as mislabelings of the corpus callosum as cerebral >>> white matter (at and/or around slice 128, sagittal). Has anyone else encountered these problems, and are there fixes that don't involve manually doctoring the mislabelings >>> (such as setting a particular flag for recon)? >>> >>> I am quite new to FS so please forgive any rudimentary misunderstandings. >>> >>> Thank you! >>> >>> Warren >>> >>> -- >>> Warren Winter >>> Lab Coordinator >>> Children's Hospital Boston >>> Division of Developmental Medicine >>> 1 Autumn Street, AU 650 >>> Boston, MA 02215 >>> 857-218-5224 >>> >>> >>> >> >> >> 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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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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cannot save edited main volume
by Wei-Ta Chen 11 Oct '11

11 Oct '11

Hi: When I finish white matter editing and try to save the edited main volume by "Save Main Volume" of the "File" menu on TKMedit Tools window, there is a dialogue asking me:"Are ou sure you wish to save the changes to the main volume". When I clicked yes, error message appeared as follows:" Error. Couldnt save volume. This session was started in read-only mode. you cannot save changes." I changed my file permission to 777 (but I forgot to check my original permission settings) and saved again but in vain. Why was this error message? What should I do for now to avoid losing the edited WM results? Thanks for your help. Best, Wei-Ta Chen

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WM hypointensities
by carolina.mr 11 Oct '11

11 Oct '11

2 1

QDEC analysis
by krista kelly 11 Oct '11

11 Oct '11

I'm using QDEC to analyze cortical thickness differences between groups and I have a few questions: 1) There are a few variables that I need to control for. First variable is scanner - I used two different scanners of different field strengths (1.5T GE and 3T Siemens) so I wanted to control for scanner. I also wanted to control for age and gender. Here's my ideal design setup: discrete variables - groups, scanner, gender nuisance variable - age contrast would be 1 -1 0 0 0 0 I realize that scanner, gender, and group are all discrete variables, and that age would be a continuous one. However, in the design tab, I am not able to select all 3 discrete variables (groups, scanner, and gender). Should I designate scanner or gender as a nuisance variable instead? Would it matter which one I use as the nuisance variable? Possible setup: discrete vars - groups, scanner nuisance vars - age, gender contrast - 1 -1 0 0 (Correct?) 2) If I use DODS, should I demean the ages if age is a nuisance variable? 3) If I use a smoothing kernel during the analysis, then create an ROI and map that ROI to each individual subject, will the resulting .stats file in each subjects stats folder reflect the smoothed data or does mapping onto each ROI just extract the raw unsmoothed data from each vertex? Thanks! Krista

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question about contrast file during group analysis with command line
by ZhiLiangLong 11 Oct '11

11 Oct '11

Hi all : I'm performing general linear model (GLM) analysis in the surface,the attachments above are FSGD file and contrast files(the last three attachments).i wonder if my contrast files are correct. the attachment named diff-C-H-thickness.txt is about difference between C and H and the last two are about difference between C and p and difference between P and H,Here,C H and P represent three groups Any suggestions appreciated

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Freesurfer October 2011