Freesurfer April 2011

freesurfer@nmr.mgh.harvard.edu

121 participants
166 discussions

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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display error
by Cris Lanting 20 Jun '11

20 Jun '11

Dear Freesurfer community, I have a display problem that affects especially tkmedit and tksurfer. We run freesurfer ( freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0) on a remote unix server and use Exceed (v. 14.0.0.376) to port the display to a local (windows) computer. At first we got a openGL error stating that OpenGL was not supported when calling e.g. tksurfer. Now we have installed Exceed 3D to support OpenGL it seems to continue beyond the previous error message but comes up with a different one (see snippet) <snippet> subject is js hemi is rh surface is pial surfer: current subjects dir: /home/cris/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/cris Reading image info (/home/cris/freesurfer/subjects/js) Reading /home/cris/freesurfer/subjects/js/mri/orig.mgz surfer: Reading header info from /home/cris/freesurfer/subjects/js/mri/orig.mgz fsurfer: vertices=156376, faces=312748 surfer: single buffered window surfer: tkoInitWindow(js) Window type not found! surfer: failed, trying double buffered window Window type not found! surfer: failed, no suitable display found <end snippet> Any ideas? Note that other programs that do not use OpenGL seem to run fine (i.e. fslview and gedit) Kind regards, Cris Lanting Career Development Fellow MRC Institute of Hearing Research Science Road, University Park Nottingham NG7 2RD cris(a)ihr.mrc.ac.uk

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Re: [Freesurfer] I/O performance mitigation
by Bruce Fischl 26 May '11

26 May '11

Hi David, I'm surprised you didn't have to do this in the past. We always space our jobs out. Glad there's an easy workaround cheers Bruce On Fri, 3 Sep 2010, David Mischel wrote: > We took the suggestion of staggering the launch of Freesurfer 5.0 recon-all > jobs. The attached Word doc (I don't know how to contribute this information > other than attaching the image and text using Word) shows a load graph on > our file server. When 20 FS jobs began at once (all processing servers using > a single file server) the load on the file server bulged up. When we spaced > out the launch of each job by 15 seconds the load hardly budged. > > > > We have not had to do this in the past with earlier versions of Freesurfer > but this is an obvious work around to the problem we encountered. > > > > < david > > > > > > David Mischel > > Manager of IT > > Center for Imaging of Neurodegenerative Diseases (CIND) > > <http://www.cind.research.va.gov/> http://www.cind.research.va.gov/ > > VA Medical Center > > 4150 Clement Street, 114M > > San Francisco, CA 94121 > > voice: 415-221-4810 x3864 > > fax: 415-668-2864 > >

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No inflated brain...
by jim kroger 17 May '11

17 May '11

Hello, I am following the sequence in the "FreeSurfer Troubleshooting Reconstruction Work Flow" instructions, and am at step 8, FsTutorial/WhiteMatterEdits. It looks like the thalamus and corpus callosum are included as white matter, and the pial surface surrounds some subcortical structures. Assuming this is not correct, I decided to look at the inflated surface as suggested in the referenced page " Making Edits to the White Matter." Unfortunately when I issue: tksurfer wm1_edits_before rh inflated I only see what looks like a very small fraction of an egg shell for the rh, and nothing for lh. Can I check somehow to see why I have almost no inflated brain? Thanks, Jim -- Cell: 575-571-8274 Email: jkk251(a)gmail.com

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Smaller Virtual Machine
by Fidel 05 May '11

05 May '11

Hi all, I have been trying the virtual disk image, and it works well. Nevertheless, I think that more than 7GB is a lot of space if somebody wants to use it as a Virtual Machine in a cloud environment, in which you are charged for used storage and maybe for used bandwidth in the data communication. Is anybody thinking about creating a lighter version of this virtual disk image? Thanks and best regards, Fidel.

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How to proceed after manual edit of segmentation
by Tetiana Dadakova 05 May '11

05 May '11

Dear FreeSurfer list, I am making some manual correction to subcortical structures using Edit Segmentation Tool. And my question is: how should I proceed after saving aseg.mgz? Should I re-run autorecon2 with some options? Thank you, Tanja.

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Re: [Freesurfer] Interpreting results from Qdec
by Gallen, Courtney (NIH/NIDA) [F] 05 May '11

05 May '11

Hi Doug Have a follow up question regarding significance levels in Qdec related to extracting means from ROIs, etc. I'm posting to the entire mailing list in case anyone else has ideas. Basically, I extracted mean volumes (from my set of participants) of ROIs for which Qdec reports an interaction between two variables. I want to look at these mean volumes in something like SPSS to see what is driving the interaction/generate figures, etc. I'm having an issue with one such ROI, in that when I extract the mean volumes and look for this interaction in SPSS, it is not significant (p ~ 0.5, so really not significant at all). Is there any way that an ROI could be significant in Qdec (p of 0.05, Monte Carlo sim), but not in SPSS when I extract means for each participant? Let me know if this isn't clear. Any thoughts would be appreciated! Courtney Courtney Gallen Post-baccalaureate IRTA Neuroimaging Research Branch National Institute on Drug Abuse (IRP) 251 Bayview Blvd Suite 200 Baltimore, MD 21224 Tel: (443) 740-2631 -----Original Message----- From: Douglas Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tuesday, April 26, 2011 1:06 PM To: Gallen, Courtney (NIH/NIDA) [F] Subject: Re: [Freesurfer] Interpreting results from Qdec Those are the values outside (first column) and inside (2nd col) the ROI. You can add "--id 1" to only report the values inside the ROI. doug On 4/26/11 1:02 PM, Gallen, Courtney (NIH/NIDA) [F] wrote: > It worked! > Now, last question. The txt file has two separate values (?averages). What do they each represent? > > -----Original Message----- > From: Douglas Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Tuesday, April 26, 2011 12:53 PM > To: Gallen, Courtney (NIH/NIDA) [F] > Subject: Re: [Freesurfer] Interpreting results from Qdec > > try "--slabel fsaverage lh ROI-drawn-on-QDEC-brain.label" > > > On 4/26/11 12:52 PM, Gallen, Courtney (NIH/NIDA) [F] wrote: >> Actually, I hope I'm wrong about what I thought below. If I specify individual subject's label and run: >> >> mri_segstats --in /prot/Mprot/CTQ/freesurferDone/8579/surf/lh.volume.fwhm10.fsaverage.mgh --slabel 8579 lh /prot/Mprot/CTQ/freesurferDone/8579/label/lh.SupTemp_CTQxBDNFctrls.label --avgwf lhSupTempctrls.txt >> >> I still get the same error about dimension mismatch >> >> >> -----Original Message----- >> From: Gallen, Courtney (NIH/NIDA) [F] >> Sent: Tuesday, April 26, 2011 12:43 PM >> To: 'Douglas Greve' >> Subject: RE: [Freesurfer] Interpreting results from Qdec >> >> Ah I think I see the problem now. >> >> The label I originally specified is the general label created from the ROI drawing in Qdec. Instead, I should use the individual subject's label (from 'Map Label to Subjects') instead, right? >> >> Thank you! >> >> -----Original Message----- >> From: Douglas Greve [mailto:greve@nmr.mgh.harvard.edu] >> Sent: Tuesday, April 26, 2011 12:38 PM >> To: Gallen, Courtney (NIH/NIDA) [F] >> Subject: Re: [Freesurfer] Interpreting results from Qdec >> >> You have to use the subject that matches the input, fsaverage in this >> case. How did you define your label? If you defined it on subject 123, >> you can transfer it to fsaverage using mri_label2label. >> doug >> >> On 4/26/11 12:28 PM, Gallen, Courtney (NIH/NIDA) [F] wrote: >>> Not a problem at all! >>> >>> If I use --in, I get an error saying that there is a dimension mismatch between input volume and seg. >>> >>> Any other thoughts? Thanks again! >>> >>> -----Original Message----- >>> From: Douglas Greve [mailto:greve@nmr.mgh.harvard.edu] >>> Sent: Tuesday, April 26, 2011 11:40 AM >>> To: Gallen, Courtney (NIH/NIDA) [F] >>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>> >>> >>> Hi Courtney, sorry for the delay. If more than a few days go by without >>> a response, feel free to repost -- I promise not to get annoyed! >>> Sometimes, things get pushed up and out of my mail browser window, and I >>> often don't get back to them. Sorry! >>> >>> To answer your question, try using --in where you have --seg. The >>> "segmentation" is actually already specified because you've specified a >>> label. >>> >>> doug >>> >>> On 4/26/11 11:03 AM, Gallen, Courtney (NIH/NIDA) [F] wrote: >>>> Hi Doug, >>>> Sorry to keep bugging you but any thoughts about my response to your e-mail from 2 weeks ago? I've given the exact command line I'm using with mri_segstats. >>>> Thanks again for all your help >>>> Courtney >>>> >>>> -----Original Message----- >>>> From: Gallen, Courtney (NIH/NIDA) [F] >>>> Sent: Tuesday, April 12, 2011 10:59 AM >>>> To: 'Douglas N Greve' >>>> Subject: RE: [Freesurfer] Interpreting results from Qdec >>>> >>>> That may be the problem. ${sub} is an actual person's directory >>>> >>>> E.g., sub# 123--command line would be: >>>> mri_segstats --seg /prot/Mprot/CTQ/freesurferDone/123/surf/lh.volume.fwhm10.fsaverage.mgh --slabel 123 lh \ >>>> lh.SupTemp_CTQxBDNFctrls.label --avgwf lhSupTempctrls.txt >>>> >>>> >>>> >>>> -----Original Message----- >>>> From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] >>>> Sent: Tuesday, April 12, 2011 10:55 AM >>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>> >>>> What is your full command-line? Without variables, just something that >>>> you could put directly into the terminal. Make sure that you are >>>> specifying fsaverage as your subject (can't tell below because your use >>>> ${sub}). >>>> >>>> doug >>>> >>>> >>>> Gallen, Courtney (NIH/NIDA) [F] wrote: >>>>> Sorry, but I can't seem to figure out how to specify input data. I tried '--in' but get an error that the input vol and seg label are not the same dimensions. I've been looking at the help options for mri_segstats (http://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats) but don't see it >>>>> >>>>> -----Original Message----- >>>>> From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] >>>>> Sent: Friday, April 08, 2011 10:38 AM >>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>> >>>>> The lh.volume.fwhm10.fsaverage.mgh should be your input. It is not a >>>>> segmentation. You've already specified the seg with the the --slabel >>>>> command. >>>>> doug >>>>> >>>>> >>>>> Gallen, Courtney (NIH/NIDA) [F] wrote: >>>>> >>>>>> One last question (hopefully). I'm specifying the input volume with --seg, but am getting an error ('cannot do frame average without input volume'). Am I missing something obvious? >>>>>> >>>>>> The entire command looks something like this: >>>>>> mri_segstats --seg /prot/Mprot/CTQ/freesurferDone/${sub}/surf/lh.volume.fwhm10.fsaverage.mgh --slabel ${sub} lh \ >>>>>> lh.SupTemp_CTQxBDNFctrls.label --avgwf lhSupTempctrls.txt >>>>>> >>>>>> Thanks again >>>>>> -----Original Message----- >>>>>> From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] >>>>>> Sent: Tuesday, April 05, 2011 4:21 PM >>>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>>> Cc: Nick Schmansky; Freesurfer Mailing List >>>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>>> >>>>>> yes, something like ?h.volume.fwhm10.fsaverage.mgh >>>>>> doug >>>>>> >>>>>> Gallen, Courtney (NIH/NIDA) [F] wrote: >>>>>> >>>>>> >>>>>>> Hi Doug >>>>>>> >>>>>>> Thanks for helping me with this! >>>>>>> >>>>>>> First time around I did everything as is outlined in 'Define a Region of Interest' here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis. >>>>>>> >>>>>>> I'll try your suggestion now. The input data would be something like ?h.volume.fwhm10.fsaverage.mgh, correct? >>>>>>> >>>>>>> Thanks again >>>>>>> Courtney >>>>>>> >>>>>>> -----Original Message----- >>>>>>> From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] >>>>>>> Sent: Thursday, March 31, 2011 5:44 PM >>>>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>>>> Cc: Nick Schmansky; Freesurfer Mailing List >>>>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>>>> >>>>>>> Hi Courtney, did you transfer the label to each individual subject using >>>>>>> mri_label2label? A better way to replicate your qdec results is to run >>>>>>> mri_segstats on the input data to qdec (y.mgh usually). Specify the >>>>>>> label with "--slabel subject hemi yourlabel". Also specify "--avgwf >>>>>>> subjectdata.txt". This will create this text file with a list of the >>>>>>> input data for each subject averaged over your label. >>>>>>> >>>>>>> doug >>>>>>> >>>>>>> Gallen, Courtney (NIH/NIDA) [F] wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>>> Hi Nick >>>>>>>> >>>>>>>> I'm revisiting this issue and have a few more questions. First, I have a significant interaction between two variables on cortical volume. I drew a label on this ROI and ran mris_anatomical_stats on the label (thank you for that suggestion). >>>>>>>> >>>>>>>> For stats in the output table file, is the column 'GrayVol' the same thing as the cortical volume I looked at in Qdec? I'm asking because when I export GrayVol values into SPSS, there is no longer a significant interaction between my variables (and if this ROI is significant after multiple comparisons across the brain, I'd expect the mean volume from the ROI to be very significant in SPSS). >>>>>>>> >>>>>>>> Please let me know if my questions aren't clear. Thanks in advance >>>>>>>> Courtney >>>>>>>> >>>>>>>> >>>>>>>> Courtney Gallen >>>>>>>> Post-baccalaureate IRTA >>>>>>>> Neuroimaging Research Branch >>>>>>>> National Institute on Drug Abuse (IRP) >>>>>>>> 251 Bayview Blvd >>>>>>>> Suite 200 >>>>>>>> Baltimore, MD 21224 >>>>>>>> Tel: (443) 740-2631 >>>>>>>> >>>>>>>> >>>>>>>> -----Original Message----- >>>>>>>> From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] >>>>>>>> Sent: Thursday, January 13, 2011 3:08 PM >>>>>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>>>>> Cc: Freesurfer Mailing List >>>>>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>>>>> >>>>>>>> Courtney, >>>>>>>> >>>>>>>> if i understand your question, i think one way to do that is to use qdec >>>>>>>> to draw a label on the blob of interest, and the run 'map label to >>>>>>>> subjects', which creates a label file in each subjects label dir, then >>>>>>>> you can run stats on that with mris_anatomical_stats. >>>>>>>> >>>>>>>> (btw, i'm putting this answer on the list, as others may have better >>>>>>>> ideas.) >>>>>>>> >>>>>>>> n. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Mon, 2011-01-03 at 16:38 -0500, Gallen, Courtney (NIH/NIDA) [F] >>>>>>>> wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> Hi Nick >>>>>>>>> >>>>>>>>> Thanks for the prompt reply. Sorry if my questions seem a bit naïve--this is my first time using Freesurfer. >>>>>>>>> >>>>>>>>> A follow up question to your answer for question 1. I see that the group data will be plotted in Qdec for significant blobs, but say there is a significant interaction between two variables and it's not entirely apparent what is driving this interaction. >>>>>>>>> Is there a way to extract the mean of this blob for each individual (i.e., treat it as an ROI or something similar) to determine what's driving the significance? >>>>>>>>> >>>>>>>>> Thanks in advance! >>>>>>>>> Courtney >>>>>>>>> >>>>>>>>> -----Original Message----- >>>>>>>>> From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] >>>>>>>>> Sent: Thursday, December 30, 2010 2:44 PM >>>>>>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>>>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>>>>>> >>>>>>>>> ans. 1. - the easiest way is to Ctrl- left mouse click on a blob, and a >>>>>>>>> plot of the data at that surface vertex will appear. the group will be >>>>>>>>> apparent from that (say, demented group is thinner than non-demented >>>>>>>>> group). this data is significance data (log p, so '2' is 0.01), so mean >>>>>>>>> and stdev wouldnt apply in that case. the file 'y.mgh' is the raw data >>>>>>>>> of all subjects in the analysis, so you could extract mean and stdev >>>>>>>>> from that. >>>>>>>>> >>>>>>>>> ans. 2. - slide the 'annotation' opacity slider to show the annotation >>>>>>>>> data (cortical parcellation). the ctrl left click will also put the >>>>>>>>> region info for that vertex on the lower left of the display. >>>>>>>>> >>>>>>>>> see also: >>>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis >>>>>>>>> >>>>>>>>> n. >>>>>>>>> >>>>>>>>> On Wed, 2010-12-29 at 10:49 -0500, Gallen, Courtney (NIH/NIDA) [F] >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> I’m currently running analyses in Qdec and have identified areas that >>>>>>>>>> show significant effects in my contrasts. I have two questions related >>>>>>>>>> to interpreting these results. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> 1. How can you interpret the effect in each “blob?” (i.e., which >>>>>>>>>> group has a greater cortical surface area, etc.). Right now, all I >>>>>>>>>> know is that there is an effect in certain areas. Can you export this >>>>>>>>>> data to get means and standard errors? >>>>>>>>>> >>>>>>>>>> 2. Is there a way to localize where these effects are? E.g., a >>>>>>>>>> tool that tells you this effect is located in __ area of the brain? >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks in advance >>>>>>>>>> >>>>>>>>>> Courtney >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Courtney Gallen >>>>>>>>>> >>>>>>>>>> Post-baccalaureate IRTA >>>>>>>>>> >>>>>>>>>> Neuroimaging Research Branch >>>>>>>>>> >>>>>>>>>> National Institute on Drug Abuse (IRP) >>>>>>>>>> >>>>>>>>>> 251 Bayview Blvd >>>>>>>>>> >>>>>>>>>> Suite 200 >>>>>>>>>> >>>>>>>>>> Baltimore, MD 21224 >>>>>>>>>> >>>>>>>>>> Tel: (443) 740-2631 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> 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 >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >

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unable to use cuda 4.0.13 and cuda 3.2.16 with nvidia 270.41.03, fedora 14
by Knut J Bjuland 04 May '11

04 May '11

It appears that fressurfer 5.0 is compiled against cuda 3.2.x rather than cuda 4. Is there any workaround to force freesurfer 5.0 apart from recompilation for it use cuda 4.0. AS the latest version of the nvidia driver has change cuda version from 3.2 to 4.0. Knut J Cuda 4.0 *[knutjbj@super-knut lib64]$ mri_em_register_cuda Acquiring CUDA device Using default device Segmentation fault (core dumped) Cuda 3.2 [knutjbj@super-knut Downloads]$ mri_em_register_cuda Acquiring CUDA device Using default device CUDA Error in file 'devicemanagement.cu' on line 46 : CUDA driver version is insufficient for CUDA runtime version. Output from deviceQueryDrv CUDA Device Query (Driver API) statically linked version There is 1 device supporting CUDA Device 0: "GeForce GTX 460" CUDA Driver Version: 4.0 CUDA Capability Major/Minor version number: 2.1 Total amount of global memory: 1072889856 bytes Multiprocessors x Cores/MP = Cores: 7 (MP) x 48 (Cores/MP) = 336 (Cores) Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 49152 bytes Total number of registers available per block: 32768 Warp size: 32 Maximum number of threads per block: 1024 Maximum sizes of each dimension of a block: 1024 x 1024 x 64 Maximum sizes of each dimension of a grid: 65535 x 65535 x 65535 Maximum memory pitch: 2147483647 bytes Memory Bus Width: 256-bit Memory Clock rate: 1800.00 Mhz Texture alignment: 512 bytes GPU Clock rate: 1.40 GHz Concurrent copy and execution: Yes # of Asynchronous Copy Engines: 1 Run time limit on kernels: Yes Integrated: No Support host page-locked memory mapping: Yes Concurrent kernel execution: Yes Device has ECC support enabled: No Device is using TCC driver mode: No PASSED Press ENTER to exit... *

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Freesurfer April 2011