Freesurfer November 2012

freesurfer@nmr.mgh.harvard.edu

105 participants
177 discussions

shared installation of freesurfer
by Lilley, John F. 19 Nov '12

19 Nov '12

Hi, We have setup a central install of free surfer but are having some difficulty with the license management aspect. Is there a way to run a single install instance yet have each user provide individual license location variables out side of $FREESURFER_HOME? (~/.license etc.) If not, would registering a single freesurfer license for the cluster in question be acceptable under the license conditions? If there's a better place for this email please let me know. Thanks, John

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Subgroup analysis
by Mahinda Yogarajah 19 Nov '12

19 Nov '12

Dear Experts, I have a two groups - a control group and patient group. The patient group can also be divided into 4 subgroups (but not control gp). Both groups are evenly split between male and female. So far I have compared the patient and control groups as a whole (age and icv as continuous/nuisance variables) but now i want to compare each of the subgroups to controls. I have tried doing this in qdec very crudely by running 4 analyses in qdec where I exclude all the subgroup cases execpt for those belonging to the subgroup I am looking at. My questions are 1) Is this valid (I would correct for the multiple tests) ? How does qdec cope with exclusions given that variables (age) have been demeaned across a whole group. 2) Is there a better way of comparing my subgroups to controls ? Thanks. Mahinda

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Re: [Freesurfer] fieldsign-sess problem in retinotopy
by Zhou, Wei 19 Nov '12

19 Nov '12

Hi Doug, It seems the previous fieldsign-sess problem is due to that I stored data on one server while freesurfer is on the other server. But when I put the data and freesurfer on the same server and run the retinotopy analysis again, it reported fail msg for "selxavg3-ses" : -- ntptot = 80, nX = 27, DOF = 53 Saving X matrix to /media/local_home/zhouw4/testf/retinotopy/SUBJ01/bold/rtopy.self.lh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 39) s = svd(A); Error in fast_selxavg3 (line 254) XCond = cond(XtX); --- I checked Xtmp.mat. There is NaN in Xn and XtX. My rtopy par is: eccen and pos. Would you please give me some idea about this error? Best Wei >> Try using this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fieldsign-sess doug On 11/01/2012 11:47 AM, Zhou, Wei wrote: > Hi Doug, > > The subject name for structural is "SUBJ1" when I did recon-all, which > is also the content of file "subjectname". My dir structures of > "structural" and "retinotopy" are the same as > http://www.alivelearn.net/?p=65 . "SUBJ1" is stored under > "structural". if I set SUBJECTS_DIR as "....../structural", > $SUBJECT_DIR/SUBJ1 does exist, then still I get the same error msg. > > The following is the log file: > > fieldsign-sess log file $Id: fieldsign-sess,v 1.2 2010/05/04 22:00:18 > greve Exp $ Thu Nov 1 10:36:52 CDT 2012 Linux rii-appserv-02 > 2.6.32-279.11.1.el6.x86_64 #1 SMP Sat Sep 22 07:10:26 EDT 2012 x86_64 > x86_64 x86_64 GNU/Linux /media/users/zhouw4/testf/retinotopy > /usr/local/freesurfer/fsfast/bin/fieldsign-sess -a rtopy.self.lh > -occip -s SUBJ1 uid=20120(zhouw4) gid=22000(rii_users) > groups=22000(rii_users),21100(rii_appservers),23000(domain^users) > context=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 > > Best > Wei > > > >What is the name of FreeSurfer subject? This is not necessarily the > same >> > >as SUBJ01 in your command line below. That is the session (which may or > >may not be the same as the "subject name"). What ever the subjectname > is, does SUBJECT_DIR/subject exist? > On 10/31/2012 03:07 PM, Zhou, Wei wrote: > > > > Hi, Doug > > > > Thank you for your reply. I have tried exporting SUBJECTS_DIR to the > > directory of upper fold, retinotopy or SUBJ01 But none of them works. > > Still the same error msg. > > > > So what should SUBJECTS_DIR be exported to for this analysis? > > > > Best > > > > Wei > > > > > > > > >Hi Wei, this is a bug in the error msg. It is trying to say that your > > >source subject is not in the $SUBJECTS_DIR. > > >doug > > > > >On 10/27/2012 02:27 PM, Zhou, Wei wrote: > > > Dear freesurfers, > > > > > > I am trying retinotopy analysis in freesurfer. For "fieldsign-sess", I > > > encounter the following problem when I type "fieldsign-sess -a > > > rtopy.self.lh -occip -s SUBJ01" or "fieldsign-sess -a rtopy.self.lh > > > -occip -sf sessid": > > > > > > */media/users/zhouw4/testf/retinotopy/SUBJ01/log/fieldsign-sess.log* > > > *subject: Undefined variable.* > > > > > > my structure of retinotopy fold is : > > > retinotopy > > > | |--sessid > > > |--SUBJ01 > > > |--subjectname > > > > > > |--bold > > > |--001 > > > |--f.nii > > > |--rtopy.par| > > > > > > I really appreciate it if you could give me some idea about that > > > problem. Thanks a lot in advance. > > > > > > Best > > > Wei Zhou > > > Medical Physics Ph.D. Student > > > Diagnostic Imaging Track > > > cgxz...(a)gmail.com<mailto:cgxz...@gmail.com> > > > zho...(a)livemail.uthscsa.edu<mailto:zho...@livemail.uthscsa.edu> > > > > > > > > > _______________________________________________ > > > 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 > > gr...(a)nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > Best > Wei Zhou > Medical Physics Ph.D. Student > cgxz...(a)gmail.com <mailto:cgxz...@gmail.com> > zho...(a)livemail.uthscsa.edu <mailto:zho...@livemail.uthscsa.edu> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Best Wei Zhou

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Re: [Freesurfer] interpretation of vertexwise thickness, area, volume analysis
by Mahinda Yogarajah 19 Nov '12

19 Nov '12

Hi, Thanks for the reply. I am using the new script and I should correct myself in that my significant volume changes do seem to correspond (although they are not completely identical) to areas where there are significant area differences (I see no significant thickness differences between my groups) - using this kind of vertex wide analysis how does one interpret (biologically) these area differences. One other quick question regarding monte Carlo correction in qdec - when I use more stringent p thresholds my significant clusters get smaller as one might expect but I also see a completely new, small cluster in the Cingulum which is not seen at less stringent thresholds - is this kind of behaviour ok ? Thanks. Mahinda

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mismatch of parcellation and pial surface
by 嘉逸劉 19 Nov '12

19 Nov '12

Dear Freesurfer experts, I met a problem as shown in the appended figuer. You can see that in the insula, the pial surface abnormally curves in but the parcellation seems recognize the boundary of gray and white matter quite well. The tutorial tells us how to correct pial problem which generally incorporates dural as gray matter. However, in my case, the pial is too conservative in that region, ignores the gray matter, and nearly overlaps with white matter boundary. I cannot get help from the tutorial/manual. Could you please guide me how to correct this problem? Thanks in advance, JoJo

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variable
by xiangbo_2010 18 Nov '12

18 Nov '12

Dear experts: I want to ask the question: the gender (1;2) can be as a continuous variable? I hope that have experts to help me. Thanks! Bo Xiang

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Tksurfer display issue
by Maleki, Nasim 18 Nov '12

18 Nov '12

Hi all, This issue was posted by someone else in October (please see below). I have the EXACT same problem. Does anyone have any ideas how fix this? Thanks, Nasim =================================================== Hi, everyone. The tksurfer can't initial a window in iOS 10.7.5. Has anyone met this before? Last login: Mon Oct 15 10:57:04 on ttys001 -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl $ system_profiler SPSoftwareDataTypeSoftware: System Software Overview: System Version: Mac OS X 10.7.5 (11G63) Kernel Version: Darwin 11.4.2 Boot Volume: Macintosh HD Boot Mode: Normal Secure Virtual Memory: Enabled 64-bit Kernel and Extensions: Yes Time since boot: 1:56 $ tksurfer bert lh pial subject is bert hemi is lh surface is pial surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/canlab06 checking for nofix files in 'pial' Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=132501, faces=264998 surfer: single buffered window surfer: tkoInitWindow(bert) then it stopped here and does#t have any respond. I tried several times with different subjects, but failed with the same issue. Does anyone have any ideas? Thanks a lot. Best Wishes Meng

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Measures on Overall Registration Quality in Freesurfer
by Xinian Zuo 17 Nov '12

17 Nov '12

Dear FS Developers, Is there any metrics output by Freesurfer for measuring the overall quality or error of the surface registration from an individual brain to the fsaverage brain? I mean something like the bbregister.dof6.dat.mincost given by bbregister. Many thanks! -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn) Google Scholar Citations: http://scholar.google.com/citations?user=a3-gVGMAAAAJ&hl=en

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Freesurfer v5.2
by Sourena Soheili-Nezhad 17 Nov '12

17 Nov '12

Hello Freesurfer Development Team, I am in a dilemma to either postpone starting of a work (~400 subjects) till next FS release or not. What do you advise, and does there exist an approximate ETA for v5.2? Thanks in advance, Sourena Soheili-N.

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contrast matrix
by xiangbo_2010 17 Nov '12

17 Nov '12

Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes three discrete factors: factor 1 with three levels (A,B,C ); factor 2 with three levels (O,P,Q); gender (F, M), and one covariate. So I can get 18 classes: FAO, FAP,FAQ,FBO,FBP,FBQ,FCO,FCP,FCQ,MAO, MAP,MAQ,MBO,MBP,MBQ,MCO,MCP,MCQ. I want to perform the interaction between factor 1 and factor 2 regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 is it correct? Any help will be very appreciated. Best wishes, Bo Xiang

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Freesurfer November 2012