Freesurfer December 2009

freesurfer@nmr.mgh.harvard.edu

77 participants
105 discussions

FW: a question about the mris_volmask ERROR
by Guang Zeng 10 Dec '09

10 Dec '09

Hello, Allison, Thanks a lot for your help and sorry for my delay! Yes, I agree. If I use -autorecon3 to rerun it, everything should be fine. But I also find something interesting. Please check the attached recon-all.log, >From line 10812 to line 10847, you will see "ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x270e3480): Unable to create a thread. pthread_create() returned 12" Normally, after this line, we will see something like, "Segmentation fault (core dumped) recon-all exited with ERRORS at Thu Dec 10 00:58:33 CST 2009" Once, I call -autorecon3, we can see the following lines in the recon-all.log, and the results will be fine. " New invocation of recon-all Thu Dec 10 15:50:19 CST 2009 /data1/radiology/m047599/subjects/002_S_0413_20060519 /usr/local/biotools/freesurfer/freesurfer-v4.5.0/bin/recon-all -s 002_S_0413_20060519 -autorecon3 -no-isrunning " However, in the recon-all.log I sent to you, we only can see something like, " ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x30bf9d90): Unable to create a thread. pthread_create() returned 12 loading input data... hemi masks overlap voxels = 4 writing volume /data1/radiology/m047599/subjects/002_S_0413_20060502/mri/ribbon.mgz writing ribbon files #----------------------------------------- #@# AParc-to-ASeg Wed Dec 9 20:07:25 CST 2009 /data1/radiology/m047599/subjects/002_S_0413_20060502 mri_aparc2aseg --s 002_S_0413_20060502 --volmask " The trick thing is I do not do anything, it looks like to me, after few rounds of calling vtkMultiThreader and getting ERRORs, FS automatically go to the next step with a wrong ribbon.mgz by itself. And it will finish the whole process without "errors", however, when we load the results into tkmedit, we find lots of wm parcellation are wrong. I have 38 subjects have this kind of problem, do you think it is because of FS or the SGE I use to run the subjects? Thanks a lot! Guang > Date: Tue, 8 Dec 2009 17:43:09 -0500 > From: astevens(a)nmr.mgh.harvard.edu > To: freesurfer_zg(a)hotmail.com > Subject: Re: [Freesurfer] a question about the mris_volmask ERROR > > Oh I just saw your earlier message which had a bit more detail. > > If you are using -autorecon3 to rerun it so it finishes, you shouldn't see > a difference in the stats. You may see a difference if you are running on > different platforms. > > -- > > On Mon, 7 Dec 2009, Guang Zeng wrote: > > > > > Hi, there, > > > > I have question about the mris_volmask ERROR. > > > > I ran multiple subjects on our SUN Grid Engine system. sometimes some subjects are sent to the same cluster node, and limited memory is assigned to each subject. > > Because of this, I often met an ERROR at the mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance sub1 step > > in autorecon3., which gave me an error like: > > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 372 > > vtkMultiThreader (0x33d05a90): Unable to create a thread. pthread_create() returned 12 > > > > I knew this error is caused by some VTK function FS used to allocate memory. What I did is everytime when I met this kind of error, > > I use recon-all -s subj -autorecon3 -no-isrunning , and the process will finish. > > > > However, I found if I did something like this, it will cause problems at the wm parcellation step. For example, I have the same subject which is sent to SGE, fails at mris_volmask, and then I call autorecon3 to finish the process, and I go to wmparc.stats, lotf of rois such as isthumus ctx-cingluate, ctx-posterior singulate are 0. > > While I ran the same subject at a local machine, and finished without any problems, I looked at isthumus cingluate and posterior singulate, they are not zeros. > > > > So, does it mean that I need start from beginning when I met the errors cause by mris_volmask? > > > > Thanks a lot! > > guang > > > > _________________________________________________________________ > > Chat with Messenger straight from your Hotmail inbox. > > http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?o… Windows Live Hotmail gives you a free,exclusive gift. Click here to download. _________________________________________________________________ Windows Live Hotmail gives you a free,exclusive gift. http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?o…

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func2roi-sess bug?
by John Richey 10 Dec '09

10 Dec '09

Dear freesurfer experts: I am trying to extract roi from my fMRI data using func2roi-sess. However, I encounter an error that I wonder might be a bug in the code? My input is func2roi-sess -roidef l_lingual -analysis hrf -anatlabel lh.lingual -maskcontrast AllvFix -maskthresh 0 -masktail pos -maskmap sig -sf subjects.txt (the last 25 or so lines of the log are pasted below). Basically, I believe that line in the log that reads: /fmcsm8= bold/007 should read: srcvol = bold/007/fmcsm8.nii The result is that the func2roi-sess routine terminates with the error displayed on the last line: /fmcsm8. Does it exist?lume bold/007 Has anyone else encountered this problem? Or maybe I am skipping a step? I am using v4.5.0. If it helps, I can also paste my source code that seems to produce this error. Thanks in advance John Richey -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/fmcs.txt07 version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ -------------------------------------------------------- roifile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 .txtxtfile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 oldtxtstyle = 0 /fmcsm8= bold/007 srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label labelreg unspecified label fill thresh = 1e-07 mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii mskfmt unspecified msk volume same as source msk tail = pos msk threshold = 0.000000 msk invert = 0 msk frame = 0 /fmcsm8. Does it exist?lume bold/007

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rebuild_gca_atlas.csh
by Jared Price 10 Dec '09

10 Dec '09

Freesurfer gurus: When using rebuild_gca_atlas.csh it fails due to the fact that not all of the TRs TEs and FlipAngles are identical across all scans I am using for the atlas. Is there any major concern if we artificially change these values using mri_modify so that they are identical? Much thanks, Jared

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Rotating to chiasmato-commissural plane
by Jordan Poppenk 10 Dec '09

10 Dec '09

Dear list, I would like to rotate my orig.mgz volume into chiasmato-commissural space to assess the length of a freesurfer-obtained hippocampal segmentation along the main axis of the hippocampus. I am doing this to enable use of a slice-counting method. Now, I know that tkregister2 allows me to both rotate volumes and load aseg files, but I can only rotate the movable volume. I'm not clear on how I would set this up a) to rotate my target image in native / subject space (orig.mgz), so as not to disturb the raw length values; or b) to rotate the aseg segmentation along with it. Is anyone able to offer any suggestions on how I might be able to use freesurfer to accomplish this task (or whether there is a different approach that would be simpler)? Thanks in advance for any help. Cheers, Jordan _____________________________________ Jordan Poppenk Ph.D. Candidate, Department of Psychology University of Toronto, Canada http://individual.utoronto.ca/poppenk There is no way to peace; peace is the way. - A.J. Muste

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2009 Destrieux Parcellation for FSAverage?
by Michael Waskom 09 Dec '09

09 Dec '09

Hi all, Is there a way to get aparc.a2009s.annot files (the updated Destrieux parcellation) for fsaverage? Doesn't seem to be in the labels directory for fsaverage for 4.5.0. Thanks! Best, Mike

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linux ppc64 build
by Bradley Buchsbaum 09 Dec '09

09 Dec '09

Hi, There was a previous request from Andre Gouws (Nov. 19th 2009) about the possiblity of obtaining a linux-ppc build. We would also like to run freesurfer on a (64-bit) linux-ppc IBM cluster. Here's hoping two independent requests in the last three weeks constitutes overwhelming demand... cheers, Brad Buchsbaum -- Bradley R. Buchsbaum, Ph.D. Rotman Research Institute 3560 Bathurst St. Toronto, ON Canada M6A 2E1 email: bbuchsbaum(a)rotman-baycrest.on.ca

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mris_volmask ERROR
by Guang Zeng 08 Dec '09

08 Dec '09

Hi, there, I submit several subjects to FS piepline using our Sun Grid Engine System, all of them failed at the same place which is the mris_volmask step in autorecon3. It gave me an error like: ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x33d05a90): Unable to create a thread. pthread_create() returned 12 I knew this error is caused by some VTK function FS used to allocate memory. So what I did is I use recon-all -s subjectid , and the process will finish. What happen is the same subjects have been run on our local machines, and finished without any problems. However, when I looked at the wmparc.stats file of the same subject, the results are quite different. For example, ctx_isthumus cingluate and ctx_posterior singulate value are not zeros for my local machine results, while ctx_isthumus cingluate and ctx_posterior singulate value are zeros for my SGE machine results. And this problem have to all these subjects. Another funny thing is if I look at the ?h.aparc.stats file, the results from SGE and local machine are the same, while when I load the results to tksurfer, they are quite different. So my question is: Since I need use SGE to run multiple subjects again, next time when I met this mris_volmask ERROR, I need rerun the process from the beginning, not from autorecon3, right? Thank! Guang _________________________________________________________________ Chat with Messenger straight from your Hotmail inbox. http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?o…

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optseq post-hoc sorting
by Kathrine Shepherd 08 Dec '09

08 Dec '09

Hello-- I'm designing an event-related task that does not have predefined conditions. instead, I plan to do some post-hoc sorting based on performance and stimuli characteristics. I expect that after sorting, I will have 5 conditions- but it could be more or less. Is it advisable to determine the stim presentation schedules in optseq as if I had already specified predefined conditions? Or is it optimal to just completely randomize the jitter without making any assumptions about the response function? Also is there a tool available to estimate the stat power of my schedules after I've defined them? Many thanks for your advice, -Kathrine

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fixed versus random effects
by Kathrin-Sophie Herbst 08 Dec '09

08 Dec '09

Hi, for my second-level statistics I have been running a fixed-effects analysis as well as a random-effects-a. with mri_glmfit (11 subjects). It turns out that the fixed-effect-analyis shows hardly any effect while in the random-effects-analysis there are results (at a low threshold: 1.6 or 2). Vision versus rest looks fine in both and gets even stronger in the fixed effects. Is there a statistical reason for stonger outcomes in random-effects for results around the threshold or is this a hint for an error in my analysis? Thanks, Kathrin my command was: mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ ffxdof.dat --surf fsaverage rh my computer: snapjudge my path: autofs/space/bomba_020/users/ksherbst/data/brightghosts_loc/ loc_group_11 and I am running freesurfer stable 4

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Registration for Upcoming Freesurfer Course now open, Feb. 1 & 2
by Allison Stevens 08 Dec '09

08 Dec '09

Hello, The Freesurfer group will be offering a two-day Freesurfer Tutorial and Workshop on February 1st and 2nd at the Martinos Center in Charlestown, MA. A description of the February course and a list of the topics covered can be found on the Course wiki page here: http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription On that website, you will find a link to register for the course. There is only room for 28 total participants and registration is on a first-come, first-serve basis. Shortly after all spots are filled, information will be sent out about hotels and parking. If you would like to arrange those details now, you can find all the information that will be sent out on the Course wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription THINGS TO KNOW BEFORE YOU REGISTER: 1. The registration AND payment deadline is January 8, 2010. 2. fMRI analysis is not a component that is taught in this course. 3. Payment can only be done in the form of a check or if you are from within the Partners network, a fund transfer can be arranged. Credit Cards are *not* accepted. 4. There are no refunds if you cannot attend the course. You can put the tuition payment towards the next course or send someone else in your spot. 5. All questions about payment should go to Stacey Ladieu (sladieu(a)nmr.mgh.harvard.edu) Before e-mailing Stacey, please read the Course wiki page (listed above) and the registration page, carefully. Most questions participants have are answered there. 6. If the course is full, please register to be placed on the waiting list *only* if you think you could attend the course on short notice if a spot were to open up. Regards, The FreeSurfer Team

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Freesurfer December 2009