Freesurfer December 2006

freesurfer@nmr.mgh.harvard.edu

49 participants
59 discussions

error message during autorecon1: Can't find the talairach xform
by Bum Seok Jeong 14 Dec '06

14 Dec '06

During autorecon1, I find error message below during autorecon1, eventhough recon-all-status.log said 'recon-all finished without error ' Is it not considerable error message or important thing? Thank you bsjeong --------------------- Can't find the talairach xform 'spgr_nifti/N3/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /spgr_nifti/N3/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /spgr_nifti/N3/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.26912/nu0.mnc... ........... #@# Talairach Thu Dec 14 14:00:02 EST 2006 /spgr_nifti/N3/mri talairach --i nu.mgz --xfm transforms/talairach.auto.xfm /spgr_nifti/N3/mri /freesurfer/bin//talairach --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.4 2006/04/18 23:05:05 nicks Exp $ Linux b2_tm128.bwh.harvard.edu 2.6.17-1.2157_FC5 #1 SMP Tue Jul 11 22:53:56 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux Thu Dec 14 14:00:03 EST 2006 tmpdir is transforms/tmp.talairach.27507 /spgr_nifti/N3/mri mri_convert nu.mgz transforms/tmp.talairach.27507/src.mnc mri_convert nu.mgz transforms/tmp.talairach.27507/src.mnc Can't find the talairach xform '/spgr_nifti/N3/mri/transforms/talairach.xfm' Transform is not loaded into mri

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RE: [Freesurfer] Freesurfer and Grid computing
by Andries van der Leij 14 Dec '06

14 Dec '06

Hi Darren, Nick and freesurfers, Thanks very much for your replies! I've discussed this and have a couple of questions. I would be very glad if you could help me out. I'm currently talking with my group to decide where to go. Like I said, we will get a research-only 3T scanner, which (if used as much as we hope) will deliver about 20 GB of raw data each week. We need to think of a solid processing and storage pipeline in order to be able to do something with the data ;) We discussed this and are trying to come up with a good solution, both storage and analyses-wise. One solution for the enhancement of the analyses would be to buy a couple of solid workstations. The other would be a grid solution. The main problem isn't as much finance as it is manpower. No current member of the faculty has the time to invest in setting up and maintaining a grid if that will be a very difficult task to do. Hopefully we will get the money to hire an ICT person to do this. However, this is not certain. So I have a question concerning the difficulty of setting up the grid like proposed by Nick: semi-parallel in the sense that different commands of a batch are distributed to different nodes. We are wondering just how difficult this is. I address this question to both of you. Darren: you have SUN grid and Nick you have something like SUN grid. Nick, you state: <snip> You are on-track with the first scenario. If you have the technical skills and time to install the Sun Grid Engine, or PBS (which does nearly the same thing), then the batch interface will be easy for others to submit as many 'recon-all' instances as they want and will handle balancing. Once a batch system is setup, you can expect to have to spend some time maintaining the system (help-line, monitoring for stalled jobs, failed nodes, or failed disks, etc). You could also write your own scripts implementing a simple batch system, if you don't mind semi-manually tracking the resources, and if you will oversee it or use it yourself, and keep it small-scale. </snip> The issue of course is this: 1. Just how much technical skills and time does the installation and maintenance of a Grid cost? It is my impression that the implementation of the SUN grid is not that hard. But I'm always an optimist if it comes to computers, although at times this has proven to be a great overestimation of my own knowledge and skills. 2. How 'intuitive' is the usage of a batch system like SUN grid and how stable is it? That is: given that we write guidelines, howtos, and set up a Wiki, how difficult will drag&drop type users will be able to work with such a system? The final maintenance issues that Nick addresses concerns failure. 3. Hardware failure: freezing nodes and disk failures I expect to cost as much time as it will cost when we buy individual workstations, Maybe even less? 4. Software failure. Maybe I'm way off here, but it's my impression that the host running the batch system uploads the input data from a central server to a node, which analyses the data and then downloads the resulting output again, deleting the data on the node. If this is correct and if a single job fails, do you have to manually delete working data on a node? I hope you can help me out with this. Thank you! Andries

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3.0.3 for Debian (RedHat 9)
by Christopher L. Hamilton 14 Dec '06

14 Dec '06

We are looking at deploying a debian install to all of our linux machines but need the 3.0.3 version of freesurfer until we can test 3.0.4. Where can we download older versions? Chris Hamilton

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problem in runnign tkmedit on linux...
by Shahabuddin Ansari 14 Dec '06

14 Dec '06

Hi I am getting the following error when I run tkmedit or tksurfer: Couldn't create output file .xdebug_tkmeditfreeglut (tkmedit): OpenGL GLX extension not supported by display ':0.0' It seems X11 server configuration is not set properly to run OpenGL applications. Any ideas? Thanks Shahab ____________________________________________________________________________________ Need a quick answer? Get one in minutes from people who know. Ask your question on www.Answers.yahoo.com

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compatability between 32 and 64 bit versions
by Glenn Lawyer 13 Dec '06

13 Dec '06

Hi, Is there any problem mixing subjects processed with the 32 bit version and the 64 bit version, using FS 3.? How about between the RH9 build and the Centos build? I would be very surprised if this did present a problem, but my supervisor wants me to check. Yes, I did see Nick's email (28 mar 2006) on the slight differences in the floating point optimizations, which he felt were minor. +glenn -- -------------------------------------- I'm only in it for the glory. > Glenn Lawyer < > +352 661 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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combining conditions
by Cameron Ellis 13 Dec '06

13 Dec '06

Hi, I have three conditions specified in my paradigm files that I have been comparing to one another. Two conditions I would like to combine and compare to the third in one contrast and was wondering if this would require modifying my paradigm files to refer to these two conditions with the same number or if I can just positively weight the two I want to combine in mkcontrast-sess and negatively weight the other. That's all. Thanks, Cameron

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GLM analysis question
by Avram Holmes 13 Dec '06

13 Dec '06

FSFast support folks, I am looking for some support running an analysis in FSFast. As far as we can tell we have successfully run every step in a random effects analysis but we are having trouble viewing/interpreting the results. I was hoping that I would be able to post my processing stream and see if anyone would give us feedback on what we have or havent done correctly (see below). My understanding is that after I run mkanalysis-sess.new, selxavg-sess, mkcontrast-sess, stxgrinder-sess, and isxavg-re-sess, I have fit a model to the data and I am testing the fit of the model across our contrasts. However, Im not seeing the expected effects and I am wondering if I am missing a step or if my stream is not optimized. I have spent a considerable amount of time searching the wiki page and I havent been able to track down a detailed description of how to conduct and interpret a complete GLM analysis in FSFast so I am a little unsure if I have everything correct. Any help would be greatly appreciated, Avram #! /bin/csh -f Step1 set mypath = . set sub = $1 mc-sess -fstem f -fmcstem fmc -s ${sub} -d ${mypath} stc-sess -i fmc -o fmcstc -so siemens -s ${sub} -d ${mypath} spatialsmooth-sess -i fmcstc -o fmcstcsm5 -fwhm 5 -d ${mypath} -s ${sub} mkbrainmask-sess -s ${sub} -d ${mypath} Step2 set analysis = 'moneygamma_test' set subj = 'FPPREW01 FPPREW02 FPPREW03 FPPREW04 FPPREW05 FPPREW06 FPPREW07 FPPREW08 FPPREW09 FPPREW10 FPPREW11 FPPREW12 FPPREW13 FPPREW14 FPPREW15 FPPREW16 FPPREW17 FPPREW18' mkanalysis-sess.new -analysis ${analysis} -gammafit 2.25 1.25 -TR 2.5 -paradigm moneygame.par -designtype event-related -timewindow 30 -funcstem fmcstcsm5 -nconditions 5 -polyfit 1 -mcextreg -taumax 20 -mask brain foreach s ($subj) selxavg-sess -s ${s} -d . -analysis ${analysis} end mkcontrast-sess -analysis ${analysis} -contrast omnibus -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 -nosumconds mkcontrast-sess -analysis ${analysis} -contrast pun_v_noinc -a 1 -c 2 mkcontrast-sess -analysis ${analysis} -contrast rew_v_noinc -a 3 -c 2 mkcontrast-sess -analysis ${analysis} -contrast pun_v_rew -a 1 -c 3 mkcontrast-sess -analysis ${analysis} -contrast rew_v_pun -a 3 -c 1 foreach s ($subj) autoreg-sess -d . -s ${s} -fsd bold end Step3 set mypath = . set analysis = 'moneygamma_test' set subj = 'FPPREW01 FPPREW02 FPPREW03 FPPREW04 FPPREW05 FPPREW06 FPPREW07 FPPREW08 FPPREW09 FPPREW10 FPPREW11 FPPREW12 FPPREW13 FPPREW14 FPPREW15 FPPREW16 FPPREW17 FPPREW18' foreach s ($subj) stxgrinder-sess -contrast omnibus -analysis ${analysis} -s ${s} -d ${mypath} stxgrinder-sess -contrast pun_v_noinc -analysis ${analysis} -s ${s} -d ${mypath} stxgrinder-sess -contrast rew_v_noinc -analysis ${analysis} -s ${s} -d ${mypath} stxgrinder-sess -contrast pun_v_rew -analysis ${analysis} -s ${s} -d ${mypath} stxgrinder-sess -contrast rew_v_pun -analysis ${analysis} -s ${s} -d ${mypath} end Step4 set analysis = 'moneygamma_test' set subj = 'FPPREW01 FPPREW02 FPPREW03 FPPREW04 FPPREW05 FPPREW06 FPPREW07 FPPREW08 FPPREW09 FPPREW10 FPPREW11 FPPREW12 FPPREW13 FPPREW14 FPPREW15 FPPREW16 FPPREW17 FPPREW18' set glist = 'GROUPLIST' set group = 'Controls' set contrasts = 'omnibus pun_v_noinc rew_v_noinc pun_v_rew rew_v_pun' foreach s ($subj) foreach anal ($analysis) func2tal-sess -res 4 -analysis ${anal} -d . -s ${s} foreach hemi (lh rh) func2sph-sess -analysis ${anal} -hemi ${hemi} -projfrac .3 -d . -s ${s} sphsmooth-sess -smoothsteps 10 -analysis ${anal} -insphdir sph -outsphdir sphsm10 -hemi ${hemi} -d . -s ${s} end end end foreach c ($contrasts) isxavg-re-sess -analysis ${analysis} -group ${group} -space tal -d . -sf ${glist} -contrast ${c} foreach hemi (lh rh) isxavg-re-sess -analysis ${analysis} -group ${group} -space sph -hemi ${hemi} -d . -sf ${glist} -contrast ${c} end end ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: [Freesurfer] A Possible Bug in Making Labels in Tksurfer
by Reza Rajimehr 13 Dec '06

13 Dec '06

Hi Kevin, on machine monkeylove source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /space/ship/4/users/Retinotopy_Project/Human_Retinotopy/subjects cd /space/ship/4/users/Retinotopy_Project/Human_Retinotopy/Human_Eccen/Katie/MYSTUDY surf-sess -sf sf.txt -df df.txt -analysis Analysis_Human_Eccen -contrast 123456 -map sig -hemi rh I changed the min threshold to 4 (linear) in the Tksurfer window (view - config overlay ...). Reza > Thanks for this report. Can you point me at the data you were using, > whether you were using the std or dev environment, and what command > you used to start tksurfer? > > On Tue, Dec 12, 2006 at 11:28:45PM -0500, Reza Rajimehr wrote: >> Hi (Doug, Kevin, ...), >> >> I am experiencing a problem with making labels in Tksurfer (for doing a >> subsequent ROI analysis). I did something as follows: >> >> 1) I loaded a functional activity map by surf-sess (human cortex). >> >> 2) Then, I loaded the full flattened cortical surface. >> >> 3) After right-clicking in the Tksurfer window, I clicked >> (left-clicking) >> on the center of 4 spatially distinct activity patches (i.e. 4 yellow >> spots of activity, which had no overlap with each other and no overlap >> with other yellow or blue patches). So 4 vertices were selected (as I >> saw >> in the command-line window). >> >> 4) Then, I openned the "Custom Fill" dialog box, and selected the >> following options: >> >> Fill Conditions: Up to and including paths, Up to functional values >> below >> threshold >> >> Fill From: All marked vertices >> >> Action: Create a new label >> >> After clicking the "Fill" button (in the "Custom Fill" dialog box) and >> then clicking the "Mark Label" button (in the Tksurfer window), the 4 >> patches were appropriately selected as white labels. In the command-line >> window: >> >> % surfer: filling (ctrl-c to cancel).. done, 123 vertices filled >> surfer: filling (ctrl-c to cancel)... done, 542 vertices filled >> surfer: filling (ctrl-c to cancel). done, 105 vertices filled >> surfer: filling (ctrl-c to cancel)..... done, 954 vertices filled >> >> 5) I saved the selected label. In the command-line window: >> >> writing 2913 labeled vertices to >> /space/ship/4/users/Retinotopy_Project/Human_Retinotopy/subjects/katie/label/DFPRHKAS.label. >> >> >> The problem is that the number of saved vertices is much more than the >> sum >> of vertices in the 4 patches (2913 vs. 123+542+105+954). I do not have >> this problem when I click on just 2 patches (rather than 4), and the >> number of saved vertices is the sum of vertices in the 2 patches. I also >> had this problem before, and I am worried that some additional vertices >> (voxels) are saved out of my control, which might affect the ROI >> analysis. >> >> Thanks for any help, >> >> Best, >> Reza >> >> ******************************** >> Reza Rajimehr, MD >> >> NMR Athinoula A. Martinos Center >> Department of Radiology >> Massachusetts General Hospital (MGH) >> Building 149, 13th St. >> Charlestown, MA 02129 >> >> Email: reza(a)nmr.mgh.harvard.edu >> ******************************** >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Kevin Teich ******************************** Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: reza(a)nmr.mgh.harvard.edu ********************************

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A Possible Bug in Making Labels in Tksurfer
by Reza Rajimehr 12 Dec '06

12 Dec '06

Hi (Doug, Kevin, ...), I am experiencing a problem with making labels in Tksurfer (for doing a subsequent ROI analysis). I did something as follows: 1) I loaded a functional activity map by surf-sess (human cortex). 2) Then, I loaded the full flattened cortical surface. 3) After right-clicking in the Tksurfer window, I clicked (left-clicking) on the center of 4 spatially distinct activity patches (i.e. 4 yellow spots of activity, which had no overlap with each other and no overlap with other yellow or blue patches). So 4 vertices were selected (as I saw in the command-line window). 4) Then, I openned the "Custom Fill" dialog box, and selected the following options: Fill Conditions: Up to and including paths, Up to functional values below threshold Fill From: All marked vertices Action: Create a new label After clicking the "Fill" button (in the "Custom Fill" dialog box) and then clicking the "Mark Label" button (in the Tksurfer window), the 4 patches were appropriately selected as white labels. In the command-line window: % surfer: filling (ctrl-c to cancel).. done, 123 vertices filled surfer: filling (ctrl-c to cancel)... done, 542 vertices filled surfer: filling (ctrl-c to cancel). done, 105 vertices filled surfer: filling (ctrl-c to cancel)..... done, 954 vertices filled 5) I saved the selected label. In the command-line window: writing 2913 labeled vertices to /space/ship/4/users/Retinotopy_Project/Human_Retinotopy/subjects/katie/label/DFPRHKAS.label. The problem is that the number of saved vertices is much more than the sum of vertices in the 4 patches (2913 vs. 123+542+105+954). I do not have this problem when I click on just 2 patches (rather than 4), and the number of saved vertices is the sum of vertices in the 2 patches. I also had this problem before, and I am worried that some additional vertices (voxels) are saved out of my control, which might affect the ROI analysis. Thanks for any help, Best, Reza ******************************** Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: reza(a)nmr.mgh.harvard.edu ********************************

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mri_surf2surf
by Lars M. Rimol 12 Dec '06

12 Dec '06

Hi, I want to resample a number of subjets' (e.g.) thickness files to ico (atlas space). It seems that mir_surf2surf has been changed, can I still use a list of subject names to specify the subjects with the flag --f? Also, what is source and what is target? I assume source is the file that is mapped onto the target, so that the output file will contain the data from the source file in the coordinate system of the target file? I used this command line to resample subject 20543 to ico: mri_surf2surf --hemi lh --srcsubject subj20543 --srcsurfval thickness --src_type curv --trgsubject ico --trgicoorder 7 --trgsurfval TEST.mgh If I want to do this with a list of subjects, is there any way to specify such a list on the command line? Is --src_type curv correct? Is this flag valid for both thickness files, sulc files, any type of .mgh files (if I e.g. calculate some ratio based on a set of surface files and store the result as an .mgh)? Can I use make_average_subject and use -trgsubject <average_subject> instead of -trgsubject ico Would that make any difference? Thank you! Lars -- yours, LMR

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Freesurfer December 2006