Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

Re: [Freesurfer] y values from glmfit-sim
by Laura M. Tully 21 Mar '13

21 Mar '13

Thank you! On Thu, Mar 21, 2013 at 10:56 AM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > wrote: > Yes, the average thickness over the cluster for each subject. > doug > > On 03/21/2013 01:54 PM, Laura M. Tully wrote: > >> Thanks - one last clarification: just to confirm - the values of >> thickness.ocn.y.dat (i.e. analyses with thickness as input) are avg >> thickness over the whole cluster for each subject? If not, how would I get >> the avg thickness value for that cluster for each subject? >> >> LT >> >> >> On Thu, Mar 21, 2013 at 10:49 AM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>> >> wrote: >> >> >> On 03/21/2013 01:11 PM, Laura M. Tully wrote: >> >> yes the input is area - so to clarify, in order to get the >> average area for each subject in that cluster I would multiply >> each subject's values in the xxx.ocn.y.dat file by the number >> of vertices in the cluster (denoted as NVtxs in the cluster >> summary?) e.g. 0.761374 * 998 = 759.85mmsq? >> >> Yes, correct >> >> >> Does the same hold for the y values in a thickness analysis, >> i.e. when thickness is the input, does each value in the >> xxx.ocn.y.dat file (e.g. 2.54) represent the average thickness >> of each vertex and so I must multiply that by the number of >> vertices to get the average thickness for each subject for >> that cluster? >> >> No, you probably just want to report the average thickness, not >> the sum of the thicknesses within the cluster >> >> >> I'm using 5.1.0 - I have no idea if I have the patch for area >> and volume analyses because I run all my analyses remotely on >> the harvard imaging server (ncf) - how would I know? And what >> are the bugs in area/volume analyses in 5.1.0(how could I >> detect them)? >> >> You will need a new version of mris_preproc which you can get from >> here: >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> greve/mris_preproc<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc> >> You can compare this version against the one you have. If they are >> different, then copy this version into $FREESURFER_HOME/bin. If >> you are using QDEC, then rerun qcache (recon-all -qcache ...). If >> you are using the command-line stream, re-run it starting at >> mris_preproc. >> >> doug >> >> >> >> LT >> >> >> >> On Thu, Mar 21, 2013 at 10:02 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>> >> wrote: >> >> Hi Laura, I assume the input is area? Then this will >> compute the >> average area of each vertex. The area of a vertex is the >> average >> area of the triangles around it. To get total area, you can >> multiple the number that you get from xxx.ocn.y.dat by the >> number >> of vertices in the cluster. >> >> doug >> >> ps. What version of FS are you using? If not 5.2, do you >> have the >> patch to fix the area and volume analysis? >> >> >> >> On 03/21/2013 12:52 PM, Laura M. Tully wrote: >> >> hi Doug, >> A follow up question: when I look at the >> xxx.ocn.y.dat for a >> cluster where group differences in surface area have been >> identified the values are all less than 1 (e.g. >> 0.761374) even >> though the cluster size is reported as 680 mmsq. does >> the y >> value correspond to .76 mmsq average area for that >> subject in >> that cluster or does the y value in the context of surface >> area analyses represent something else? (or does it >> need to be >> multiplied by some factor?) >> >> Thanks! >> >> >> On Wed, Mar 20, 2013 at 2:39 PM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>>> >> wrote: >> >> They are the input (mri_glmfit --y y.mgh) averaged >> over >> the clusters. >> They are raw input, no detrending. >> doug >> On 03/20/2013 05:16 PM, Laura M. Tully wrote: >> > Hello experts, >> > >> > could someone clarify for me what the y values >> in the >> xxx.ocn.y.dat >> > files represent following glmfit-sim? are they the >> residualized y >> > values of avg cortical thickness in that specific >> cluster after >> > regressing out the effect of any predictor >> variables in >> the glm? >> > >> > Thanks! >> > >> > Laura. >> > -- >> > -- >> > Laura M. Tully, MA >> > Social Neuroscience & Psychopathology, Harvard >> University >> > Center for the Assessment and Prevention of >> Prodromal >> States, UCLA >> > Semel Institute of Neuroscience >> > ltully(a)mednet.ucla.edu >> <mailto:ltully@mednet.ucla.edu**> <mailto:ltully@mednet.ucla.edu >> <mailto:ltully@mednet.ucla.edu**>> >> <mailto:ltully@mednet.ucla.edu >> <mailto:ltully@mednet.ucla.edu**> <mailto:ltully@mednet.ucla.edu >> <mailto:ltully@mednet.ucla.edu**>>> >> <mailto:ltully@mednet.ucla.edu >> <mailto:ltully@mednet.ucla.edu**> >> <mailto:ltully@mednet.ucla.edu >> <mailto:ltully@mednet.ucla.edu**>> >> <mailto:ltully@mednet.ucla.edu <mailto:ltully@mednet.ucla.edu**> >> <mailto:ltully@mednet.ucla.edu >> <mailto:ltully@mednet.ucla.edu**>>>> >> > ltully(a)fas.harvard.edu >> <mailto:ltully@fas.harvard.edu**> <mailto:ltully@fas.harvard.edu >> <mailto:ltully@fas.harvard.edu**>> >> <mailto:ltully@fas.harvard.edu >> <mailto:ltully@fas.harvard.edu**> <mailto:ltully@fas.harvard.edu >> <mailto:ltully@fas.harvard.edu**>>> >> <mailto:ltully@fas.harvard.edu >> <mailto:ltully@fas.harvard.edu**> >> <mailto:ltully@fas.harvard.edu >> <mailto:ltully@fas.harvard.edu**>> >> <mailto:ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu**> >> <mailto:ltully@fas.harvard.edu >> <mailto:ltully@fas.harvard.edu**>>>> >> > 310-267-0170 <tel:310-267-0170> >> <tel:310-267-0170 <tel:310-267-0170>> <tel:310-267-0170 >> <tel:310-267-0170> >> >> <tel:310-267-0170 <tel:310-267-0170>>> >> >> >> > -- >> > My musings as a young clinical scientist: >> > http://theclinicalbrain.**blogspot.com/<http://theclinicalbrain.blogspot.com/> >> > Follow me on Twitter: @tully_laura >> > >> > >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >>> >> >> > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> >>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 >> <tel:617-724-2358>>> >> Fax: 617-726-7422 <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 >> <tel:617-726-7422> >> >> <tel:617-726-7422 <tel:617-726-7422>>> >> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** >> BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** >> BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> FileDrop: >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >>> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >> >> >> >> >> -- -- >> Laura M. Tully, MA >> Social Neuroscience & Psychopathology, Harvard University >> Center for the Assessment and Prevention of Prodromal >> States, >> UCLA Semel Institute of Neuroscience >> ltully(a)mednet.ucla.edu <mailto:ltully@mednet.ucla.edu**> >> <mailto:ltully@mednet.ucla.edu <mailto:ltully@mednet.ucla.edu**>> >> <mailto:ltully@mednet.ucla.edu >> <mailto:ltully@mednet.ucla.edu**> <mailto:ltully@mednet.ucla.edu >> <mailto:ltully@mednet.ucla.edu**>>> >> ltully(a)fas.harvard.edu <mailto:ltully@fas.harvard.edu**> >> <mailto:ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu**>> >> <mailto:ltully@fas.harvard.edu >> <mailto:ltully@fas.harvard.edu**> <mailto:ltully@fas.harvard.edu >> <mailto:ltully@fas.harvard.edu**>>> >> 310-267-0170 <tel:310-267-0170> <tel:310-267-0170 >> <tel:310-267-0170>> >> -- My musings as a young clinical scientist: >> http://theclinicalbrain.**blogspot.com/<http://theclinicalbrain.blogspot.com/> >> Follow me on Twitter: @tully_laura >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 >> <tel:617-726-7422>> >> >> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** >> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> >> >> -- -- >> Laura M. Tully, MA >> Social Neuroscience & Psychopathology, Harvard University >> Center for the Assessment and Prevention of Prodromal States, >> UCLA Semel Institute of Neuroscience >> ltully(a)mednet.ucla.edu <mailto:ltully@mednet.ucla.edu**> >> <mailto:ltully@mednet.ucla.edu <mailto:ltully@mednet.ucla.edu**>> >> ltully(a)fas.harvard.edu <mailto:ltully@fas.harvard.edu**> >> <mailto:ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu**>> >> 310-267-0170 <tel:310-267-0170> >> -- My musings as a young clinical scientist: >> http://theclinicalbrain.**blogspot.com/<http://theclinicalbrain.blogspot.com/> >> Follow me on Twitter: @tully_laura >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> >> >> -- >> -- >> Laura M. Tully, MA >> Social Neuroscience & Psychopathology, Harvard University >> Center for the Assessment and Prevention of Prodromal States, UCLA Semel >> Institute of Neuroscience >> ltully(a)mednet.ucla.edu <mailto:ltully@mednet.ucla.edu**> >> ltully(a)fas.harvard.edu <mailto:ltully@fas.harvard.edu**> >> 310-267-0170 >> -- >> My musings as a young clinical scientist: http://theclinicalbrain.** >> blogspot.com/ <http://theclinicalbrain.blogspot.com/> >> Follow me on Twitter: @tully_laura >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > -- -- Laura M. Tully, MA Social Neuroscience & Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltully(a)mednet.ucla.edu ltully(a)fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura

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y values from glmfit-sim
by Laura M. Tully 21 Mar '13

21 Mar '13

Hello experts, could someone clarify for me what the y values in the xxx.ocn.y.dat files represent following glmfit-sim? are they the residualized y values of avg cortical thickness in that specific cluster after regressing out the effect of any predictor variables in the glm? Thanks! Laura. -- -- Laura M. Tully, MA Social Neuroscience & Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltully(a)mednet.ucla.edu ltully(a)fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura

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installation problem
by Xue Zhang 21 Mar '13

21 Mar '13

dear freesurfer experts, I tried to install freesurfer in a remote linux cluster, when I completed the installation, and began to run the freesurfer gui use my own windows PC, the command line showed erro belowing information : [wanglhlab@node01 freesurfer]$ tkmedit bert orig.mgz GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by display: localhost:11.0 could anyone tell me the reason why my installation failed? The video card on cluster is Matrox Graphics, Inc. MGA G200eW WPCM450 (rev 0a), my own PC video card is AMD Radeon HD 7800 Series. regards Xue Zhang

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Re: [Freesurfer] fs-fast processing questions
by Douglas N Greve 21 Mar '13

21 Mar '13

Oh, yes, I was thinking you were starting at 1 not 0. Sorry about that. doug On 03/21/2013 12:45 PM, preciado(a)nmr.mgh.harvard.edu wrote: > So, to clarify I got the number of the acquisitions that I want to exclude > from an fs-fast output file: fmcpr.dat in .../project/session/bold/008/ > > This file starts with scan number 0. So if > Scan 0 is seconds 0, 1, 2 > Scan 1 is seconds 3, 4, 5 > ..... > Shouldn't then; > Scan 134 be 402, 403, 404 > > > -Ronny > > >> Hi Ronny, >> >> On 03/20/2013 05:57 PM, preciado(a)nmr.mgh.harvard.edu wrote: >>> Hello all, >>> I am starting to run some analysis using fs-fast and I had a few basic >>> questions that I couldn't find answers on the wiki/tutorial. >>> >>> 1) Format of files for mkanalysis-sess -tpexclude tpexclude.dat >>> What is the format of the input file for -tpexclude? Is it simply a >>> single >>> column of integers representing the seconds that need to be excluded? My >>> example, my TR is 3 and I know I want to remove acquisitions 134 and 140 >>> because of motion. Do I simply need to have a file that has the >>> following >>> content? >>> 402 >>> 403 >>> 404 >>> 420 >>> 421 >>> 422 >> This is correct, except that time starts at 0. So time point 1 = 0, tp2 >> = 3sec, etc. So tp134 = (134-1)*3 = 399, not 402 >>> >>> 2) bold data - Resampling to "common space" >>> In the preprocessing step, the bold data is resampled to 76x76x93. My >>> data >>> is 96x96x50. Does starting with data that is larger than the "common >>> space" cause a problem in the analysis? >> No >>> 3) Viewing analysis for individual bold data runs >>> When the First level analysis is completed, the resulting files are a >>> combination of all of the bold data runs of the session. Is there a way >>> to >>> make it so that I can also see the different activity for individual >>> runs >>> within the session or does the analysis only do it by combining data for >>> all runs within a session? >> By default it combines all the runs. If you want to see what it looks >> like in each run, there are two things you can do. First, you can run >> selxavg3-sess with the -run-wise option. This causes it analyze each run >> separately. This the easy way. Second, you could recode your stimulus >> numbers to be run specific. This means you have to create a new analysis >> and specify new contrasts. >> doug >>> Thanks in advance! >>> -Ronny >>> _______________________________________________ >>> 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 >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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 greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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mri_info crashing (bits stored vs bits allocated?)
by Ostuni, John (NIH/NINDS) [E] 21 Mar '13

21 Mar '13

We have a data set that mri_info cannot work with. We've tried multiple architectures and freesurfer versions, but mri_info either crashes with segmentation fault or generates errors such as *** glibc detected *** mri_info: free(): invalid pointer: 0x000000000000006b *** One feature of the data set is that the bits stored(12) is different than the bits allocated(16). Could this be the problem? I have an anonymized version of the data set I can upload if that helps. Thanks for any assistance, John

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Talairach General Question
by obregon＠nmr.mgh.harvard.edu 21 Mar '13

21 Mar '13

Hi, I have a rather general, and perhaps even naive, concern regarding the Talairach transform. I've noticed that the coronal and/or horizontal views of the Talairach transform viewed under tkregister2, though generally correctly aligned with respect to the midline of the brain, they tend to have a scaling offset compared to the orig volume, i.e., smaller in size in the XZ and XY planes, respectively. A minor rotation around the x-axis is also generally present in the sagittal view. Considering that everything in both the volume and surface pipelines is affected by the Talairach transform, is it adviseable to manually stretch and rotate the moveable volume so it matches the orig volume as closely as possible, or will this have negligible effects on the surface reconstructions? Thanks, --G

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recon-all errors
by Marcos Martins da Silva 21 Mar '13

21 Mar '13

Hi, freesurfers I am trying to execute the post installation tests as recommended at freesurfers website. Using a CentOS6 Virtual Machine (kernel 2.6.32-358.2.1.el6.x86_64) over Fedora 18 using VirtualBox 4.2.8. Tkmedit, Tksurfer, qdec and freeview all work great. But recon-all tests return errors. Thanks in advance for your help. _______________________________________ recon-all -s bert -autorecon1 running loop to estimate saturation parameter: A or b constain NAN or infinity values!! _______________________________________ recon-all -s bert -all talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log _______________________________________ The log indicated above shows: imgrege: no voxels in register ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted

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Re: [Freesurfer] Tracula bbr errors
by Douglas N Greve 21 Mar '13

21 Mar '13

Hi Salil, I'm posting this to the list since others (i,e Zeke and/or Nick) can better diagnose installation problems. doug On 03/20/2013 05:21 PM, Salil Soman wrote: > Hi Doug, > > Following up on our previous emails, I have been able to get the > entire tracula process to work on our sun grid engine using FLT and > disabling bbr. > > However, if I enable bbr I still get a number of errors, the first of > which appears to be > > mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory > > The log file and a text file with the lines with the word error are > attached. > > Any suggestions on how to address this issue would be greatly appreciated. > > Best wishes, > > Salil > > > On Wed, Mar 13, 2013 at 9:55 PM, Salil Soman <salsoman(a)stanford.edu > <mailto:salsoman@stanford.edu>> wrote: > > Dear Doug, > > Thank you for your email. I apologize for the delay in responding. > At present the file > /mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregister.30396/template.nii > does not exist. > > These are the files in the directory > /mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregister.30396: > > fslregister reg.init.dat.fslregister.log > reg.init.dat.fslregister.log.old > > the 2 files are attached. > > Best wishes, > > Salil > > > > > On Sun, Mar 10, 2013 at 10:17 AM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hmmm, I think that these failures are happening because it is > looking for an input that does not exist. Does > /mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregister.30396/template.nii > exist? This was in a temporary directory, and it is likely > that it was deleted when the script was run. > > doug > > > > > On 3/8/13 8:43 PM, Salil Soman wrote: >> Dear Doug, >> >> Thank you for your email. >> >> Please find the output attached. >> >> Best wishes, >> >> Salil >> >> >> On Fri, Mar 8, 2013 at 8:47 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >> Salil, can you run fslregister with --debug as the first >> option, capture the terminal output, and send it to me? >> thanks >> doug >> >> >> >> On 03/07/2013 09:02 PM, Anastasia Yendiki wrote: >> >> >> Hi Salil - I'm cc-ing Doug who may be able to help. >> The error happens when bbregister invokes >> fslregister, in this particular line of fslregister: >> set refvol = `stem2fname >> $SUBJECTS_DIR/$subjid/mri/$fsvol` >> >> When run on brainmask.mgz, it returns "ERROR: could >> not determine file". >> >> a.y >> >> On Wed, 6 Mar 2013, Salil Soman wrote: >> >> >> Thank you for your email. Changing the mask >> option got me past the error I >> was having initially, but now I get these new errors: >> >> mri_convert ERROR: could not determine file for >> /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis >> >> ter.30396/fslregister/refvol.fslregister.nii >> mri_convert ERROR: could not determine file for >> /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis >> >> ter.30396/fslregister/refvol.fslregister.nii >> >> Thank you for your consideration. >> >> Best wishes, >> >> -S >> >> On Wed, Mar 6, 2013 at 1:15 PM, Anastasia Yendiki >> <ayendiki(a)nmr.mgh.harvard.edu >> <mailto:ayendiki@nmr.mgh.harvard.edu>> wrote: >> >> Hi Salil - The problem is that you've set dob0 = >> 1 but you haven't set >> b0mlist and b0plist, so it doesn't know where to >> find your field maps to do >> the B0 unwarping. >> >> a.y >> >> >> >> >> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> >> >> >> 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. >> >> >> ---------- Forwarded message ---------- >> From: *Salil Soman* <salsoman(a)stanford.edu >> <mailto:salsoman@stanford.edu>> >> Date: Fri, Mar 8, 2013 at 11:41 AM >> Subject: fslregister output >> To: salsoman(a)gmail.com <mailto:salsoman@gmail.com> >> >> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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(no subject)
by martina.andellini＠fastwebnet.it 21 Mar '13

21 Mar '13

Hi FreeSurfer experts, I would need to use the registration tools in freesurfer because the fsl ones ga ve me some problem. Just to try I have run mri_ca_registration and mri_cvs_registration and so I hav e three questions: 1) mri_ca_registration generates a talairach tansform file in .m3z format and I would need to apply it to my high res image. Any hint? 2) Converting RB_all_2008-03-26.gca to nii and opening it to mricron it seems to superimposable to the mni atlas. does it mean that what it comes out from mri_c a_registration coincides to an mni atlas image? 3) Running mri_cvs_registration (on bert data...just to try) I do not know where to find the registered volume file (I have tried few volume .mgz but with no su ccess...). Should i look for a transform file too? Thanks so much! Martina

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fs-fast processing questions
by preciado＠nmr.mgh.harvard.edu 21 Mar '13

21 Mar '13

Hello all, I am starting to run some analysis using fs-fast and I had a few basic questions that I couldn't find answers on the wiki/tutorial. 1) Format of files for mkanalysis-sess -tpexclude tpexclude.dat What is the format of the input file for -tpexclude? Is it simply a single column of integers representing the seconds that need to be excluded? My example, my TR is 3 and I know I want to remove acquisitions 134 and 140 because of motion. Do I simply need to have a file that has the following content? 402 403 404 420 421 422 2) bold data - Resampling to "common space" In the preprocessing step, the bold data is resampled to 76x76x93. My data is 96x96x50. Does starting with data that is larger than the "common space" cause a problem in the analysis? 3) Viewing analysis for individual bold data runs When the First level analysis is completed, the resulting files are a combination of all of the bold data runs of the session. Is there a way to make it so that I can also see the different activity for individual runs within the session or does the analysis only do it by combining data for all runs within a session? Thanks in advance! -Ronny

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Freesurfer March 2013