Freesurfer February 2016

freesurfer@nmr.mgh.harvard.edu

123 participants
179 discussions

Re: [Freesurfer] selxavg3-sess problem: SVD input matrix contains NaN
by Douglas N Greve 16 Feb '16

16 Feb '16

It appears that you do not have any events for condition 3. Is that correct? Check your par files. doug On 02/08/2016 08:28 PM, Mcnorgan, Christopher wrote: > Hi Doug, > Thanks for looking at this. The .mat file is attached. Can you send me the Xtmp.mat file? On 2/2/16 6:40 PM, Mcnorgan, Christopher wrote: > Hi, > I'm attempting an inaugural run through the FS pipeline on some event-related > data collected over 6 runs. I'm not sure if this makes any difference, but > the experiment is self-paced, and the events are of varying duration (it's a > lexical decision task, and participants can take up to 4 seconds to respond > but typically respond between 600 - 800ms, with an exponentially-decreasing > jittered ITI between trials). > > When I run selxavg3-sess on this single participant, the following error is > generated: > > /********************************** > Saving X matrix to /home/kali/fMRI/LDT/1001_001/bold/LDT.sm6.lh/Xtmp.mat > Error using svd > Input to SVD must not contain NaN or Inf. > > Error in cond (line 35) > s = svd(A); > > Error in fast_selxavg3 (line 279) > XCond = cond(XtX); > >>> ------------------------------------------ > ERROR: fast_selxavg3() failed\n > *******************************************/ -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

unpacking error
by Ji Won Bang 16 Feb '16

16 Feb '16

Dear. Freesurfer team. Hi. Our lab tried to unpack DICOM files using both freesurfer v4.5.0 and v5.3.0. The command line is: unpacksdcmdir -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ $DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK And I get the error message: $Id: unpacksdcmdir,v 1.19.2.2 2008/03/11 19:56:38 nicks Exp $ /home/jbang/Projects/replay/log -src /home/jbang/Projects/replay/epi//replay01/DICOM/day1 -targ /home/jbang/Projects/replay/epi//replay01/bold_decode -fsfast -seqcfg /home/jbang/Projects/replay/log// Wed Feb 3 18:12:41 EST 2016 mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2016/02/03-23:12:41-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ User: jbang Machine: cpu166.cabiatl.com Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 cpu166.cabiatl.com Linux cpu166.cabiatl.com 2.6.32-358.6.2.el6.x86_64 #1 SMP Tue May 14 15:48:21 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux Wed Feb 3 18:12:41 EST 2016 Log File is /home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log INFO: Logfile is /home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is /home/jbang/Projects/replay/epi//replay01/bold_decode/dicomdir.sumfile INFO: status file is /home/jbang/Projects/replay/epi//replay01/bold_decode/parse.status Scanning directory Wed Feb 3 18:12:41 EST 2016 mri_parse_sdcmdir --sortbyrun --d /home/jbang/Projects/replay/epi//replay01/DICOM/day1 --o /home/jbang/Projects/replay/epi//replay01/bold_decode/dicomdir.sumfile --status /home/jbang/Projects/replay/epi//replay01/bold_decode/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 Done scanning Wed Feb 3 18:17:33 EST 2016 ------------------------------------------ 2 localizer ok 512 512 3 1 00002_loc02.dcm 3 fMRI_physio_1_decoder ok 74 74 33 150 00001_dec01.dcm 5 fMRI_physio_2_decoder ok 74 74 33 150 00001_dec02.dcm 7 fMRI_physio_3_decoder ok 74 74 33 150 00001_dec03.dcm 9 fMRI_physio_4_decoder ok 74 74 33 150 00001_dec04.dcm 11 fMRI_physio_5_decoder ok 74 74 33 150 00001_dec05.dcm 13 fMRI_physio_6_decoder ok 74 74 33 150 00001_dec06.dcm 15 fMRI_physio_7_decoder ok 74 74 33 150 00001_dec07.dcm 17 fMRI_physio_8_decoder ok 74 74 33 150 00001_dec08.dcm 19 fMRI_physio_9_decoder ok 74 74 33 150 00001_dec09.dcm 21 fMRI_physio_10_decoder ok 74 74 33 150 00001_dec10.dcm 23 fMRI_physio_1_retinotopy ok 74 74 33 120 00001_retino01.dcm 25 fMRI_physio_2_retinotopy ok 74 74 32 120 00001_retino02.dcm 27 fMRI_physio_3_retinotopy ok 74 74 32 120 00001_retino03.dcm 29 fMRI_physio_4_retinotopy ok 74 74 32 120 00001_retino04.dcm 31 fMRI_physio_5_retinotopy ok 74 74 32 120 00001_retino05.dcm 35 T1_MEMPRAGE ok 256 256 176 4 00001_T1_MEMPRAGE_35.dcm 36 T1_MEMPRAGE ok 256 256 176 1 00001_RMS.dcm error reading "file4": illegal operation on a directory while executing "gets $FileId line" (procedure "ReadSeqCfg" line 11) invoked from within "ReadSeqCfg $seqcfgfile" invoked from within "if { [info exists seqcfgfile] } { set SeqCfgList [ReadSeqCfg $seqcfgfile]; }" (file "/home/jbang/freesurfer//bin/unpacksdcmdir.tcl" line 1048) This same error message appeared on both v4.5.0 and v5.3.0. Do you have any clue to fix it? Thank you for your help. Best, Ji Won Bang

3 6

Extract LGI at MaxVertex of a significant Cluster, Effect sizes
by Bittner, Nora 16 Feb '16

16 Feb '16

Dear FreeSurfer Experts, I have two questions, which you can hopefully answer to: 1) I calculated several analyses with LGI as my dependent variable, resulting in several significant clusters. Now, I would like to extract the individual LGI value at the maximum vertex of each significant cluster to plot it against my experimental variables (instead of working with the mean LGI values of the clusters). What I tried so far is to use mri_segstats to extract the LGI at the maximum vertex: mri_segstats --i $SUBJECTS_DIR/qdec/glm/y.mgh --crs vertexno 84367 0 0 --avgwf vertexno84367.dat where y.mgh is my input file from the glm and vertexno 84367 is the maximum vertex of the cluster as reported in the cluster.summary-file. I found the command in the FS helpline documentation (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42655.html) but regrettably<http://dict.leo.org/ende/index_en.html#/search=regrettably&searchLoc=0&resu…> I get the following error message: "ERROR: Option --crs unkown" In the fswiki I also couldn´t find the "mri_segstats - - crs option" in the user description. Is there any other option or argument I can use in mri_segstats (or in any other command) to extract the LGI value per person at the given vertex? 2) I would like to calculate effect sizes of my results. Therefore I used fscalc: fscalc $SUBJECTS_DIR/qdec/glm/contrast/gamma.mgh div $SUBJECTS_DIR/qdec/glm/rstd.mgh -o $SUBJECTS_DIR/qdec/ glm/contrast/effectsize.mgh This worked fine and resulted in a surface overlay displaying the effect sizes. Is there any way to convert this effectsize.mgh-file to a table format? Such that I would get numerical values, let´s say, vertexwise effect sizes or similar? Thank you in advance, Nora Bittner ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

2 1

Correct_all_vols_4_sphinx_position
by Casas, Rafael (NIH/CC/DRD) [F] 16 Feb '16

16 Feb '16

Hello, I'm a rookie and I had issues with the unpack_CIT script, so I went ahead and created the data structure similar to "bert testsubjects". I also converted my raw dicom files to mgz format. I'm currently trying to run "00.05_correct_all_vols_4_sphinx_position.csh" . Is there anything wrong with my current file structure? And how/what lines should I be editing the lines on the current script? [cid:image001.jpg@01D168C5.DD5D72B0] Any help would be appreciated Thanks, Rafael

1 0

MNI coords in GLM cluster
by Bronwyn Overs 16 Feb '16

16 Feb '16

Hi Freesurfer mailing list, Is there a way to determine if a specific MNI location is included in any of the clusters that are significant in a freesurfer GLM analysis (after monte-carlo)? We have a specific coordinate of interested from a previous analysis (e.g. -21, 11, -17) and wish to know if this is included in any of the significant clusters from an alternate GLM in freesurfer. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

2 1

more on comparing runs on the same scan
by Krieger, Donald N. 16 Feb '16

16 Feb '16

We have been able to establish that we are getting identical results when running recon-all -all on the same scan on different machine for the following: All .mgz files in directories mri, mri/orig, and mri/transforms, by comparing using mri_diff ... All of the .label and .annot files in directory label with md5sum ... Many of the files in directory surf with mris_diff. We see differences in the BA*.annot files. We are still seeing difference in about 20 of the files in surf including [lr]h.inflated|orig|pial . We do see identity for lh.area.pial but not for lh.pial for instance. I've attached the output of our test routine. Your thoughts would be welcome on this pesky question. Best - Don

1 0

freesurfer with infants MRI
by Chiara Bulgarelli 16 Feb '16

16 Feb '16

Dear All, I would like to ask you for some advice about segmenting MRI from infants data. In particular, these are my questions: 1. if I have two different templates related to two different time points in the 1st year of life, and one of this two is clearly a bad quality MRI image (even visible from the T1 image), the other one is quite good. While with the good one I can reconstruct and segment the image perfectly, with the bad one the software is of course missing lots of part during the reconstruction. Is there the possibility to set up some lower threshold in the ‘recon-all' script to allow the segmentation to get more areas considered, even with this bad quality image? 2. I know that the program register the volume with the MNI305 atlas, that is supposed to work well with adults but not with infants: I am actually trying to avoid in my whole neuroimaging analyses (also with other softwares) to “stretch” the infants brain to an adult one. From the high quality MRI infants image that I was able to segmented, the output seems to be fine, but my concern was whether using as a reference an adult brain could affect the results in my case, although the segmentation seems to be well done. I checked the FreeSurfer website but I couldn’t find this information! Any advice would be really appreciated! Best Regards Chiara ---------------- Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London cbulga01(a)mail.bbk.ac.uk // bulgarelli.chiara3(a)gmail.com

3 3

wm-hypointensities variables
by Otília 14 Feb '16

14 Feb '16

Greetings, I am wondering if there is some information regarding the meaning of "wm-hypointensities" and "non-WM-hypointensities" variables from the aseg.stats file, ie, what features are included in these variables and how FS computes them. I checked previous posts that have the same issue I have now. I find some non-zero, (some cases have "quite big") WM-hypointensities values for healthy young brains. I find it odd. I would appreciate some additional information about these issues. Thank you! Best regards,

2 4

curved Surface projection
by Ashkan Faghiri 13 Feb '16

13 Feb '16

Hello I know it is not the best place to ask this kind of question. But I don't know any place to ask a question like this. I am looking to display "curved Surface projection" for brain mri (like explained in http://www.ajnr.org/content/24/6/1045.full) Can any one suggest me a tool to do this. Regards, Ashkan -- -- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology

1 0

Longitudinal analysis--mass univariate
by John Anderson 12 Feb '16

12 Feb '16

4 7

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Freesurfer February 2016