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I: R: R: R: Re: To use a ROI.label as seed in FS-FAST
by stdp82＠virgilio.it 16 Feb '16

16 Feb '16

1 0

v.6.0 Permissions Error
by Grafe,Brendan P. (BIDMC - Neurology) 16 Feb '16

16 Feb '16

Hello all, I am in the middle of a FreeSurfer v.6.0 longitudinal analysis, running on the Martinos cluster, and I received an error today during the (-base) template creation step regarding a file that the pipeline calls upon: GCAread(/usr/local/freesurfer/stable6/average/RB_all_2016-02-11.gca): could not open file I noticed that permissions access to this file are limited at present to the greve group and that the file was last modified earlier today. I'm unfamiliar with this component's functionality, but am assuming access to it is necessary for template creation. Would this simply be the issue? Preemptive thanks, Brendan Grafe ----------------------------- Brendan P. Grafe MSc Clinical Research Assistant Berenson-Allen Center for Noninvasive Brain Stimulation Beth Israel Deaconess Medical Center 330 Brookline Avenue Boston, MA 02215 Tel: 617-667-0256 Fax: 617-975-5322 ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

tkregister visualization issue
by Philip Brandner 16 Feb '16

16 Feb '16

Dear Freesurfer team, I encountered a visualization error with tkregister-sess after trying to look at the overlays of my 1st level analysis in a standard fMRI block designed localizer. tkregister loads without errors (menu plus window) but only very faint and small colored dots are visible, no inflated hemisphere as a surface no significant overlay of the contrast, nothing. It might seem like a specific problem with my setup, because from another computer in the lab the surface is visible (but no overlay). *Here is the terminal output during tkregiter-sess:* -bash-3.2$ tksurfer-sess -s NC211pre/ -analysis face.object.sm5.lh -c face-vs-object Surface fsaverage lh Map Surface fsaverage lh $Id: tksurfer-sess,v 1.16.2.2 2012/11/19 22:35:56 greve Exp $ Linux wiener 2.6.18-407.el5 #1 SMP Fri Oct 16 12:04:40 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux Tue Feb 9 11:51:24 EST 2016 /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/bin/tksurfer list face-vs-object con/map face-vs-object /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/face-vs-object/sig.nii maplist /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/face-vs-object/sig.nii mri_concat /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/face-vs-object/sig.nii --o /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii cd /Freiwald/cpressl/imaging/tle setenv SUBJECTS_DIR /Freiwald/cpressl/imaging/tle/ tksurfer fsaverage lh inflated -overlay /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii -label-outline -colscalebarflag 1 -annot aparc -fthresh 2 -fmid 3.00000000000000000000 -fslope .50000000000000000000 Contrasts 0 face-vs-object setting colscalebarflag to 1 setting fthresh to 2.0000 setting fmid to 3.0000 setting fslope to 0.5000 subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /Freiwald/cpressl/imaging/tle/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Freiwald/cpressl/imaging/tle checking for nofix files in 'inflated' Reading image info (/Freiwald/cpressl/imaging/tle//fsaverage) Reading /Freiwald/cpressl/imaging/tle//fsaverage/mri/orig.mgz surfer: Reading header info from /Freiwald/cpressl/imaging/tle//fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 tkmedit: Trying to open /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.dat surfer: Interpreting overlay volume /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii as encoded scalar volume. surfer: curvature read: min=-0.673989 max=0.540227 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Found embedded color table in annotation. 13887 vertices did not have an annotation! surfer: double buffered window surfer: tkoInitWindow(fsaverage) surfer: using interface /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tksurfer.tcl Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tkm_common.tcl Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tkm_wrappers.tcl Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/lib/tcl/fsgdfPlot.tcl Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % Please let me know if you have encountered this before and whether you might have a solution for this issue. Best regards, Philip Brandner

2 1

mri_annotation2label
by Worker, Amanda 16 Feb '16

16 Feb '16

Hi All, I am trying to run a vertex-wise analysis on a pre-defined ROI - the caudal anterior cingulate label as defined by the Desikan atlas. I have used mri_annotation2label to get these labels for each subjects ./label directory. I assumed that as these labels were created in fsaverage space, it would be ok to get these labels for each subject without further sampling to fsaverage? If not, how can I do this? I have also tried to run mri_glmfit, using --label instead of --cortex, but I don't have the label 'lh.caudalanteriorcingulate.label' in standardised space, only in each subjects directory. How can I specify that this is the label I'd like to confine my analysis to (this might be answered by the first question). Thanks in advance, Amanda

2 1

Fwd: Specifying color table file
by Faeze Vedaei 16 Feb '16

16 Feb '16

Hi Freesurfer experts, In order to using mris_label2annot command to create annot files, I've got an error: need to specify color table file. Does anyone know how can I create and specify color table file? In advance, I'd appreciate your consideration and time. Bests, Faezeh Vedaei

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Re: [Freesurfer] comparison between two hemisphere in single
by Ashkan Faghiri 16 Feb '16

16 Feb '16

Thank you Douglas for your reply. I have perforemed surfreg --s subj1 --t fsaverage_sym --lh surfreg --s subj1--t fsaverage_sym --lh --xhemi mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff --srcsurfreg fsaverage_sym.sphere.reg --meas thickness --out lh.lh-rh.thickness.sm00.mgh --s subj1 for my *one* subject. as I understand "lh.lh-rh.thickness.sm00.mgh" file is the difference between the two hemisphere of my one subject (it's dimension is 163842 x 1 x 1). so I should check if these values are significantly different than zero, right? but DOF of this vector is 0 so mri_glmfit returns "ERROR: DOF = 0". which is correct I think. I believe I can't do this procedure for single subject. I want to check if there is thickening or thinning between two hemisphere for one subject. what should I do exactly? Regards, Ashkan -- -- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology

2 1

How to convert a surface label to .nii
by Afzal, Afsana 16 Feb '16

16 Feb '16

Hi, How can I convert a surface .label file to a .nii format? I'm using mri_label2label in the following way but the output is always in .label not .nii: mri_label2label --srclabel dlpfc-lh.label --outmask dlpfc-lh_mask.nii --s fsaverage --trglabel dlpfc-lh_mask.nii --regmethod surface --hemi lh Thanks for your help, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

3 3

fwhm issue with mri_glm-sim
by Domenico Zacà 16 Feb '16

16 Feb '16

Dear FS team, I am running a surface based analysis on GWR on a group of 203 subjects. I generated left and right GWR maps, smoothed with a Gaussian kernel of FWHM 15 mm. However when I try to run the multiple comparisons correction analysis (mri_glmfit-sim --glmdir lh.w-g.pct_aesint.15.glmdir --cache 2 pos --cwp 0.05 --2spaces) I get the following error message: fwhm = 46.240061 ERROR: cannot find /opt/freesurfer/freesurfer-stable5/average/mult-comp-cor/fsaverage/lh/cortex/fwhm46/pos/th20/mc-z.csd Any idea how to get around this? Thanks Domenico Zacà, PhD MR Lab Research Fellow Center for Mind/Brain Sciences University of Trento, Italy Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3069 Fax: +39-0461-28-3066 Email: domenico.zaca(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri

2 1

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

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