Freesurfer

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30099 discussions

tracula preproc complains about missing bvec-file
by Parzer, Peter 05 Feb '16

05 Feb '16

Hi, trying to do my first steps with tracula I got stuck early in the preprocessing step. The DICOM import and preparation for FSL seem to work (mri_convert, mri_probedicom, flip4fsl, fslswapdim, fslorient). But then trac-preproc wants to move a file named dwi_orig_flip.mghdti.bvecs that does not exist. What did I wrong? The command I used was trac-all -prep -c dmrirc The content of the configuration file "dmrirc" was the minimum as described in the tutorial: setenv SUBJECTS_DIR /dat/Hirnreifung/Auswertung/freesurfer set dtroot = /dat/Hirnreifung/Auswertung/freesurfer set subjlist = (3001LT) set dcmroot = /dat/Hirnreifung/Daten/DICOM set dcmlist = (3001LT/d_Diff_ax_64dir_1av_b0_1000_3000/IM-0001-0001.dcm) dcminfo.dat and trac-all.log are in the attachments. Peter

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Re: [Freesurfer] freeview command line generic overlay colormap question
by Gardumi Anna (PSYCHOLOGY) 05 Feb '16

05 Feb '16

Dear all, I am currently trying to automatically generate Freesurfer screenshots and, to this purpose, I need to change the color scale of the surface overlay to "Color Wheel - Inverse" and with specific min and max threshold. Looking for a way to achieve this, I found this thread with similar request, but unfortunately no solution was posted. Thus Heath (who kindly replied to my email) suggested to re-post the question to the entire FreeSurfer community. So far I am able only to set the min max threshold with the following command: freeview -f $SUBJECTS_DIR/subj01/surf/lh.inflated:overlay=/pathToOverlay/MyOverlay.mgh:overlay_threshold=-10,10 Does anybody know the command line to set the overlay color scale to "Color Wheel (Inverse)"? Thank you! Any help is very much appreciated! Best regards, Anna ------------------------- Anna Gardumi Department of Cognitive Neuroscience | Faculty of Psychology & Neuroscience | Maastricht University Postal address: PO Box 616, 6200MD, Maastricht, The Nederlands Visiting address: Oxfordlaan 55, room 2.012, 6229EV anna.gardumi(a)maastrichtuniversity.nl

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(no subject)
by Ачча Чимагомедова 05 Feb '16

05 Feb '16

Hello! My name is Achcha. I am a PhD student of Russian Medical Academy for Postgraduate Education. In my research "Dementia with Lewy bodies" (DLB) I am going to determine the association between the focal atrophy measures on MRI and to compare it with clinical features of DLB. I try to install FreeSurfer on my computer. But I have only Windows Operating System, that's why I have got and installed VirtualBox. Could you please send me detailed instructions and help to install FreeSurfer. Thank you, Kindest regards Achcha Chimagomedova

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Brain stem segmentation-- FS6
by Alshikho, Mohamad J. 05 Feb '16

05 Feb '16

Dear Freesurfer experts, I am working on brain stem segmentation analysis using the new module included in FS6. The analysis ran properly for 38/40 subjects. I have an issue with two subjects. I sent my jobs to the cluster as always using the following command line: pbsubmit -c " recon-all -subjid <SUBJECT ID> -brainstem-structures " -f <email address> & After a while I received an email that the job is done: PBS Job Id: 11020983.launchpad.nmr.mgh.harvard.edu Job Name: pbsjob_2045 Exec host: compute-0-111/3 Execution terminated Exit_status=0 resources_used.cput=00:42:33 resources_used.mem=3220236kb resources_used.vmem=7319444kb resources_used.walltime=00:44:45 I checked the subject's folder /mri/ looking for the files : "brainstemSsLabels.v10.1mm.mgz" , "brainstemSsLabels.v10.mgz" but I was unable to find them. I checked the job history in the cluster and it returns as ( quotation -- the last lines): Resolution level 3 iteration 3 deformation iterations 19 Number of Meshes: 1 Using CG optimizer Did one deformation step of max. 0.0097272 voxels in 4.1676 seconds minLogLikelihoodTimesPrior = 1.0786e+07 Resolution level 3 iteration 3 deformation iterations 20 Number of Meshes: 1 Using CG optimizer Did one deformation step of max. 0.016365 voxels in 4.1717 seconds minLogLikelihoodTimesPrior = 1.0786e+07 Fitting mesh to image data mask took 2144.0218 seconds Error using kvlAtlas3D_Matlab std::bad_alloc Error in kvlRasterizeAtlasMesh (line 11) Error in segmentSubject (line 1078) Started at Thu Feb 4 15:57:18 EST 2016 Ended at Thu Feb 4 16:41:59 EST 2016 #@#%# recon-all-run-time-hours 0.745 recon-all -s CTRL039 finished without error at Thu Feb 4 16:42:00 EST 2016 It stated that the job was ended properly without errors but the previous lines ( before the final stamp) showed errors and the files "brainstemSsLabels.v10.1mm.mgz" , "brainstemSsLabels.v10.mgz" are missing ... Kindly what I am doing wrong? Any suggestions are highly appreciated !! Mohamad

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problem mri_convert
by Righart, Ruthger 05 Feb '16

05 Feb '16

Dear FreeSurfers, On one of our Linux machines we encounter the following error message when calling mri_convert: /lib64/libz.so.1: no version information available (required by mri_convert) /usr/lib64/libstdc++.so6: version GLIBCXX_3.4.11 not found (required by mri_convert) Mri_convert has worked before without any problem. Any advices how to resolve this would be very welcome! Best Regards, Ruthger

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Viewing nifti file in freeview
by Worker, Amanda 04 Feb '16

04 Feb '16

Hi All, I was hoping someone could help with an issue that I'm having that I'm sure has a simple explanation. I have a proton density map in nifti format that I am trying to convert to mgz using mri_convert. However, when I load the original nifti file into freeview, I get a blank screen and the same when I try to load the converted .mgz - but I have no issue with loading this file into fslview. Other nifti and .mgz files are also loading fine into freeview. Has anyone seen this problem before? Thanks, Amanda

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Re: [Freesurfer] TRACULA Longitudinal can't find subject folder
by Anastasia Yendiki 04 Feb '16

04 Feb '16

Hi Deniz - It seems that it finds the folders of the 2 time points, but not the folder of the longitudinal base template. This is the template that longitudinal recon-all creates in its 2nd processing step. In your case, it would be /data_august/Deniz/DTI_long/subjects/med_AhJa94 Does this exist? a.y On Thu, 4 Feb 2016, Gürsel, Deniz wrote: > Dear Tracula Experts, > > I'm having trouble with longitudinal analysis using tracula. Just to try out, I am > using one subject with 2 time points. I defined the parameters in dmrirc file as: > > set subjlist = (med_AhJa94_1 med_AhJa94_2) > set baselist =(med_AhJa94 med_AhJa94) > > My subject folder which contains the longitudinal templates of reconstruction is > located as "/data_august/Deniz/DTI_long/subjects/med_AhJa94_1.long.med_AhJa94" > "/data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94" > > Tracula can't seem to find this subject folder, although I am providing the correct > parameters for it. I get the error message when I ran trac-all -prep -c > dmrirc.long : > ERROR: cannot find /data_august/Deniz/DTI_long/subjects/med_AhJa94 > > I attached the trac-all.log and dmrirc files for your reference. > Thank you very much. > > > Best regards, > > >

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Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)
by will brown 04 Feb '16

04 Feb '16

Message: 3 Date: Tue, 2 Feb 2016 14:17:02 -0500 From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <E8AA9D81-BB67-446A-BDD8-2000A5AAC28B(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="us-ascii" Hi Will There was no attachment Bruce > On Feb 2, 2016, at 3:27 AM, will brown <willbrown1987(a)gmail.com> wrote: > > Hi Bruce, > > I've attached a shot of the misalignment as seen in freeview. > > Yes the original images were DICOM created in Siemens machine T1, 0.8 slice thickness, can provide all DICOM tags if needed. > - Ignored: > Thanks, > > Will > > > On Tue, Jan 26, 2016 at 6:00 AM, < freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > > > Message: 1 > Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mritotal failed - help with manual > registration > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1601241858240.29174(a)door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Will > > can you take the same images with freeview and send them along? Also: > tell us a bit about your images. What format did they start in? Were they > dicoms? > > Bruce > > On Mon, 25 Jan 2016, will brown wrote: > > > Hi all, > > After attempting recon-all I received the error "mritotal failed, see > > transforms/talairach.log" etc which I understand may have something to do > > with bad output from registration. I've checked orig.mgz which does look out > > of line - the orientation is off so that it appears the subject has their > > head tilted off to one side (see Image1.jpg). > > > > I have tried to fix this manually with the help of this tutorial: > > > > http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview > > > > Hovever, the "movable" blurry image that I'm trying to line up with my > > subjects image does not match the coronal, sagittal or horizontal views, > > e.g. when I click "coronal" my subject is displayed correctly but the > > movable image is displayed horizontally (see Image2.jpg and Image3.jpg). > > > > Am I missing something obvious? (and am I even on the right track given this > > error?) > > > > Thanks in advance for any help. > > > > Cheers, > > Will - Done. 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: will brown <willbrown1987(a)gmail.com> To: freesurfer-request(a)nmr.mgh.harvard.edu Cc: Date: Thu, 4 Feb 2016 17:07:23 +1300 Subject: Re: mritotal failed - help with manual registration (Bruce Fischl) (Bruce Fischl) Sorry - attached now Message: 3 Date: Tue, 2 Feb 2016 14:17:02 -0500 From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <E8AA9D81-BB67-446A-BDD8-2000A5AAC28B(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="us-ascii" Hi Will There was no attachment Bruce > On Feb 2, 2016, at 3:27 AM, will brown <willbrown1987(a)gmail.com> wrote: > > Hi Bruce, > > I've attached a shot of the misalignment as seen in freeview. > > Yes the original images were DICOM created in Siemens machine T1, 0.8 slice thickness, can provide all DICOM tags if needed. > > Thanks, > > Will > > > On Tue, Jan 26, 2016 at 6:00 AM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > > > > Message: 1 > Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mritotal failed - help with manual > registration > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1601241858240.29174(a)door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Will > > can you take the same images with freeview and send them along? Also: > tell us a bit about your images. What format did they start in? Were they > dicoms? > > Bruce > > On Mon, 25 Jan 2016, will brown wrote: > > > Hi all, > > After attempting recon-all I received the error "mritotal failed, see > > transforms/talairach.log" etc which I understand may have something to do > > with bad output from registration. I've checked orig.mgz which does look out > > of line - the orientation is off so that it appears the subject has their > > head tilted off to one side (see Image1.jpg). > > > > I have tried to fix this manually with the help of this tutorial: > > > > http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview > > > > Hovever, the "movable" blurry image that I'm trying to line up with my > > subjects image does not match the coronal, sagittal or horizontal views, > > e.g. when I click "coronal" my subject is displayed correctly but the > > movable image is displayed horizontally (see Image2.jpg and Image3.jpg). > > > > Am I missing something obvious? (and am I even on the right track given this > > error?) > > > > Thanks in advance for any help. > > > > Cheers, > > Will

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Unpacking error
by Ji Won Bang 03 Feb '16

03 Feb '16

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

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Regarding: T2w and HcV analysis
by Dr Sampada Sinha 03 Feb '16

03 Feb '16

Dear freesurefr experts, Hope this mail finds you all doing well. I want to calculate hippocampal subfield volume using T2w mages. Is the recon-all command same as we do for the T1images (recon-all -i input to T1.nii.gz -s 001 -all)? I was not able to understand the recon-all command for the T2w images. if you can please explain it to me: recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume -T2pial -all what is -i here (which input volume)? Since, -T2 is the T2 images (dcm or nifti) I am going to feed for processing. Appreciate all you help! Best wishes and regards, Sampada -- Sampada Sinha

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