Freesurfer

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11 participants
30080 discussions

recon-all error
by Ebru Ayyürek 25 Apr '19

25 Apr '19

External Email - Use Caution Hi FreeSurfer Developers, I'm attempting to perform a full recon-all on the dicom/nifti file for test my freesurfer installation as described on the website https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall but I have an error like this; recon-all -s file1 -i /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm -all Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux sid 4.18.0-17-generic #18-Ubuntu SMP Wed Mar 13 14:34:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/file1 mri_convert /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz mri_convert /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm... Starting DICOMRead2() dcmfile = /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm dcmdir = /home/ebru/Desktop/den01_org/T1_1 Ref Series No = 201 Found 182 files, checking for dicoms Found 180 dicom files in series. First Sorting Computing Slice Direction Vs: -0.0462818 0.24329 0.968857 Vs: -0.0462815 0.243288 0.968849 Second Sorting Counting frames nframes = 1 nslices = 180 ndcmfiles = 180 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=8.39, TE=3.86, TI=0.00, flip angle=8.00 i_ras = (-0.996607, -0.0773363, 0.0281873) j_ras = (0.0680693, -0.966865, -0.246046) k_ras = (0.0462815, -0.243288, 0.968849) writing to /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Çrş Nis 24 11:45:57 +03 2019 Found 1 runs /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz /usr/local/freesurfer/subjects/file1 mri_convert /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz /usr/local/freesurfer/subjects/file1/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz /usr/local/freesurfer/subjects/file1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz... TR=8.39, TE=3.86, TI=0.00, flip angle=8.00 i_ras = (-0.996607, -0.0773363, 0.0281873) j_ras = (0.0680693, -0.966865, -0.246046) k_ras = (0.0462815, -0.243288, 0.968849) Original Data has (0.976562, 0.976562, 1) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/file1/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/file1/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/file1/mri/orig.mgz /usr/local/freesurfer/subjects/file1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Çrş Nis 24 11:46:09 +03 2019 /usr/local/freesurfer/subjects/file1/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux sid 4.18.0-17-generic #18-Ubuntu SMP Wed Mar 13 14:34:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s file1 exited with ERRORS at Çrş Nis 24 11:46:11 +03 2019 For more details, see the log file /usr/local/freesurfer/subjects/file1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Ubuntu version:18.10 3) uname -a: Linux sid 4.18.0-17-generic #18-Ubuntu SMP Wed Mar 13 14:34:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached DownloadAndInstall - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall> Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. surfer.nmr.mgh.harvard.edu

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fsaverage error with recon-all
by chen 25 Apr '19

25 Apr '19

External Email - Use Caution Dear All, I ran recon-all using single MPRAGE data set. Processing exited with an error pasted below indicating there is not fsaverage/surf/lh.sphere.reg. According to the fsaverage-recon-all.log, it completed without error. I was able to run a subject before without any error not sure why all the subjects I ran now over the weekend ended up with same error. Secondly, i have studied the multi-site reliability of young traveling subjects which scanned in multi-site with the same scanner and protocol across 12 month. I ran these data with cross-pipeline. But, our results showed that the amygdala volumes have significantly lower reproducibility in inter-site than hippocampus and entorhinal cortex (ICC scores less than 0.5) with FreeSurfer rather than manual tracing. So, i want to assure that recon-all -all is the optimal process pipeline. If not, can you give me some advice? Should i use the longitudinal pipeline in multi-site study with traveling subjects? Thanks. ------------------ 首都医科大学宣武医院杜佳晨

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Alignment of segmented brainstem in Freesurfer
by Sadia Sheikh 25 Apr '19

25 Apr '19

External Email - Use Caution Dear FreeSurfer experts I did brainstem segmentation using BrainstemSubstructure method. Then after segmentation, I aligned all my segmented brainstem to Talairach coordinates using transform=$SUBJECTS_DIR/$s/mri/transforms/talairach.xfm. Alignment seems to be fine. But the boundary of the aligned brainstem looks distorted with different other colors. Why does the boundary look like this? and how can I improve this? I have attached the image of brainstem after alignment. Thanks in advance. Regards Sadia Research Student <https://www.avast.com/en-in/recommend?utm_medium=email&utm_source=link&utm_…> I’m protected online with Avast Free Antivirus. Get it here — it’s free forever. <https://www.avast.com/en-in/recommend?utm_medium=email&utm_source=link&utm_…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Re: [Freesurfer] Fwd: mri_surfcluster ERROR
by Greve, Douglas N.,Ph.D. 24 Apr '19

24 Apr '19

This is pretty weird. Can you try this version https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surfcluster On 4/24/19 2:56 PM, Javier Navas wrote: > > External Email - Use Caution > > > ---------- Forwarded message --------- > De: *Javier Navas* <fjnavas2(a)gmail.com <mailto:fjnavas2@gmail.com>> > Date: mié., 24 abr. 2019 a las 19:22 > Subject: Re: [Freesurfer] mri_surfcluster ERROR > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > Yes, the file ($SUBJECTS_DIR/fsaverage/surf/rh.white) exists and I can > open it with freeview. The mri_surfcluster worked well in the past. > However, I recently downloaded the fspalm and the mri_surfcluster > attached for the fspalm. I do not know if it could interfere...?? > > I'm using Ubuntu 18.04 x86_64 > > El mié., 24 abr. 2019 a las 19:13, Greve, Douglas N.,Ph.D. > (<DGREVE(a)mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>) escribió: > > The "locale" error is probably not a problem. Does > *//media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white exist? > What operating system are you using?/* > > On 4/24/2019 6:41 AM, Javier Navas wrote: >> >> External Email - Use Caution >> >> Dear freesurfer experts, >> >> I want to create an annot from the output of PALM, the vertexwise >> file corrected by TFCE-FWEp. The values of this files are in >> 'p-values'. >> >> However, the mri_surfcluster has some problems: it could not >> recognize the fsaverage and it shows a problem with the 'locale' >> also. I have permissions of 'write' and 'read' in the fsaverage >> folder. I use the last dev version,but also it occurs with the >> stable version of FS 6.0. >> >> I send you the command, with the outputs and the errors. >> >> />$ mri_surfcluster --in >> ./PALM_results/rh_thickness_n34_10000_PALM_tfce_tstat_fwep.mgz >> --thmin 0.99 --hemi rh --subject fsaverage --sign pos --surf >> white --oannot >> /media/Data/PEH/NEW_FS_analysis/PALM_results/rh_thickness_n34_10000_PALM_tfce_tstat_fwep.annot/ >> */Could not set locale/* >> */No such file or directory/* >> */Could not set locale/* >> /thsign = pos, id = 1/ >> /version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve >> Exp $/ >> /hemi = rh/ >> /srcid = >> ./PALM_results/rh_thickness_n34_10000_PALM_tfce_tstat_fwep.mgz/ >> /srcsubjid = fsaverage/ >> /srcsurf = white/ >> /srcframe = 0/ >> /thsign = pos/ >> /thmin = 0.99/ >> /thmax = -1/ >> /fdr = -1/ >> /minarea = 0/ >> /xfmfile = talairach.xfm/ >> /nth = -1/ >> /subjectsdir = /media/Data/PEH/NEW_FS_analysis/ >> /FixMNI = 1/ >> /------------- XFM matrix (RAS2RAS) ---------------/ >> //media/Data/PEH/NEW_FS_analysis/fsaverage/mri/transforms/talairach.xfm/ >> / 1.00000 0.00000 0.00000 0.00000;/ >> / 0.00000 1.00000 0.00000 0.00000;/ >> / 0.00000 0.00000 1.00000 0.00000;/ >> / 0.00000 0.00000 0.00000 1.00000;/ >> /----------------------------------------------------/ >> */Reading source surface >> /media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white/* >> */MRISread(): could not open file/* >> */No such file or directory/* >> */mri_surfcluster: could not read surface >> /media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white/* >> */No such file or directory/* >> / >> / >> />$ more error.log/ >> */Could not set locale/* >> */MRISread(): could not open file/* >> >> Thank you in advance >> -- >> /**********************************************************\ >> Francisco Javier Navas Sánchez >> Laboratorio de Imagen Médica U.M.C.E. >> Hospital General Universitario Gregorio Marañón >> Dr Esquerdo 46, 28007 Madrid, Spain >> Phone : (+34) 91 426 50 67 Fax: (+34) 91 426 5108 >> e-mail:jnavas@hggm.es <mailto:e-mail%3Ajnavas@hggm.es> >> http://image.hggm.es >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > /**********************************************************\ > Francisco Javier Navas Sánchez > Laboratorio de Imagen Médica U.M.C.E. > Hospital General Universitario Gregorio Marañón > Dr Esquerdo 46, 28007 Madrid, Spain > Phone : (+34) 91 426 50 67 Fax: (+34) 91 426 5108 > e-mail:jnavas@hggm.es <mailto:e-mail%3Ajnavas@hggm.es> > http://image.hggm.es > > > -- > /**********************************************************\ > Francisco Javier Navas Sánchez > Laboratorio de Imagen Médica U.M.C.E. > Hospital General Universitario Gregorio Marañón > Dr Esquerdo 46, 28007 Madrid, Spain > Phone : (+34) 91 426 50 67 Fax: (+34) 91 426 5108 > e-mail:jnavas@hggm.es <mailto:e-mail%3Ajnavas@hggm.es> > http://image.hggm.es

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Re: [Freesurfer] FreeSurfer 6.0 disk image for VirtualBox?
by fsbuild 24 Apr '19

24 Apr '19

External Email - Use Caution Hello Gonzola, I use a CentOS7 VM image (on virtualbox) originally downloaded from osboxes.org.  After downloading and bringing up the image, I installed various packages for freesurfer.  But apart from my image being CentOS7 (and not CentOS6), I think it is currently too large for it to be practical to upload/download. You can download CentOS6 images from osboxes.org, https://www.osboxes.org/centos/If you scroll down that page you will see the latest CentOS6 image is 6.10, followed by previous 6.X releases. Some of the packages I installed are, qt-create qt-config.x86_64 qt5-qtx11extras.x86_64 qt5-qtx11extras-devel.x86_64 boost.x86_64 boost-devel.x86_64 tk-devel.x86_64 opencl-filesystem.noarch opencl-headers.noarch opencv.x86_64  opencv-devel.x86_64 git-annex - R. On Apr 24, 2019, at 11:21, Gonzalo Rojas Costa <gonzalo.rojas.costa(a)gmail.com> wrote:       External Email - Use Caution        Hi: Where can I find the FreeSurfer 6.0 disk image for VirtualBox? Sincerely,Gonzalo Rojas Costa

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QDEC ROI Analysis
by Kraft, Jessica N 24 Apr '19

24 Apr '19

External Email - Use Caution Hello FreeSurfers, I had the same question as below, but did not see a response. Does anyone know if this feasible in QDEC? Best, Jessica --------------------------------------------------------------------------------------------- fabrizio piras<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Mon, 20 Jun 2011 09:54:38 -0700<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> Hi Nick, Thank you for your response. I carefully read the whole tutorial but still did not find what I was looking for. I don't want to manually draw an ROI but rather use one of the existing labels (i.e. the middle orbitofrontal). Moreover, I don't wanto to extract mean ROI thickness and analyze it with SPSS or whatever, I simply want to compute my vertex to vertex difference map limiting the analysis to that region. Is it possible with qdec? Best, Fabrizio --------------------------- Fabrizio Piras Ph.D. --------------------------- Fondazione I.R.C.C.S. Santa Lucia Laboratorio di Neuropsichiatria via Ardeatina 306 tel +390651501547 fax +390651501213 Jessica Kraft, M.A. Neuroscience Graduate Student Woods Lab Center for Cognitive Aging and Memory McKnight Brain Institute Department of Clinical and Health Psychology College of Public Health and Health Professions University of Florida Phone: 352-294-5744 Email: jkraft(a)phhp.ufl.edu<mailto:jkraft@phhp.ufl.edu>

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Obtaining stats for a custom label
by Nillo, Ryan Michael R 24 Apr '19

24 Apr '19

External Email - Use Caution Hello Freesurfer developers, I am using the code below to generate the stats table for the ROI. mris_anatomical_stats -l /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label -b subject rh white However, when I run this command, I get this output: limiting computations to label /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label. reading volume /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/mri/wm.mgz... reading input surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white... reading input pial surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.pial... reading input white surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white... table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name I am getting no values for any of the metrics listed above. Is this a bug? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging

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Re: [Freesurfer] Followup on the mystery of the missing mcprextreg file
by Mcnorgan, Christopher 24 Apr '19

24 Apr '19

External Email - Use Caution Thanks for looking into the matter Doug, and I now have gotten to the bottom of the problem based on your suggestion about dropping volumes. For context, I have been collecting functional runs from a Phillips scanner using a self-paced task, and terminating the run prior to the 256-volume finishing time. The MRI center has been providing us with reconstructed .NII files, rather than DICOM files, but the .NII file headers incorrectly report the files as containing 256 frames, rather than the actual number of full frames collected. When opening the .nii file headers using fsledithd, the mismatch between observed and expected data size is detected, and the data are zero-padded until the 4D files have 256 frames worth of data. The problem we had was during motion correction, when motion correction for some runs (but not others) failed to generate a mcprextreg file, though all other indications suggested that motion-correction had been successfully applied to the data. When I used fslplit on the padded files to inspect individual frames, there were some instances of partial volumes in the last non-zero data frame, as though a partially-acquired data frame would be included in the reconstructed data. In many cases, only a few slices were missing, but in a few others (likely the ones that were problematic), most slices were missing, which is surely catastrophic for realignment. In the end, I went back to the original data, used fslsplit to split the volumes into individual frames which also generated a series of dummy volumes, and then inspected the series to identify where the padded volumes start. After deleting the padded and/or partial volumes, I merged the individual 3D volumes into a 4D series, and preproc-sess went off without a problem. /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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trac-all -prep b0 inhomogeneity correction error
by Daniel Callow 24 Apr '19

24 Apr '19

External Email - Use Caution Hello Doug, When running trac-all -prep and including b0 inhomogeneity correction with epidewarp.fsl I get the following error. FSL Version is $FSLVersion, must be 3.X or 4.X or 5.X Looking at the epidewarp.fsl source code I see that the error is occurring because of this section of the code. set FSLVersion = `cat $FSLDIR/etc/fslversion`; set FSLVerMaj = `echo $FSLVersion | cut -c 1` echo FSLVersion $FSLVersion echo FSLVerMaj $FSLVerMaj if($FSLVerMaj == 3) then set FSLPre = avw set DilFlag = -dil set FSLToFloat = avwmaths_32R set FSLToFloatFlag = () else if($FSLVerMaj == 4) then set FSLPre = fsl set DilFlag = -dilM set FSLToFloat = (fslmaths) set FSLToFloatFlag = (-odt float) else if($FSLVerMaj == 5) then set FSLPre = fsl set DilFlag = -dilM set FSLToFloat = (fslmaths) set FSLToFloatFlag = (-odt float) else echo "FSL Version is $FSLVersion, must be 3.X or 4.X or 5.X" exit 1; endif Since fsl is now at version 6.0.1 would epidewarp.fsl be compatible with this version? Could I simply include else if($FSLVerMaj == 6) then set FSLPre = fsl set DilFlag = -dilM set FSLToFloat = (fslmaths) set FSLToFloatFlag = (-odt float) or are these paramaters different under fsl 6.x+? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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mri_surfcluster ERROR
by Javier Navas 24 Apr '19

24 Apr '19

External Email - Use Caution Dear freesurfer experts, I want to create an annot from the output of PALM, the vertexwise file corrected by TFCE-FWEp. The values of this files are in 'p-values'. However, the mri_surfcluster has some problems: it could not recognize the fsaverage and it shows a problem with the 'locale' also. I have permissions of 'write' and 'read' in the fsaverage folder. I use the last dev version,but also it occurs with the stable version of FS 6.0. I send you the command, with the outputs and the errors. *>$ mri_surfcluster --in ./PALM_results/rh_thickness_n34_10000_PALM_tfce_tstat_fwep.mgz --thmin 0.99 --hemi rh --subject fsaverage --sign pos --surf white --oannot /media/Data/PEH/NEW_FS_analysis/PALM_results/rh_thickness_n34_10000_PALM_tfce_tstat_fwep.annot* *Could not set locale* *No such file or directory* *Could not set locale* *thsign = pos, id = 1* *version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $* *hemi = rh* *srcid = ./PALM_results/rh_thickness_n34_10000_PALM_tfce_tstat_fwep.mgz* *srcsubjid = fsaverage* *srcsurf = white* *srcframe = 0* *thsign = pos* *thmin = 0.99* *thmax = -1* *fdr = -1* *minarea = 0* *xfmfile = talairach.xfm* *nth = -1* *subjectsdir = /media/Data/PEH/NEW_FS_analysis* *FixMNI = 1* *------------- XFM matrix (RAS2RAS) ---------------* */media/Data/PEH/NEW_FS_analysis/fsaverage/mri/transforms/talairach.xfm* * 1.00000 0.00000 0.00000 0.00000;* * 0.00000 1.00000 0.00000 0.00000;* * 0.00000 0.00000 1.00000 0.00000;* * 0.00000 0.00000 0.00000 1.00000;* *----------------------------------------------------* *Reading source surface /media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white* *MRISread(): could not open file* *No such file or directory* *mri_surfcluster: could not read surface /media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white* *No such file or directory* *>$ more error.log* *Could not set locale* *MRISread(): could not open file* Thank you in advance -- /**********************************************************\ Francisco Javier Navas Sánchez Laboratorio de Imagen Médica U.M.C.E. Hospital General Universitario Gregorio Marañón Dr Esquerdo 46, 28007 Madrid, Spain Phone : (+34) 91 426 50 67 Fax: (+34) 91 426 5108 e-mail:jnavas@hggm.es http://image.hggm.es

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