Freesurfer April 2019

freesurfer@nmr.mgh.harvard.edu

99 participants
136 discussions

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 **********************************************/

1 0

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

2 2

Issue running recon-all
by Bhattarai, Kriti 24 Apr '19

24 Apr '19

External Email - Use Caution I am having issues running recon-all in my Mac. I have checked my permission and it is not a read-write issue. Also, I dont know any way to manually verify if I have build-stamp.txt. Could someone guide me if they have seen this before? Thanks! [cid:d493af7b-4924-4889-9844-15035836a8d4]

2 1

How to Display Specific Cortical Parcels (not the output of the recon-all) on Brain Surface
by Mahshid Fouladivanda 24 Apr '19

24 Apr '19

External Email - Use Caution Dear Freesurfer Experts, I have a predetermined cortical parcels in native space. I want to display them on brain surface, As shown in the last image of page bellow: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview I have loaded *.pial files (transferred to native space ) and then volume file (contains native space parcels not output of the recon-all) using freeview but it is not desired! Now, I have some question. First, is it possible to show determined parcels (not the output of the recon-all) on brain surface using freesurfer? Second, is my procedure correct? Then, how could I display determined parcels (not the output of the recon-all) on brain surface using freesurfer? Regards, Mahshid

2 1

FreeSurfer 6.0 disk image for VirtualBox?
by Gonzalo Rojas Costa 24 Apr '19

24 Apr '19

External Email - Use Caution Hi: Where can I find the FreeSurfer 6.0 disk image for VirtualBox? Sincerely, Gonzalo Rojas Costa

1 0

recon-all error
by 1013364183 24 Apr '19

24 Apr '19

External Email - Use Caution Dear freesurfer We run the recon-all command of freesurfer, but when it runs to the randomSeed 0 step below, it will not run anymore, that is, the running terminal has been stuck in the following statement for more than 10 days.We want to ask why this happens? How should we solve this problem? The running statement is as follows: only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/filled.mgz... reading volume /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/brain.finalsurfs.mgz... reading volume /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/../mri/aseg.presurf.mgz... reading volume /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/wm.mgz... 1792 bright wm thresholded. 583658 bright non-wm voxels segmented. reading original surface position from /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/surf/lh.orig... computing class statistics... border white: 318655 voxels (1.90%) border gray 363634 voxels (2.17%) WM (109.0): 109.3 +- 4.5 [70.0 --> 110.0] GM (109.0) : 101.3 +- 17.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 92.2 (was 70) setting MAX_BORDER_WHITE to 114.5 (was 105) setting MIN_BORDER_WHITE to 110.0 (was 85) setting MAX_CSF to 35.0 (was 40) setting MAX_GRAY to 105.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 60.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 56.6 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.26 +- 0.11 (0.00-->2.25) (max @ vno 28887 --> 31618) face area

2 1

fswiki brainstem substructures: test data unavailable
by Fabian Peter Hammerle 24 Apr '19

24 Apr '19

External Email - Use Caution Hi, Section "6. Test data" of the article "Brainstem Substructures" at https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures mentions: > Processed data of a single subject (also used to demo the hippocampal subfield segmentation) is available here: > wget -c ftp://surfer.nmr.mgh.harvard.edu/pub/data/hipposubfields-testdata.tgz At the moment `/pub/data` does not contain the mentioned file `hipposubfields-testdata.tgz`. Is the testdata file still publically available at some url? I found `pub/data/archive/hipposubfields-testdata.tgz`. However, this archive appears to be outdated (modification date: 2015-06-12). Thank you, Fabian

1 0

LGI in QDEC menu please respond soon
by Avi Gharehgazlou 23 Apr '19

23 Apr '19

External Email - Use Caution Hi experts, To give more detail re my previous post.... I have created the .Qdecrc file in my Subjects directory and QDEC folder, which contains one line : MEASURE1 = pial_lgi . However, LGI is still not appearing in the drop down menu on QDEC. When I do command more ~/.Qdecrc it gives the following output: # This file is automatically generated by the application # If you change any lines or add new lines, note that all # coments and empty lines will be deleted. Every line has # to be in format: # key = value # Qdec1\Dialogs\ExitApplication = 0 Qdec1\Dialogs\SendErrorLog = 0 Qdec1\Geometry\MainPanelSize = 375 Qdec1\Geometry\MainPanelVisibility = 1 Qdec1\Geometry\SaveUserInterfaceGeometry = 1 Qdec1\Geometry\SecondaryPanelSize = 250 Qdec1\Geometry\SecondaryPanelVisibility = 0 Qdec1\Geometry\ViewPanelPosition = Right Qdec1\Geometry\WindowGeometry = 900x700+531+190 Qdec1\RunTime\MostRecentVersionLaunched = 1.5 Qdec1\RunTime\PrintTargetDPI = 100.000000 Qdec1\RunTime\ShowBalloonHelp = 1 Qdec1\RunTime\ShowSplashScreen = 1 Qdec1\RunTime\ToolbarFlatButtons = 1 Qdec1\RunTime\ToolbarFlatFrame = 1 Based on previous archives I think my .Qdecrc was not saved properly because the line in this file (MEASURE1 = pial_lgi) doesn't appear in the above output. I know I have to put this line in the above output, but I can't seem to figure out how. Will you please be able to tell me how I can do this? Thanks so much

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Freesurfer April 2019