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30135 discussions

output file from running mri_glmfit-sim
by Yu Sun Chung 14 Jun '16

14 Jun '16

Hi, all, While working on gyrification data using Freesurfer, I have a question to confirm one of output files. First, I did run mri_glmfit using age x IQ itneraction. fsgd file in which I included intracranial volume and gender to covary out. then, I am running mri_glmfit-sim for age x IQ interaction using the following commands; mri_glmfit-sim --glmdir lh.ageIQ.glmdir --cache 3 abs --cwp 0.05 --2spaces After running simulation, I see there are several output files. Especially, I have a question about "*cache.th30.abs.y.ocn.dat*" *my question is whether these values are raw values of lgi or residualized values? * I think that these values in "cache.th30.abs.y.ocn.dat" refers to raw, non-residualized values of local gyrification index. so I extract those vales into SPSS and covaried out by running regression with ICV and gender as covariates. but I want to confirm whether my understanding is correct. Anyone who used this can confirm? Many thanks in advance!! Best, Yu Sun

2 1

Segmentation fault in mri_convert
by Christopher Finuf 14 Jun '16

14 Jun '16

I'm trying to convert the dicom to the original 001.mgz file using the following command on a Mac OSX Yosemite version 10.10.5. My SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/ . My current working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/ . The following is the output and error that I get. I'm running the latest version v 5.3.0 of freesurfer. Any suggestions on what the problem is? What is strange that it works with half my data set but the other has this error. I've run this command in the exact way many times before and have never had this issue. bash-3.2$ recon-all -i /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm -subjid Bigler_Repeatability_0005Ad_M1 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin NS112201PSY2.byu.edu <http://ns112201psy2.byu.edu/> 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1 \n mri_convert /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz \n mri_convert /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm... Getting Series No INFO: Found 178 files in /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1 INFO: Scanning for Series Number 2 Scanning Directory INFO: found 176 files in series INFO: loading series header info. RunNo = 1 INFO: sorting. INFO: (224 256 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Bigler_Repeatability_AD_M Date and time StudyDate 20160512 StudyTime 075942.531000 SeriesTime 081401.859000 AcqTime 080647.620000 Acquisition parameters PulseSeq *tfl3d1_ns Protocol t1_mpr_sag_iso_ave2_ipat2_(mprage) PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.26 InversionTime 900 RepetitionTime 1900 PhEncFOV 218.75 ReadoutFOV 250 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 256 NImageCols 224 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 75.8389 136.8499 125.0000 VolRes 0.9766 0.9766 1.0000 VolDim 224 256 176 Vc 0.0767 -0.9971 0.0000 Vr -0.0000 0.0000 -1.0000 Vs -0.9971 -0.0767 0.0000 VolCenter -3.5106 21.0460 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) Segmentation fault Darwin NS112201PSY2.byu.edu <http://ns112201psy2.byu.edu/> 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 recon-all -s Bigler_Repeatability_0005Ad_M1 exited with ERRORS at Wed Jun 8 13:39:08 MDT 2016 For more details, see the log file /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

2 1

fs development version
by shi yao wang 14 Jun '16

14 Jun '16

Dear Experts: I set up FS development version. And now it shows error message: -------------------------------------------------------------------------- GNU libc version: 2.17 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html -------------------------------------------------------------------------- How can I upgrade this license? thanks Lawrence Emory

2 1

swapped dimensions?
by Marja Caverlé 14 Jun '16

14 Jun '16

Hi guys, Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere. Thanks! Best, Marja

4 14

QA Tools : All in errors for aseg outliers detection
by Matthieu Vanhoutte 14 Jun '16

14 Jun '16

Dear FS experts, I tried to run the QA Tools on a subject with the following command: *${QA_TOOLS}/recon_checker -s 207043_M0_2010-10-07 -outputFOF ${SUBJECTS_DIR}/FOF -gen-outputFOF -gen-asegLUT ${SUBJECTS_DIR}/AsegOutliers* But I got all errors concerning the detection of Aseg outliers: *Making aseg look-up table, /NAS/tupac/matthieu/FS5.3//AsegOutliers* *parsing arguments ...* *checking parameters ...* *MeanFile is /NAS/tupac/matthieu/FS5.3//AsegOutliers* *checking logs ...* *done checking logs ...* *done checking parameters ...* *moving previous log files to *.bak* *done moving previous log files* *Processing each subcortical label ...* *(standard_in) 1: syntax error* *gawk: /home/matthieu/programs/QAtools_v1.1/gstd.awk:22: (FILENAME=- FNR=1) fatal: division by zero attempted* *(standard_in) 1: syntax error* *(standard_in) 1: syntax error* *(standard_in) 1: syntax error* *(standard_in) 1: syntax error* *(standard_in) 1: syntax error* *(standard_in) 1: syntax error* *-----Checking asegs for outliers...Using asegLUT: /NAS/tupac/matthieu/FS5.3//AsegOutliersparsing arguments ...checking parameters ...checking logs ...done checking logs ...done checking parameters ...moving previous log files to *.bakdone moving previous log filesProcessing each subcortical label ...(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error(standard_in) 1: syntax error* Please find attached the recon_checker summary. Thanks in advance for any help ! Best regards, Matthieu

1 0

Remove zeroes from mri_segstats in mean calculation?
by Lakhani, Bimal 13 Jun '16

13 Jun '16

Hello, I am running mri_segstats to get the intensity mean of a custom image volume, but I do not want zeroes to be included in the calculation of the mean. Is there an option to remove zeroes from this calculation or another potential workaround? Thanks very much! Bimal

2 1

FreeView updating
by Chiu, Bryan (PHTH) 13 Jun '16

13 Jun '16

Hello, I would like to download the latest version of FreeView so I could use the Recon Edit option. I've downloaded the latest version of FreeSurfer (v5.3), but it seems that I have an older version of FreeView (v1.0). Could someone please assist me in updating FreeView - I can't find the download for it. Regards, _______________________________________ Bryan Chiu Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia

2 1

Skull Strip and Bad Surfaces
by Katherine Reiter 13 Jun '16

13 Jun '16

Dear FreeSurfer experts, I am working on a data set and am having particular difficulty with one subject. It appeared the skull strip was mistakenly removing occipital regions. These regions were absent from the brainmask, T1, and resulting surfaces. I attempted to solve this in 2 different ways. I first adjusted the watershed and reran the recon-all -autorecon2 in order to redraw the surfaces. Adjusting the watershed worked to include these regions in both the brainmask and T1 but the resulting surfaces hugely inaccurate (see the attached screenshot '4003_badsurfs_parietal_cerebellum2'; Oddly enough, the frontal surfaces are largely accurate but the parietal regions include gray matter in the white surface and even large amounts of the cerebellum, while excluding occipital regions. I then reran it from the raw dicoms and had the same issue with occipital regions being excluded so I adjusted the watershed and tried to manually fix the surfaces, but this resulted in similar inaccurate surfaces. See the second attached screenshot '4003_badsurfs'. ll surfaces are fairly messy, but some regions are more accurage, where the appears to distinguish between gray and white and other areas are over inclusive, but cerebellar and some superior and medial regions are excluded. Any and all help would be much appreciated. Thanks in advance! Kate Katherine Reiter, M.S. Clinical Psychology Doctoral Student Marquette University Phone: (414) 288-3807 Email: katherine.reiter(a)marquette.edu

1 0

Cortical Thickness Processing Error
by Navena Rebecca Lingum 13 Jun '16

13 Jun '16

Dear FreeSurfer experts, I am currently in the process of running the mris_anatomical_stats command line to look at cortical thickness however, the output states that the annotation file could not be read. Please see below for command line and output: navenalingum% mris_anatomical_stats -a N1/label/lh.aparc.annot -b N1 lh computing statistics for each annotation in N1/label/lh.aparc.annot. reading volume /Users/navenalingum/Applications/freesurfer/subjects/N1/mri/wm.mgz... reading input surface /Users/navenalingum/Applications/freesurfer/subjects/N1/surf/lh.white... reading input pial surface /Users/navenalingum/Applications/freesurfer/subjects/N1/surf/lh.pial... reading input white surface /Users/navenalingum/Applications/freesurfer/subjects/N1/surf/lh.white... could not read annot file N1/label/lh.aparc.annot No such file or directory mris_anatomical_stats: could not read annotation file N1/label/lh.aparc.annot No such file or directory Could it be that there was an error in the recon-all processing stage? Your help would be greatly appreciated! Thanks, Navena Lingum

2 1

Help resolving ERROR: Invalid FreeSurfer license key found in license file
by Suzanne Witt 13 Jun '16

13 Jun '16

Hej. I recently tried to create a license file for a Unix-based installation of FreeSurfer that previously had no license file associated with it. With the help of our IT people, I have tried copying the lines I received via email into a file named ‘license.txt’ and then following responses I found on the message board to similar problems, into a file named ‘.license’. In both cases, I get the same error: ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt or ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license I have since tried performing a completely new installation of freesurfer, recreating the .license file using a text editor (per a previous message found about this error on the message boards). I am still receiving the same invalid FreeSurfer license error message. To the best that I can figure out, there do not appear to be any sort of ‘end of line’ characters in any of the iterations of our attempts to create this license file. I have noticed many messages about this error in the archives, but none of the suggested fixes seem to be working for me. Any help at this point would be much appreciated. Thanks in advance, suzanne

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