Freesurfer June 2016

freesurfer@nmr.mgh.harvard.edu

152 participants
213 discussions

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

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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

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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

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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

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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

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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

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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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checking freesurfer output
by Gabor Perlaki 13 Jun '16

13 Jun '16

Dear all, I've a lot of patients and we are looking for the fastest solution to check the output of Freesurfer. On the troubleshooting page ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) there are a lot of steps to check, but I think not all of that should be done to find out whether there is error in the final segmentations. I think, but I am not sure, that checking the surfaces (white and pial) and checking the subcortical segmentations (aseg) is enough to realize if something is wrong. After an error is detected based on the checked outputs (surfaces and aseg), we can find out the exact nature of the error and correct it based on the troubleshooting page. Is it a good solution for verifying the performance of Freesurfer by checking only these two things (surfaces and aseg) or I need to check all of the steps listed on the troubleshooting page anyway? Best Regards, Gabor <petzinger.gabor(a)gmail.com>

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Cerebellar volumes?
by Marja Caverlé 12 Jun '16

12 Jun '16

Hi all, I am hoping to find some cerebellar volumes, but I don't know how to get them. I already did recon -all on all my subjects, but I cannot find any of these numbers in the .stats files. Am I just missing them, or does the recon all not do any cerebellar stuff? Best, Marja

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converting ME-MPRAGE files
by Limachia, Gaurang (NIH/NINDS) [F] 10 Jun '16

10 Jun '16

Hello All, We have acquired our anatomical images on a Siemens scanner as multiecho MPRAGE sequence (4 echos), and wish to unpack the runs so we can perform morphometric analysis using FreeSurfer. What is the optimal way to convert the DICOM files so we can use them with FreeSurfer tools? Specifically, what command line do you recommend for dcmunpack? When running the command: dcmunpack –src dicomdir we get the following output: Found 1 unique series: 6 6 3D_T1_MEMPRAGE 7.27 2530 7 unknown ROW 650 dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm Not sure how to interpret this. Thanks. Gaurang Limachia

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Freesurfer June 2016