Freesurfer June 2017

freesurfer@nmr.mgh.harvard.edu

116 participants
186 discussions

CT DIOCMs
by John Anderson 29 Jun '17

29 Jun '17

Dear Freesurfer experts, I have T1 images acquired using CT scan not MRI. I have the following questions please: 1. "mri_convert" failed to convert the dicoms to nifti, so I used "dcm2nii" part of mricron to convert the dicoms to nifti. I am wondering if there are any tools in Freesurfer to convert CT scan dicoms to nii or mgz formats 2. Can this type of images be processed in Freesufrer using the traditional pipeline for surfaces reconstruction. I mean using "recon-all" Thank you for your guidance Jon

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mri_normalize problem normalization2
by Chris Adamson 28 Jun '17

28 Jun '17

Hello, For one subject I'm getting a weird error on mri_normalize in normalization2. When it goes into the "3d normalization pass 1 of 2" I get an error HISTOalloc(-2147383648): could not allocate histogram The image that is produced by MRI3dGentleNormalize line 874 of mri_normalize/mri_normalize.c has a block of pixels with HUGE negative values. They are in the background and nowhere near the brain. The data comes from a public dataset so I can send it for debugging if required. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Qdec input fields
by Rockers, Elijah D. 28 Jun '17

28 Jun '17

Hi, We like using Qdec to display cortical thickness results. The only drawback is that we are unable to manually input values into the boxes for threshold values, FDR rate, etc.. We are running Centos7. We thought the graphics drivers were the problem, but even after buying a whole new GFX card with different drivers, the same problem persists. Even stranger, our colleague can SSH in from a Mac using X forwarding, and she does not experience that problem. I know this may not strictly be a Freesurfer problem, but I was hoping someone else may have run into this problem before, and has some insight that could help us. Thanks, Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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ERROR: bits = 0 not supported
by 糜超 28 Jun '17

28 Jun '17

Hi, I am preprocessing my fMRI data acquired with Philips. when I using the command 'dcmunpack -src . -targ sess01 -run 101 bold nii f.nii .....' The error occurred likes below: Found 31 total files. Found 12 unique series: 0 101 301 401 501 601 701 801 901 1001 1101 1201 Subject xxx Date xxx Time 110223 Institution xxxxx. 0 Survey unknown unknown unknown unknown unknown unknown ./PS_0002 101 Survey unknown unknown unknown unknown unknown 140 ./XX_0003 301 T1W_3D_TFE_ref unknown unknown unknown unknown unknown 190 ./IM_0004 401 FE_EPI unknown unknown unknown unknown unknown 2835 ./XX_0007 501 FE_EPI_EX1 unknown unknown unknown unknown unknown 2835 ./IM_0008 601 FE_EPI_EX2 unknown unknown unknown unknown unknown 2835 ./IM_0011 701 FE_EPI_EX3 unknown unknown unknown unknown unknown 2835 ./IM_0013 801 FE_EPI_EX4 unknown unknown unknown unknown unknown 2835 ./XX_0016 901 FE_EPI_EX5 unknown unknown unknown unknown unknown 2835 ./XX_0018 1001 FE_EPI_EX6 unknown unknown unknown unknown unknown 2835 ./IM_0019 1101 FE_EPI_EX7 unknown unknown unknown unknown unknown 2835 ./XX_0022 1201 FE_EPI_EX8 unknown unknown unknown unknown unknown 2835 ./XX_0024 mri_convert ./XX_0003 ./bold/101/f.nii --nskip 0 --ndrop 0 nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./XX_0003... Starting DICOMRead2() dcmfile = ./XX_0003 dcmdir = . WARNING: tag image orientation not found in ./XX_0003 Ref Series No = 101 ERROR: bits = 0 not supported. My os is Linux 16.04 and the Freesurfer's version is 5.3.

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QDEC Error in Analysis
by AYUSHI SHUKLA 28 Jun '17

28 Jun '17

Hi, I'm a new user of qdec and I'm trying to run a cortical thickness analysis in qdec between Schizophrenic patients and healthy controls. I have run "recon-all -i" and "recon-all -s <subjid> -qcache" on my data and it says that this has run successfully without any errors. But when I hit analyze on the qdec GUI, I get the following error- "Error in Analyze: Couldn't open /Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file." I went through the old questions with the same issue, however I could not figure a solution for my problem as when I check in the directory, the file is present. I have tried to re-run recon-all and recon-all -s as well, but it is still giving the same error. I was wondering if someone could help me with this issue. Warm Regards Ayushi Shukla

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ROI analyses using SPM AAL ROIs
by M Janani 28 Jun '17

28 Jun '17

Hi Team, Currently I'm working on ROI analyses. I saw one article related to VolumeROICorticalThickness in Free surfer wiki. Could anyone please tell me what is the anatomical file(TT_avg152T1.nii) they are referring to? I took AAL ROIs from SPM. In that case, which anatomical file should I use for my analyses? Any help would be really grateful. Thanks in advance. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

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freesufer 6.0 error
by Jinsong Tang 27 Jun '17

27 Jun '17

Dear FreeSurfer experts, When I run the FreeSurfer 6.0. the recon-all exited with ERRORS. Attached is the log file. Can you please let me know how fix this error? Thanks, Jinsong

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mghRead error (ribbon.mg: could not open file)
by Shuo Zhou 27 Jun '17

27 Jun '17

Hello FreeSurfer Developers, I am using recon-all to process the structural mri data. The autorecon1 works fine, however I got the following error when I run the recon-all autorecon2 command: mghRead(/home/acp16sz/openfmri/data/subdir/ds003_sub001/mri/ribbon.mgz, -1): could not open file. I have checked the output of the recon-all steps (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) the file ribbon.mgz is the output of autorecon3, why it is required in autorecon2. Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: 64-bit Scientific Linux (which is Redhat based) HPC 3) uname -a: Linux iceberg-login2 2.6.32-696.3.2.el6.x86_64 #1 SMP Mon Jun 19 11:23:31 CDT 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Kind regards, Shuo Sent from Mail for Windows 10

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cannot open registration file in DTI
by Yifan Xu 27 Jun '17

27 Jun '17

Hi, freesurfer team. when I check my DTI registration and run the below command: the bash terminal always tell me freeview -v $SUBJECTS_DIR/$subj/mri/orig.mgz \ lowb.nii:reg=register.dat \ -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green \ $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green \ -viewport coronal

1 0

Can new-released FS(stable v6.0.0) build in CentOS 6 x86_64 (64b) run on Ubuntu 16.04?
by zonglei.fsl Zhen 26 Jun '17

26 Jun '17

I mean the pre-complied package freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz. Thanks Zonglei

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Freesurfer June 2017