Freesurfer August 2018

freesurfer@nmr.mgh.harvard.edu

104 participants
167 discussions

hippocampal subfield segmentation
by Nillo, Ryan Michael R 21 Aug '18

21 Aug '18

External Email - Use Caution Hello FreeSurfer users, I want to segment hippocampal subfields, but did not have much luck running it. I downloaded the matlab compiler runtime according to this: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime. Now, there is a directory called MCRv80 in my FREESURFER_HOME. The first error says kvlAutoCrop: command not found. However, $FREESURFER_HOME.bin is on my path. Does anything seem incorrect? My path looks like this: /data/sugrue2/rnillo/tools:/data/sugrue2/rnillo:/netopt/afni:/working/sdl_analysis/software/dcm2niix/build/bin:/netopt/rhel7/versions/cmtk/lib/cmtk/bin:/working/sdl_analysis/software/vtk-dicom/build/bin:/netopt/dicom/bin:/working/sdl_analysis/software/ANTs/antsbin/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/mni/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin:/netopt/share/bin/local/sdl/fix:/netopt/rhel7/fsl/bin:/working/sdl_analysis/software/git_pipeline/CommandLineProg:/netopt/share/local/bin/sdl/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/bin:/usr/local/sbin:/working/sdl_analysis/software/git_unwarp:/working/sdl_analysis/software/parallel:/working/sdl_analysis/software/git_tools:/working/sdl_analysis/software/anaconda3/bin:/bin:/sbin:/usr/bin::/netopt/rhel7/bin:/netopt/rhel7/bin/local:/netopt/share/bin:/netopt/share/bin/local:/netopt/bin:/netopt/bin/local:/netopt/dicom/bin:/netopt/rhel7/matlab/bin:/netopt/ctf/bin:/netopt/share/hosts::/netopt/caret/bin:/netopt/afni:/netopt/freesurfer/bin/Linux:/netopt/freesurfer/bin/noarch:/netopt/sybase/12.5.3/OCS-12_5/bin:/netopt/rhel7/fsl/bin:/netopt/sge_n1ge6/bin/lx24-amd64:/netopt/rhel7/tivoli/tsm/client/ba/bin::/netopt/share/bin/local/sdl:/netopt/bin/local/brain:/netopt/share/bin/local/brain:/netopt/bin/local/ncl:/netopt/share/bin/local/ncl:. MatlabRuntime - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime> surfer.nmr.mgh.harvard.edu Matlab Runtime. The brainstem and hippocampal subfield modules in FreeSurfer 6.0 and the development version require the Matlab R2012b (v8.0) runtime (note that development versions from January 2018 onwards require the Matlab R2014b - v8.4 - runtime instead). ERROR MESSAGE: #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Tue Aug 21 13:45:25 PDT 2018 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/runtime/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/bin/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/os/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/working/sdl_analysis/software/freesurfer6/freesurfer/bin: Warning: Unable to open display '10.48.0.125:0'. You will not be able to display graphics on the screen. Registering imageDump.mgz to hippocampal mask from ASEG /working/sdl_analysis/software/freesurfer6/freesurfer/bin/kvlAutoCrop: line 3: kvlAutoCrop.bin: command not found gzip: /data/sugrue2/MTS/sub_0006_T1_20160920_1723/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1_autoEstimateAlveusML (line 158) MATLAB:badSwitchExpression #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Tue Aug 21 13:45:43 PDT 2018 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/runtime/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/bin/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/os/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/working/sdl_analysis/software/freesurfer6/freesurfer/bin: Warning: Unable to open display '10.48.0.125:0'. You will not be able to display graphics on the screen. Registering imageDump.mgz to hippocampal mask from ASEG /working/sdl_analysis/software/freesurfer6/freesurfer/bin/kvlApplyTransform: line 3: kvlApplyTransform.bin: command not found mv: cannot stat ‘imageDump_transformed.mgz’: No such file or directory /working/sdl_analysis/software/freesurfer6/freesurfer/bin/kvlAutoCrop: line 3: kvlAutoCrop.bin: command not found gzip: /data/sugrue2/MTS/sub_0006_T1_20160920_1723/tmp/hippoSF_T1_v10_right//hippoAmygBinaryMask_autoCropped.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1_autoEstimateAlveusML (line 158) MATLAB:badSwitchExpression Mahalo, Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging

2 2

Lesion segmentation
by Mo Izady 21 Aug '18

21 Aug '18

External Email - Use Caution Hi FreeSurfer experts, I have two questions; any hints are greatly appreciated: 1) What is considered lesion in subcortical segmentation? (tumor, MS, stroke, etc) 2) Would you pls share the reference to the algorithm that FreeSurfer uses for segmenting lesions? Thanks in advance! Mo Izady PhD Candidate in Neuroscience Arizona State University

2 3

vertex MNI305
by Trisanna Sprung-Much 21 Aug '18

21 Aug '18

External Email - Use Caution Hi there This might be a very silly question but I actually cannot find the answer in the email archive: Assuming I have loaded a label onto fsaverage in Freeview and want to get the MNI305 coordinate of that labelled vertex, am I simply using the x,y,z in brackets in the panel? I attach a photo of what I mean. Best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

4 8

Flipped left to right hemisphere subjects
by Lutz,Olivia (BIDMC - Psychiatry) 21 Aug '18

21 Aug '18

Hi Doug, Yes the brainmask volume is left-right reversed as well. Thanks! Olivia ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

AAL and freesurfer atlas concordance
by Venkateswaran Rajagopalan 21 Aug '18

21 Aug '18

External Email - Use Caution Dear All I have seen posts discussing about bringing AAL to freesurfer etc. I am wondering whether anyone has created a table of concordance between the regions in AAL to the freesurfer or the vice versa. If so can you please share with me. For my work I just want to know the mapping between the two atlases. Or is there any software or website (like the brain atlas concordance one) from where I can find the concordance between the two atlas regions Any help is greatly appreciated Thanks Venkat

1 1

Re: [Freesurfer] Flipped left to right hemisphere subjects
by Lutz,Olivia (BIDMC - Psychiatry) 20 Aug '18

20 Aug '18

Hi Doug and Bruce, thank you for the quick reply. As a follow-up question, we've edited our brainmasks for a dataset and want to flip some subjects left to right. I found instructions to flip the scans, however they are for the nu.mgz file (https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal) Is is possible to apply this mri_convert --in_orientation? command to change the left and right labels of the brainmask so we don't have to re-edit as opposed to applying it to the nu.mgz file and regenerating the brainmask? Thanks! Olivia ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

Fw: Parcellation label error
by Ali,Mohamed Tarek Mohamed 20 Aug '18

20 Aug '18

External Email - Use Caution ________________________________ From: Ali,Mohamed Tarek Mohamed Sent: Saturday, August 18, 2018 10:59 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Parcellation label error Hello FreeSurfer Developers, While I am using [vec,labels,cnames] = read_annotation('lh.aparc.annot'), I am getting values in labels which are not found in cnames.table(:,5). These values are 0. I assigned the values to the unknown area. However, when I looked at the number of vertices per brain regions I found that corpuscallosum has no vertices in the DK atlas. This is my first week using a neuroimaging software and Freesurfer is my first software to work on, so I just don't know if that's ok or if there is something wrong. I am attaching the output of a python code I wrote to count the number of vertices per brain region in the left hemisphere of a structural MRI image from our dataset. Thanks in advance, Mohamed T. Ali Ph.D. student, Bioengineering, University of Louisville.

1 0

segmentHA_T1.sh exits with error
by Antonin Skoch 20 Aug '18

20 Aug '18

External Email - Use Caution Dear experts, I am running segmentHA_T1.sh. In about 3 subjects from 200, the script exits with following error: In an assignment A(:) = B, the number of elements in A and B must be the same. Error in segmentSubjectT1_autoEstimateAlveusML (line 1856) MATLAB:subsassignnumelmismatch Command exited with non-zero status 255 Full log file is attached. I have also uploaded whole subject (named segmentHA_T1_error.tar.gz ), including content of temporary directory hippoSF_T1_v21_right, to your server. I am using dev version, build 2018-07-28. I am using customized recon-all, but it should not relate to this error. Could you please look at this issue? Regards, Antonin Skoch

2 2

How to register fMRI data without upsampling voxel size?
by Maria Hakonen 20 Aug '18

20 Aug '18

External Email - Use Caution Dear Freesurfer experts, Could you please let me know how to normalize fMRI data without upsampling the original voxel size from 5 x 5 x 7 mm to 2 x 2 x 2 mm? I have tried this as follows: 1. Register functional (data.nii) to anatomical matrix bbregister --s $subject --bold --init-fsl --mov data.nii --reg register.dof6.dat 2. Register anatomical to mni152: mni152reg --s $subject 3. Create registration between functional and mni152 mri_matrix_multiply -im register.dof6.dat -iim reg.mni152.2mm.dat -om reg.mni152.dat 4. Resample func to mni152 space mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --mov data.nii --reg reg.mni152.dat --o data.mni152.nii --no-resample I checked the registrations after each step. After step 4, the functional data and the template are not fully aligned if I use “no-resample”. Without no-resample, the registration seems successful, but the fMRI data has a voxel size of 2mm. Best, Maria

1 0

How to install Biomedical Toolkit examples in Labview 2015?
by Bellamy Baron 20 Aug '18

20 Aug '18

External Email - Use Caution Hi freesurfers, Does anyone know how to install Biomedical Toolkit examples in Labview 2015? I installed an evaluation version of Labview 2015, 2015DFDT, and 2015ASPT under Windows 7. Then, I installed the 2014BMTK but only one, I get the Biomedical Workbench, but examples (source codes) are not installed. In a second time, I marked the option of 2014_Support in the installation of 2014BMTK, then examples are installed but in another file (Labview 2014) and there are missing modules when I try to test these examples. Thanks, -------------------------------------------------------------------------------------------------------- Bellamy Specialist - iWYZE https://www.iwyze.co.za <https://www.iwyze.co.za/products/car-insurance>

1 0

← Newer
1
...
6
7
8
9
10
11
12
...
17
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer August 2018