Freesurfer January 2018

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

Re: [Freesurfer] Issues with hippo subfields / amygdala fixed
by Maksimovskiy, Arkadiy 17 Jan '18

17 Jan '18

Got it. Thank you so much for all the information. Best, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Re: [Freesurfer] Hippocampal Sub-field volume units
by Iglesias Gonzalez, Eugenio 17 Jan '18

17 Jan '18

Short answer: yes, it’s cubic mm. -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Crawford, Anna" <CRAWFOA4(a)ccf.org> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, 17 January 2018 at 19:20 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal Sub-field volume units Hello, i am using the hippocampal subfield segmentation. I am looking at the results in [lr]h.hippoSfVolumes-T1.v10.txt. I saw the following in the FAQs and was unsure of what the units were then in the .txt file. Does the .txt file give units in mm^3? * The sum of the number of voxels of a given structure multiplied by the volume of a voxel is not equal to the volume reported in [lr]h.hippoSfVolumes*.txt. This is because the volumes are computed upon a soft segmentation, rather than the discrete labels in [lr]h.hippoSfLabels*.mgz. This is the same that happens with the main recon-all stream: if you compute volumes by counting voxels in aseg.mgz, you don't get the values reported in aseg.stats. Thank you, Anna =================================== Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Hippocampal Sub-field volume units
by Crawford, Anna 17 Jan '18

17 Jan '18

Hello, i am using the hippocampal subfield segmentation. I am looking at the results in [lr]h.hippoSfVolumes-T1.v10.txt. I saw the following in the FAQs and was unsure of what the units were then in the .txt file. Does the .txt file give units in mm^3? * The sum of the number of voxels of a given structure multiplied by the volume of a voxel is not equal to the volume reported in [lr]h.hippoSfVolumes*.txt. This is because the volumes are computed upon a soft segmentation, rather than the discrete labels in [lr]h.hippoSfLabels*.mgz. This is the same that happens with the main recon-all stream: if you compute volumes by counting voxels in aseg.mgz, you don't get the values reported in aseg.stats. Thank you, Anna =================================== Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Issues with hippo subfields / amygdala fixed
by Maksimovskiy, Arkadiy 17 Jan '18

17 Jan '18

Dear Dr. Iglesias, Could you please let me know what the specific problems were that are fixed? I am asking because I have already applied this segmentation, and want to make sure that the data is valid. Thank you so much, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Cloning Voxel Tool Question
by Maksimovskiy, Arkadiy 17 Jan '18

17 Jan '18

Hi All, I was wondering if someone might be able to confirm about whether cloning a voxel is working right based on my description. My concern stems from the fact that when I follow instructions to clone a voxel from a T1 onto the brainmask, I click on the brainmask but do not see any immediate indication that the voxel(s) have been cloned. This is unlike erasing voxels, when the immediate indication is the brainmask dissappearing within the area that is erased. I was wondering if someone imght be able to confirm (1) whether this is normal and (2) whether there is no way to see if the voxel has been cloned prior to rerunning the reconstruction script with the incorporated edits. Thank you for your help, Arkadiy

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Issues with hippo subfields / amygdala fixed
by Iglesias Gonzalez, Eugenio 17 Jan '18

17 Jan '18

Dear all, The problems with the hippocampal subfield / nuclei of amygdala module (as well as with the brainstem module) in the dev version should now be fixed. I apologize for the inconvenience these issues might have caused. I rushed to leave everything ready right before the winter break and made a mistake when committing files to the repository. I have also updated the wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures Thanks for the patience, Eugenio PS: if anyone has success stories with the new tail/body/head segmentation of the hippocampus, please share them with me! -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

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Freesurfer compilation for supporting cuda9.1
by zuxfoucault Wong 17 Jan '18

17 Jan '18

Hi Freesurfers, I tried different ways to compile freesurfer for support cuda 9.1. Unfortunately, I still cannot get it work. While I tried to compile a specific module freesurfer/utils where the errors generated, I got the error message. Any suggestions would be appreciated! gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I../include/dicom -I../xml2 -I../include/NrrdIO -DTEEM_DIO=0 -DTEEM_32BIT=0 -DTEEM_QNANHIBIT=1 -DTEEM_ENDIAN=1234 -I../jpeg -I../tiff -I../expat -I/home/bc/software /environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit -I/home/bc/softwa re/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/Algorithms -I/h ome/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/Ba sicFilters -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/In sightToolkit/Common -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/i nclude/InsightToolkit/IO -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/curr ent/include/InsightToolkit/Numerics -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packag es/itk/current/include/InsightToolkit/Numerics/Statistics -I/home/bc/software/environment/freesurfer_src /centos6-x86_64-packages/itk/current/include/InsightToolkit/Review -I/home/bc/software/environment/frees urfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/Review/Statistics -I/home/bc/softwa re/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/SpatialObject - I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit /Utilities -DHAVE_ITK_LIBS -I../glut -DHAVE_GLUT_LIBS -I/home/bc/software/environment/freesurfer_src/c entos6-x86_64-packages/vxl/current/include/vxl/core -I/home/bc/software/environment/freesurfer_src/cento s6-x86_64-packages/vxl/current/include/vxl/vcl -I/home/bc/software/environment/freesurfer_src/centos6-x8 6_64-packages/vxl/current/include/vxl/v3p/netlib -I/home/bc/software/environment/freesurfer_src/centos6- x86_64-packages/vxl/current/include/vxl/v3p/netlib/opt -I/usr/local/cuda/include -DHAVE_ZLIB -g -O3 -mss e2 -mfpmath=sse -Wall -Wno-unused-but-set-variable -DUSE_SSE_MATHFUN -fopenmp -DHAVE_OPENMP -m64 -DLinx -DANSI -fdata-sections -ffunction-sections -Wl,--gc-sections -I/home/bc/software/environment/freesurfe r_src/centos6-x86_64-packages/mni/current/include -DFS_CUDA -I/usr/local/cuda/include -MT libutils_cud a_a-mrishash.o -MD -MP -MF .deps/libutils_cuda_a-mrishash.Tpo -c -o libutils_cuda_a-mrishash.o `test -f 'mrishash.c' || echo './'`mrishash.c mrifilter.c: In function ‘MRIconvolveGaussian’: mrifilter.c:2618:7: error: ‘width’ undeclared (first use in this function) if (width <= 1 || height <= 1 || depth <= 1) ^ mrifilter.c:2618:7: note: each undeclared identifier is reported only once for each function it appears in mrifilter.c:2618:21: error: ‘height’ undeclared (first use in this function) if (width <= 1 || height <= 1 || depth <= 1) ^ mrifilter.c:2618:36: error: ‘depth’ undeclared (first use in this function) if (width <= 1 || height <= 1 || depth <= 1) ^ Makefile:4419: recipe for target 'libutils_cuda_a-mrifilter.o' failed make[3]: *** [libutils_cuda_a-mrifilter.o] Error 1 make[3]: *** Waiting for unfinished jobs.... mv -f .deps/libutils_cuda_a-mriprob.Tpo .deps/libutils_cuda_a-mriprob.Po mv -f .deps/libutils_cuda_a-mrisbiorthogonalwavelets.Tpo .deps/libutils_cuda_a-mrisbiorthogonalwavelets. Po mv -f .deps/libutils_cuda_a-mrisegment.Tpo .deps/libutils_cuda_a-mrisegment.Po mv -f .deps/libutils_cuda_a-mrishash.Tpo .deps/libutils_cuda_a-mrishash.Po mv -f .deps/libutils_cuda_a-mrinorm.Tpo .deps/libutils_cuda_a-mrinorm.Po mv -f .deps/libutils_cuda_a-mripolv.Tpo .deps/libutils_cuda_a-mripolv.Po mv -f .deps/libutils_cuda_a-mriset.Tpo .deps/libutils_cuda_a-mriset.Po make[3]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer/utils' Makefile:6230: recipe for target 'all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer/utils' Makefile:1060: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer' Makefile:970: recipe for target 'all' failed make: *** [all] Error 2 Best, Foucault

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FreeSurfer LocalGI error
by Manoj Kumar 16 Jan '18

16 Jan '18

Hello Dear FreeSurfer Experts, I am trying to run "recon-all -s subject -localGI" command on my Mac bash terminal. I am getting following error. I am using using Freesurfer V 6.0 and running on MacOS High Sierra (version 10.13) I also run the istallation update :"sudo -E fs_update" as per suggestion on the release note but still getting same error. Any help to resolve this issue would be greatly appreciated. Thank you so much for all your help and support. Best regards Manoj *************************************************************** Manojs-iMac:cases manojkumar$ export SUBJECTS_DIR=/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf Manojs-iMac:cases manojkumar$ cd $SUBJECTS_DIR Manojs-iMac:surf manojkumar$ mris_compute_lgi --i lh.pial ================= rm -Rf /Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Abort ERROR: mris_fill -c -r 1 lh.pial /Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz failed! Manojs-iMac:surf manojkumar$

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POST-DOCTORAL FELLOWSHIP IN NEUROIMAGING
by Xiaosong He 16 Jan '18

16 Jan '18

*POST-DOCTORAL FELLOWSHIP* *IN NEUROIMAGING * *THOMAS JEFFERSON UNIVERSITY/ SIDNEY KIMMEL * *MEDICAL** COLLEGE, PHILA., PA.* The Department of Neurology at Thomas Jefferson University/Jefferson Medical College has an opening for a Two-Year Postdoctoral Research Fellowship in Neuroimaging focusing on both clinical brain mapping and primary cognitive neuroscience investigations. The emphasis in our neuroimaging program is on cognitive and behavioral network organization and plasticity in neurologic disorders such as epilepsy. The lab is part of the Jefferson Comprehensive Epilepsy Center, an internationally-known epilepsy surgery program. Presurgical brain mapping studies are undertaken (MRI volumetrics, task-fMRI, resting state functional connectivity, diffusion imaging, neuropsychological assessment, electrophysiology/electrocortical stimulation) as well as post-surgical neuroimaging studies investigating clinical, cognitive, and behavioral outcomes. The pre-surgical brain mapping studies are conducted on a regular basis, utilized in image-guided surgery, and then made available for research. Studies in brain recovery and the cognitive reorganization of language and memory functions are emphasized, utilizing rich multi-modal datasets for the investigation of both cognitive and pathologic (e.g., seizure) networks. Thomas Jefferson University provides a high-level interdisciplinary research environment with grand rounds, seminars, case conferences, and opportunities to collaborate with faculty across departments such as neurosurgery and radiology. Successful applicants must have a strong background in image processing and analysis using programs such as MATLAB, SPM, and FSL with a strong interest in clinical neuroimaging and cognitive neuroscience. Applicants must have a PHD or MD in neuroscience, biomedical engineering, statistics, neurology, neuropsychology, radiology, or related field. Interested applicants should send a CV and cover letter stating experience and interests, 2-3 peer-reviewed publications, and three letters of recommendation. Anticipated start date is 7/1/18, but is flexible. *Contact: Joseph I. Tracy, Ph.D., ABPP(CN). Director, Cognitive Neuroscience and Brain Mapping Laboratory, Thomas Jefferson Univ./Sidney Kimmel Medical Coll., Jefferson Hospital for Neuroscience, 901 Walnut Street, Suite #447, Phila.,PA 19107, phone:#215-955-4661, *e-mail: joseph.tracy(a)jefferson.edu. Thomas Jefferson University and Hospitals is an equal Opportunity Employer. Jefferson values diversity and encourages applications from women, members of minority groups, LGBTQ individuals, disabled individuals, and veterans.

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Re: [Freesurfer] Longitudinal Pipeline (fwd)
by Bruce Fischl 16 Jan '18

16 Jan '18

FYI ---------- Forwarded message ---------- Date: Tue, 16 Jan 2018 19:59:38 +0000 From: Mark Jenkinson <mark.jenkinson(a)ndcn.ox.ac.uk> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Cc: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal Pipeline Hi Aaron and Hi Bruce! There is code to convert ANTs format to FSL, so you can use that. It is part of this tool: https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md I've included a code snippet below to show how we've used this. Cheers, MJ ${antsFolder}/antsRegistrationSyN.sh -d 3 -f ${ref} -f ${ref2} -m ${src} -m ${src2} -o ${workdir}/${outname}_ -t 'b' -j 1 ${c3dFolder}/c3d_affine_tool -ref ${ref} -src ${src} -itk ${workdir}/${outname}_0GenericAffine.mat -ras2fsl -o ${workdir}/${outname}_affine_fsl.mat ${c3dFolder}/c3d -mcs ${workdir}/${outname}_1Warp.nii.gz -oo ${workdir}/wx.nii.gz ${workdir}/wy.nii.gz ${workdir}/wz.nii.gz ${FSLDIR}/bin/fslmaths ${workdir}/wy -mul -1 ${workdir}/i_wy ${FSLDIR}/bin/fslmerge -t ${workdir}/${outname}_warp_fsl ${workdir}/wx ${workdir}/i_wy ${workdir}/wz ${FSLDIR}/bin/convertwarp --ref=${ref} --premat=${workdir}/${outname}_affine_fsl.mat --warp1=${workdir}/${outname}_warp_fsl --out=${workdir}/${outname}_warp_fsl ${FSLDIR}/bin/invwarp -w ${workdir}/${outname}_warp_fsl -o ${workdir}/${refBN}_to_${srcBN}_warp_fsl -r ${src} On 15 Jan 2018, at 15:18, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: Hi Aaron we compute the warp and save it in the mri/transforms/talairach.m3z, but don't apply it (so don't require an extra resampling). I know we have some tools around to convert to ANTS format, but I'm not sure about fnirt. I'll cc MJ who may know (hi MJ!) cheers Bruce On Mon, 15 Jan 2018, Aaron Tanenbaum wrote: Is the warp saved anywhere and where can I find it? Also is the warp compatible with FNIRT in any way. I am interested in combining warps together to reduce the number of re-sampling steps. Thank you so much in advanced On Mon, Jan 15, 2018 at 8:53 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: in the last stage there is a nonlinear atlas alignment that is specific to each timepoint. We are working on building a nonlinear base, but it is not distributed yet. cheers Bruce On Sun, 14 Jan 2018, Aaron Tanenbaum wrote: > > I am interested in knowing what type of alignment goes into the last stage of the longitudinal > pipeline. Are each longitudinal time point non-linearly aligned to the base image? If so can I find > the warp? > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Freesurfer January 2018