Freesurfer

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30088 discussions

unable to create symbolic link, and GPU error
by John Absher 22 Jun '19

22 Jun '19

External Email - Use Caution Hi, I am testing a new installation of freesurfer. Two errors occurred, and I'm hoping someone can help me troubleshoot: First, recon-all exits with error indicating that it is unable to create a symbolic link: [GHS\026278@vmcntdsktp10 fs_sample1]$ tail /neuro_images_isilon/026278/fs_sample1/sample001/scripts/recon-all.log ICI = 216.7, FI = 1989.1, variation=32373.324 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux vmcntdsktp10 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sample001 exited with ERRORS at Sat Jun 22 17:10:41 EDT 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting The error occurs in CentOS 7 running on a virtual machine environment, with the latest stable freesurfer release, 6.0. The recon-all process was being run on the sample_001.mgz file to test the installation, and ran for about 7 hours. Second, when I tried to use the -use-gpu flag, the process seems to be missing a library: [GHS\026278@vmcntdsktp10 fs_sample1]$ recon-all -subject sample001 -i ./sample-001.mgz -use-gpu -all Testing for CUDA device: /usr/local/freesurfer/bin/mri_em_register_cuda: error while loading shared libraries: libcudart.so.5.0: cannot open shared object file: No such file or directory Linux vmcntdsktp10 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sample001 exited with ERRORS at Sat Jun 22 10:05:12 EDT 2019 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting [GHS\026278@vmcntdsktp10 fs_sample1]$ Can you suggest workarounds for one or both of these errors? Thanks, John Warm regards, Please, note my new email address, john.absher(a)prismahealth.org John R. Absher, MD, FAAN Division of Neurology, Department of Medicine Prisma Health-Upstate 200 Patewood Drive, Suite 350B City, SC 29615 864-454-4500 (office) 864-350-6655 (mobile) 864-454-4505 (fax) Inspire health. Serve with compassion. Be the difference. ---------------------------------------------------------------------- CONFIDENTIALITY NOTICE This message is intended only for the use of 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, you are hereby notified that any dissemination, distribution, or copying of this communication is strictly prohibited by law. If you have received this communication in error, please notify me immediately.

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Post-doctoral Research Position at the Yale Alzheimer's Disease Research Unit
by Adam Mecca 22 Jun '19

22 Jun '19

External Email - Use Caution The Yale University Alzheimer’s Disease Research Unit and the Yale PET Center has an opening for a highly qualified and motivated individual at the post-doctoral level to work on research involving the development of analysis techniques integrating human imaging data including PET and fMRI for NIH-funded studies and clinical trials in Alzheimer’s disease. Applicants must have obtained a Ph.D. in neuroscience, biomedical engineering, or a related field. Qualifications: Strong experimental, analytical, and programming skills are essential. Experience in fMRI, image analysis, algorithm development, and biological applications is highly desirable. The selected candidate will work under the direction of Drs. Christopher van Dyck and Adam Mecca. The successful candidate should have a Ph.D. or an M.D./Ph.D. with at least three years of experience in fMRI and/or PET imaging. Application Instructions: Interested individuals should email a CV to adam.mecca(a)yale.edu. Adam Mecca, M.D. Ph.D. Yale School of Medicine, Department of Psychiatry Geriatric Psychiatry and the Alzheimer's Disease Research Unit Tel: (203) 764-8100 Fax: (203) 764-8111

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WARNING: no voxels in AR1 computation
by Francesca Pentimalli 22 Jun '19

22 Jun '19

External Email - Use Caution Dear FreeSurfer experts, I am trying to run *mri_glmfit *on a series of concatenated volumes. mri_glmfit --y $SUBJECTS_DIR/concat/new_glm_input.mgh --fsgd Qdec/qdec.fsgd --mask fsaverage/label_volume/mask.mgz --glmdir glm_output --C $SUBJECTS_DIR/qdec/Untitled/contrasts/lh-Avg-Intercept-volume.mat I am getting the following : WARNING: no voxels in AR1 computation. I am guessing that this is due to the results of the analysis, or is this potentially a problem with the specific contrast used? If so, what should be kept in mind while creating new contrasts? Regards, Francesca *Francesca Pentimalli Biscaretti di Ruffia * Via S. Eufemia 3, 35121 Padova (Italy) Mobile: +39 3483862788 francesca.pentimallibiscarettidiruffia(a)studenti.unipd.it fpentimallibdr(a)gmail.com fpenti(a)mit.edu fpbdr(a)bu.edu

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Group mean tracer uptake images
by Boris Rauchmann 22 Jun '19

22 Jun '19

External Email - Use Caution Dear FS community, how can I create group mean tracer uptake images in surface space with FS from several overlays? Thanks, Boris Von meinem iPhone gesendet

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aseg annotation2label
by Sam W. 22 Jun '19

22 Jun '19

External Email - Use Caution Hello, I'm trying to create label files of the aparc+aseg ROIs but cannot find the aseg annotations. The ?h.aparc.annot does not contain subcortical regions that exist in the aparc+aseg.mgz volume. Is there a way to apply mri_annotation2label to aseg labels? Thanks! Best regards, Sam

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Within-subject vertexwise correlation
by Matthieu Vanhoutte 22 Jun '19

22 Jun '19

External Email - Use Caution Dear FS experts, I would like to compute within-subject correlation between two modalities based on vertexwise maps in fsaverage space. I wonder whether I have to smooth the normalized surface-based maps before computing vertexwise within-subject correlation? I have noted that smoothing surface maps before computing correlation increases the output correlation value. Thanks for your lights. Best, Matthieu

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Applying Pial edits to Longitudinal
by Sierra Ann Jarvis 22 Jun '19

22 Jun '19

External Email - Use Caution Hello Freesurfers, I am trying to apply Pial edits to my longitudinal time point. I have tried the command, recon-all -long C002d.long.C002.base/ C002.base -mprage -3T -norm2-b 20 -norm2-n 5 -autorecon2 -autorecon3 But receive the error, Unmatched “. I am using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Do you know what could be the reason for this? Sierra

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Advantage of having skull for longitudinal processing?
by Adam Martersteck 22 Jun '19

22 Jun '19

External Email - Use Caution Hi Freesurfer team, I'm thinking of pre-skullstrip'ing my brains prior to being input into FreeSurfer. My fear was this information in the skull might be useful during mri_robust_register or mri_robust_template for longitudinal analyses: Martin discusses this in his Freesurfer workshop talk at 9 minutes in (youtube: http://www.youtube.com/watch?v=vxJODPBLd3M&t=9m21s) where the heatmap covers parts of the skull and the Freesurfer wiki which mentions that the Tukey biweight will deweight regions of noise like tongue/eye/neck differences. But it appears the longitudinal stream registers everything on each cross-sectional's norm.mgz to create the fused norm -- which is skullstripped and missing neck/tongue/eyes/skull already. Am I missing something? Is it alright if my T1.mgz, rawavg.mgz, orig.mgz, etc. do not have a skull for longitudinal processing? Thanks, Adam

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translations and rotations from an affine transform matrix
by Pfannmoeller, Joerg Peter 21 Jun '19

21 Jun '19

Hello, is there a tool to extract the translations and rotations from an affine transform matrix (register.dof6.dat)? Best Joerg

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examining between group differences using DODS
by Avi Gharehgazlou 21 Jun '19

21 Jun '19

External Email - Use Caution Hi experts, I want to examine between-group differences in LGI controlling for age, sex and surface area (all except sex demeaned). To do so, I ran the DODS model on QDEC selecting: - “diagnosis” and “sex” as discrete (fixed factors) - “age” and “surface area” as nuisance factors - And selected this question à “Does the average pial_lgi, accounting for sex, differ between TD and NDD? Nuissance factors: Age Surface area” 1) I wanted to ask you what the significant results from the above analysis means? I was under the impression that the significant clusters represent clusters where there are significant group differences in LGI while controlling for age, surface area and sex. But I am confused because I know from previous threads that you recommend to run DODS to check for interactions first, and if there is no interaction to then run DOSS to see differences between groups. So: 2) Do my significant results mean that I have an interaction between diagnosis and sex OR diagnosis and age OR diagnosis and surface area? 3) Considering that I have an interaction, how do I now examine between-group differences in LGI? Is what I have done (through the DODS model) correct? I'd really appreciate your help, Thanks so much, Avi

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