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30132 discussions

Unanswered question regarding including covariates in the fsgd file and the contrast matrix
by Basavaraju, Rakshathi 24 Jun '19

24 Jun '19

External Email - Use Caution Hi all FS users, I have the basic doubt of including age and gender as co-variates for a cortical thickness comparison between 2 groups. I read extensively many mails answering these questions but still could not get a satisfactory answer for the question. As I have 2 discrete variables i.e. Group with 2 levels and gender with 2 levels and one continuous variable of age my contrast matrix should be like this: [0 0 0 0 0 0 0 0] which is [malegroup1 femalegroup1 malegroup2 femalegroup2 age.malegroup1 age.femalegroup1 age.malegroup2 age.femalegroup2] I understood that if I have to test the effect of only the groups my contrast matrix should be: [0.5 0.5 -0.5 -0.5 0 0 0 0] What should be my contrast matrix if I have to include age and gender as covariates respectively? I know gender cannot be included as columns of 1s and 0s by my reading of previous mails. In one of the mail I read that if we want to test for interaction of group and gender (disregarding effect of age) the contrast matrix file should be: [0.5 -0.5 -0.5 0.5 0 0 0 0] But is testing for gender as a covariate same as testing group*gender interaction? I do not feel so. Hence requesting you all to throw some clarity on this. If this is not the way to study gender as a covariate how else should the contrast matrix be written? And regarding age should it be four 0.5s for the last 4 columns of the matrix if we want to study age as a covariate? Kindly let know. Finally I want a contrast matrix that studies the group differences in cortical thickness covarying for the effect of age and gender. Kindly help me. Thanks, Dr. Rakshathi Basavaraju (MD Psychiatry) Postdoctoral Research Scientist Taub Institute Columbia University Irving Medical Centre 622 West, 168th Street, New York - 10032 E-Mail: rb3419(a)cumc.columbia.edu<mailto:rb3419@cumc.columbia.edu> http://www.wellcomedbt.org/fellowsprofile/dr-rakshathi-basavaraju-288

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I have a question for "matlabruntime"
by Gwang-Won Kim 24 Jun '19

24 Jun '19

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(no subject)
by fsbuild 23 Jun '19

23 Jun '19

External Email - Use Caution Hello John, You might be able to tell from the log what directory recon-all was cd'd into when the creation of the soft link failed.  You could try to cd there as your userid (which I assume you used to run recon-all), and see if you can manually create any soft link there.  if you cannot do so, there could be a problem with the directory permissions.  The uersid running recon-all should have permission to read, write, and execute on subdirectories which typically means the permission on them is set to be 755. While do not officially support cuda, I would first check to see you have the cuda libraries installed on you system.  You could do a search under /usr to see if you have it, e.g. $ sudo find /usr -name "libcudart*" - or with the package tools, look to see if any nvidia or cuda packages are installed,  e.g., $ rpm -qa | grep -i nvid $ rpm -qa | grep -i cuda If you don't find a libcudart.so.5 installed, then I think you will need to install rev 7.5 of the cuda tools on your system as that should be the version with libcudart.so.5 - R. John Absher June 22, 2019 at 22:28 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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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question for preprocessing
by ping cao 23 Jun '19

23 Jun '19

External Email - Use Caution Dear expert， Thank you for reading! I want to do these four pre-processing steps: 1. Re-sampling each MR image to 256*256*256; 2. Using the N3 algorithm for intensity inhomogeneity correction; 3. Skull stripping; 4. Removing the cerebellum. Does " *recon-all"* do all the above 4 steps automatically? If so, which file is just finished with these four steps? If not, how can I do these steps? Your help is greatly appreciated. Best, ping

3 3

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

2 1

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

2 1

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

2 1

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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