Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

about Rahul Desikan
by Lilla Zollei 14 Jun '18

14 Jun '18

Hi All, Many of you might know Rahul personally from his time spent in Boston, at the Martinos Center and on Freesurfer (eg.: 'Desikan-Killiany' cortical atlas). The below is a great piece about his current struggles with ALS (and amazing work productivity): https://www.washingtonpost.com/news/national/wp/2018/06/13/feature/devastat… And here is a site where you can support his research: https://www.donorscure.org/project/project/?projectid=201b7e93-66d8-44a4-a1… Best, Lilla

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mri_vol2surf projection
by Tom Vanasse 14 Jun '18

14 Jun '18

External Email - Use Caution Hello, I wanted to confirm that I properly performed the mri_vol2surf command. I'm interested in projecting a z-score image (in Talairach space) to an average surface (fsaverage5), using a mid-gray projection fraction. mri_vol2surf --src ICA_split0000.nii.gz --regheader fsaverage5 --hemi lh --o ICA_split0000_lh.nii --projfrac 0.5 My --src volume has array size (80 x 96 x 70) with 2mm isotropic voxels in Talairach space. The command ran without error, but I wanted to be sure it is indeed the correct approach. Thanks, Tom Vanasse Thomas J. Vanasse Medical Physics PhD Candidate UT Health San Antonio Research Imaging Institute, Office 2.312

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Error during QDEC
by Seung-Gul Kang (강승걸) 14 Jun '18

14 Jun '18

This message contained a link to a web site whose IP address has recently been associated with malicious activity. Due to that activity, the site is not accessible from within the Partners Healthcare network. The link has been modified in the message below. If you feel this is an error, please contact the IS Service Desk and open a ticket with the network security - phs assignment group. IS Service Desk BWH 617-732-5927 BWFH 617-983-7454 BWH-RICS 617-525-0848 DFCI 617-632-3399 LCC 857-307-4150 MCL 781-416-8940 MGH 617-726-5085 NHP 617-643-2020 NSMC 978-354-2014 NWH 617-243-6001 PCPO 781-433-3757 PHH 617-726-0790 PHS 857-282-4357 SRN 617-952-5555 CDHC 413-582-50051 ********************************* External Email - Use Caution Dear Freesurfer experts, I see the error message when I perform QDEC. The error message is as below. Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/sgk cmdline mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat sysname Linux hostname localhost.localdomain machine x86_64 user sgk FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh logyflag 0 usedti 0 FSGD /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd labelmask /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label maskinv 0 glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /mnt/hgfs/share/suicide/qdec/LH_area_SSI Loading y from /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /mnt/hgfs/share/suicide/qdec/LH_area_SSI/Xg.dat Normalized matrix condition is 24522.5 Design matrix ------------------ 1.000 0.000 0.000 0.000 15.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000 21.000 0.000 0.000 0.000 149457.594 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 19.000 0.000 0.000 0.000 50.000 0.000 0.000 0.000 20.000 0.000 0.000 0.000 161540.203 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 7.000 0.000 0.000 0.000 55.000 0.000 0.000 0.000 26.000 0.000 0.000 0.000 167295.906 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 10.000 0.000 0.000 0.000 31.000 0.000 0.000 0.000 27.000 0.000 0.000 0.000 175241.703 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 15.000 0.000 0.000 0.000 59.000 0.000 0.000 0.000 23.000 0.000 0.000 0.000 165616.797 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 11.000 0.000 0.000 0.000 57.000 0.000 0.000 0.000 22.000 0.000 0.000 0.000 183255.594 0.000; 1.000 0.000 0.000 0.000 26.000 0.000 0.000 0.000 37.000 0.000 0.000 0.000 23.000 0.000 0.000 0.000 159212.203 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 14.000 0.000 0.000 0.000 50.000 0.000 0.000 0.000 22.000 0.000 0.000 0.000 170017.094 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 16.000 0.000 0.000 0.000 26.000 0.000 0.000 0.000 19.000 0.000 0.000 0.000 190217.906 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 39.000 0.000 0.000 0.000 19.000 0.000 0.000 0.000 156341.000 0.000; 1.000 0.000 0.000 0.000 18.000 0.000 0.000 0.000 49.000 0.000 0.000 0.000 32.000 0.000 0.000 0.000 168844.297 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 21.000 0.000 0.000 0.000 39.000 0.000 0.000 0.000 26.000 0.000 0.000 0.000 149945.406 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 11.000 0.000 0.000 0.000 39.000 0.000 0.000 0.000 22.000 0.000 0.000 0.000 166132.906 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 17.000 0.000 0.000 0.000 41.000 0.000 0.000 0.000 25.000 0.000 0.000 0.000 139924.406 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 27.000 0.000 0.000 0.000 45.000 0.000 0.000 0.000 34.000 0.000 0.000 0.000 133331.797 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 11.000 0.000 0.000 0.000 47.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000 164844.703 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 23.000 0.000 0.000 0.000 46.000 0.000 0.000 0.000 26.000 0.000 0.000 0.000 163024.203 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 31.000 0.000 0.000 0.000 42.000 0.000 0.000 0.000 33.000 0.000 0.000 0.000 140203.797 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 18.000 0.000 0.000 0.000 21.000 0.000 0.000 0.000 29.000 0.000 0.000 0.000 186282.297 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 18.000 0.000 0.000 0.000 21.000 0.000 0.000 0.000 17.000 0.000 0.000 0.000 171746.094; 0.000 1.000 0.000 0.000 0.000 17.000 0.000 0.000 0.000 34.000 0.000 0.000 0.000 15.000 0.000 0.000 0.000 145005.203 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 15.000 0.000 0.000 0.000 54.000 0.000 0.000 0.000 27.000 0.000 0.000 0.000 168633.203; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 17.000 0.000 0.000 0.000 27.000 0.000 0.000 0.000 20.000 0.000 0.000 0.000 186731.297; 0.000 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 61.000 0.000 0.000 0.000 28.000 0.000 0.000 0.000 154627.500 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 10.000 0.000 0.000 0.000 44.000 0.000 0.000 0.000 22.000 0.000 0.000 0.000 154626.297 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 4.000 0.000 0.000 0.000 59.000 0.000 0.000 0.000 20.000 0.000 0.000 0.000 177918.500; 0.000 1.000 0.000 0.000 0.000 4.000 0.000 0.000 0.000 56.000 0.000 0.000 0.000 27.000 0.000 0.000 0.000 157687.797 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 8.000 0.000 0.000 0.000 58.000 0.000 0.000 0.000 32.000 0.000 0.000 0.000 173899.094; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 21.000 0.000 0.000 0.000 20.000 0.000 0.000 0.000 18.000 0.000 0.000 0.000 175980.500; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 59.000 0.000 0.000 0.000 28.000 0.000 0.000 0.000 162526.703 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 2.000 0.000 0.000 0.000 37.000 0.000 0.000 0.000 20.000 0.000 0.000 0.000 198622.797; 0.000 1.000 0.000 0.000 0.000 3.000 0.000 0.000 0.000 32.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000 157633.906 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 17.000 0.000 0.000 0.000 21.000 0.000 0.000 0.000 21.000 0.000 0.000 0.000 164236.297; 0.000 1.000 0.000 0.000 0.000 22.000 0.000 0.000 0.000 46.000 0.000 0.000 0.000 23.000 0.000 0.000 0.000 144559.703 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 7.000 0.000 0.000 0.000 32.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000 156151.500 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.000 0.000 0.000 0.000 46.000 0.000 0.000 0.000 27.000 0.000 0.000 0.000 154306.406; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 19.000 0.000 0.000 0.000 20.000 0.000 0.000 0.000 188334.203; 0.000 1.000 0.000 0.000 0.000 20.000 0.000 0.000 0.000 55.000 0.000 0.000 0.000 26.000 0.000 0.000 0.000 134977.406 0.000 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 24522.5 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat --C /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat I also attach the error message. Could you tell me how I can fix this problem? I am looking forward to receiving your reply. Best regards, Seung-Gul *S**eung-Gul Kang, M.D., Ph.D. * Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center 연구부학장. Dean, Department of Research Affairs; Gachon University College of Medicine 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea ᐧ

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Is longitudinal lme analysis invalid when it doesn't converge?
by Knut J Bjuland 14 Jun '18

14 Jun '18

External Email - Use Caution Dear FreeSurfer experts I ran the lme scripts in FreeSurfer on FA-data (dMRI). The script doesn't crash but 70% of the models yield this message: "Algorithm does not converge after 50 iterations!!!" Does that mean the results (pvalues) are invalid? I would appreciate any input on this topic. Thank you! Best regards Knut Jørgen Bjuland

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Post-doc position in neuroimaging pain research
by Lussier,Desiree 13 Jun '18

13 Jun '18

External Email - Use Caution Postdoctoral Research Positions in Neuroimaging Pain Research Pain Research & Intervention Center of Excellence University of Florida, Gainesville, Florida Dr. Yenisel Cruz-Almeida and Dr. Natalie Ebner are currently accepting applications for postdoctoral research fellows and/or research associates to advance research on cognitive neuroscience and chronic pain using multi-modal brain neuroimaging. While the primary candidate will work on an NIH funded position to support neuroimaging aspects of characterizing chronic pain and treatment effects in older individuals, the candidate will be directly interacting with a large group of interdisciplinary UF researchers involved with multiple studies involving acute and chronic pain including: real-time fMRI control of brain activity, neuroimaging-based pain biomarkers, individual difference in pain and cognitive/affective dimensions of pain across a number of departments and institutes. Qualifications: Applicants should have (or anticipate having) a Ph.D. and research background in Cognitive Neuroscience, Neurophysiology, Neuropsychology, or related fields. Individuals with backgrounds in Electrical Engineering, Physics, Mathematics, Computer Science or similar fields and a strong interest/background in Psychology and human neuroimaging are also encouraged to apply. Applicants should be experienced at designing and implementing cognitive neuroscience experiments. Preference will be given to candidates who have experience with conducting fMRI studies, working with MRI scanners, processing MRI and fMRI datasets, and running neuroimaging data analysis using software packages, such as Matlab, SPM, FSL EPrime, and AFNI. Applicants should also possess strong interpersonal skills and be able to work independently and in groups. Application Process: Applications are accepted on an ongoing basis. To apply, potential candidates should submit: - Curriculum Vitae - Personal Statement describing research interests and goals - Three letters of recommendation Address applications or inquiries to: Yenisel Cruz-Almeida, M.S.P.H., Ph.D.; cryeni(a)ufl.edu And Natalie Ebner, Ph.D.; natalie.ebner(a)ufl.edu Thank you, Désirée Lussier, MS Graduate Student Department of Psychology University of Florida [1509730522218_github]<https://github.com/dllussier> [1509730529145_linkedin-icon-14small.png] <https://www.linkedin.com/in/desiree-lussier/> [1509730538655_twitter-icon] <https://twitter.com/desiree_lussier> <http://www.psych.ufl.edu/ebnerlab/> <https://people.clas.ufl.edu/desireelussier/> [1509730546740_website] <https://people.clas.ufl.edu/desireelussier/>

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Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 13 Jun '18

13 Jun '18

External Email - Use Caution Thank you for your response! Just to clarify: if my input is volume, does the cache.th20.abs.sig.y.ocn.dat contain the average unadjusted volume values for each participant in each significant cluster? Since the file I just mentioned contains the average values, I used mri_segstats to calculate total volume for the cluster. mri_segstats --i <pathway to rh.volume.Study.10.mgh> --seg cache.th20.abs.sig.ocn.mgh --excludeid 0 --sumwf ClusterVolumeValues.dat However, this just calculates the sum of the unadjusted values in the cluster. I guess my main question is, is there a way to extract or calculate the adjusted values for each participant in each cluster after accounting for covariates (age, sex, and ICV)? --- Jessica ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Wednesday, June 13, 2018 11:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 172, Issue 21 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: crypt_gkey = (null) (Dicamillo, Robert) 2. tractstats2table - all tracts for multiple subjects (Alexopoulos, Dimitrios) 3. Re: tractstats2table - all tracts for multiple subjects (Yendiki, Anastasia) 4. dwi.ecclog file (Daumail, Loic Jean) 5. Re: dwi.ecclog file (Yendiki, Anastasia) 6. Re: tractstats2table - all tracts for multiple subjects (Alexopoulos, Dimitrios) 7. Re: Missing Control Points and QATools (Matthew Peverill) 8. Re: Missing Control Points and QATools (Bruce Fischl) 9. Re: Extract the entorhinal cortex as a mask (Erik O'Hanlon) 10. PREDOCTORAL POSITION at King's College London (Walter Hugo Lopez Pinaya) 11. Re: Extract the entorhinal cortex as a mask (Bruce Fischl) 12. Re: "WARNING: Image geometries differ across time" upon running base step of longitudinal pipeline (Tudor Popescu) 13. Re: dwi.ecclog file (Daumail, Loic Jean) 14. Re: Running qcache on old FS data (Douglas N. Greve) 15. Re: Group Analysis Covariates (Douglas N. Greve) 16. Re: Error during QDEC (Douglas N. Greve) ---------------------------------------------------------------------- Message: 1 Date: Tue, 12 Jun 2018 19:52:52 +0000 From: "Dicamillo, Robert" <RDICAMILLO(a)mgh.harvard.edu> Subject: Re: [Freesurfer] crypt_gkey = (null) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <5024346D-6C53-4E0F-8189-FAAE089D2108(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hello Aaron, The build timestamp from the output below shows mri_convert is from 8/2014. When I look at the build timestamp on our stable 5.3 version of mri_convert I see it is from 5/2013. So the version that you listed is about 1 year newer than the 5.3 release I can see. It is possible that someone downloaded a daily/dev build of freesurfer at that time. You might want to consider running the latest 6.0 release of Freesurfer (released in January 2017), which should be fine on CentOS 7. It can be downloaded from, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall I also suggest that you start out in a default/clean shell, set FREESURFER_HOME, and then source the setup script for linux, You can see the instructions on that same web page under ?Setup and Configuration?. The setup steps should work for version 5 or 6. - rob On Jun 12, 2018, at 2:43 PM, Aaron Tanenbaum <aaron.b.tanenbaum(a)gmail.com<mailto:aaron.b.tanenbaum@gmail.com>> wrote: External Email - Use Caution I checked my system is not encrypted. I had someone else run the command on the same machine. It worked for them. So I changed my BASH environment to a default environment. I still get the same error. I tried this again but with a different FreeSurfer 5.3. turns out the one I was using has been altered version of FreeSurfer. I do not know how it was altered. It worked. so it has to do with the altered FreeSurfer. I ran the command mri_convert -version on both FreeSurfer. for the unaltered i get the out put mri_convert -version stable5 altered version i get mri_convert -version dev build (use --all-info flag for full version info) with this output i type in mri_convert --all-info mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/12-18:32:17-GMT BuildTimeStamp: Aug 22 2014 21:04:47 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: tanenbauma Machine: rocky Platform: Linux PlatformVersion: 3.10.0-862.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Wondering is this version of mri_convert a developmental version? Also both version are the CentOS 6 build. On Tue, Jun 12, 2018 at 1:01 PM Dicamillo, Robert <RDICAMILLO(a)mgh.harvard.edu<mailto:RDICAMILLO@mgh.harvard.edu>> wrote: Hello Aaron, You could check to see if the CentOS 7 system is using disk encryption, e.g., if the following command return 1, then it would mean encryption is in use (which can be an issue with FreeSurfer). $ cat /proc/sys/crypto/fips_enabled If it returns zero, it could be an issue with a system library like glibc on CentOS 7.5 (that does not happen on older versions of CentOS). Either way, this is not your doing ;-) On Jun 12, 2018, at 11:51 AM, Aaron Tanenbaum <aaron.b.tanenbaum(a)gmail.com<mailto:aaron.b.tanenbaum@gmail.com>> wrote: External Email - Use Caution I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3. When i get to the part where MRI_convert is creating the the orig001.mgz its gives me a segmentation fault. if i run this on a centos 6 system it works fine. below is the output of the program. /data/gizmo/data1/freesurfer5.3/bin/mri_convert /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm /data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm... crypt_gkey = (null) Segmentation fault (core dumped) Did I do anything wrong? _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Postdoctoral Fellowship in Spinal Cord and Parkinson's Disease
by Arnaud Boré 13 Jun '18

13 Jun '18

External Email - Use Caution *Postdoctoral Fellowship in Spinal Cord and Parkinson's Disease* We are looking to recruit a post-doctoral fellow in Dr. Julien Doyon’s *Motor Learning and Plasticity Laboratory*, at McGill University. The suitable candidate will join a team of post-doctoral fellows and PhD students who are conducting neuroimaging research in motor learning, both fundamental and clinical. For the current job opening, we seek to recruit a post-doctoral fellow who will *conduct neuroimaging and behavioral studies on healthy individuals and Parkinson’s Disease (PD) patients*. These studies are part of a research program aiming to characterize motor learning related plasticity in both brain and spinal cord, as well as to identify neuronal correlates of early stages of PD at both spinal and supra-spinal levels. The position is based at the Montreal Neurological Institute (MNI). The ideal candidate is expected to take the lead in regards to the methodological aspects of the study, addressing specifically the challenges related to the functional neuroimaging of the spinal cord, and to the analysis of complex data sets. The fellow will be involved in all stages of the research projects, from experimental design to data analysis and manuscript writing. The following requirements are mandatory: - PhD degree in neuroscience or a related field; - Experience with functional neuroimaging in human participants and with neuroimaging data analysis techniques and software (i.e. SPM, FSL or similar); - Ability to work independently and to collaborate with other team members; - Excellent organizational and social skills, especially when dealing with patient participants; - Established publication record attesting the above-mentioned requirements; - Good English proficiency (especially scientific writing and oral communication). The following requirements are assets: - Experience with spinal cord imaging; - Experience with multivariate data analysis approaches as implemented in established neuroimaging data analysis software; - Good proficiency with programming (such as Python or Matlab); - French proficiency; - Research experience with PD patients (or other movement-related disorders); - Availability to start as soon as possible. If you are interested in this position, please send your CV, a cover letter and the contact information of two individuals who can provide references at the following e-mail address: *francine.belanger(a)mcgill.ca <francine.belanger(a)criugm.qc.ca>*

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Re: [Freesurfer] hippocampus subfields and manual editing
by Iglesias Gonzalez, Eugenio 13 Jun '18

13 Jun '18

External Email - Use Caution Hi Lara, A little trick you can do (it shouldn’t be too hard to implement in Matlab with the functions in $FREESURFER_HOME/matlab) For each subject: 1. make a copy of aseg.mgz 2. create a binary mask for your edited hippocampi. 3. in aseg.mgz, replace each voxel labeled as hippo by the label of the closest, non-hippocampal structure. 4. Paint your hippocampi from step 2 on the hippocampal-less aseg. I hope this helps, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 13/06/2018, 17:18, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Lara Foland-Ross" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of lfoland(a)stanford.edu> wrote: External Email - Use Caution Hello, I am running an analysis of hippocampus volume on a set of T1-weighted scans with 1mm^3 isotropic resolution. Due to flow and other artifacts, a moderate degree of manual editing was required to correct the boundaries of each subject's hippocampus. Final volumes of manually edited hippocampi were submitted to a repeated measures ANOVA which showed a significant main effect of diagnosis on the overall size of this structure (controlling for age and TBV). We recently submitted this paper and just received a request from a reviewer that asked that we run a subfield analysis on these data to better understand the regions driving this overall effect. What I'd like to know is: would the subfield approach *not* be recommended on this dataset considering that artifacts necessitated a good deal of manual intervention for the entire region? Second, if it a subfield approach *is* okay to run on these data, how can I feed in my manually edited volumes to ensure that the corrected segmentations of the entire hippocampus is used during subfield creation? thanks very much in advance! Lara Lara Foland-Ross, Ph.D. Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 _______________________________________________ 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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hippocampus subfields and manual editing
by Lara Foland-Ross 13 Jun '18

13 Jun '18

External Email - Use Caution Hello, I am running an analysis of hippocampus volume on a set of T1-weighted scans with 1mm^3 isotropic resolution. Due to flow and other artifacts, a moderate degree of manual editing was required to correct the boundaries of each subject's hippocampus. Final volumes of manually edited hippocampi were submitted to a repeated measures ANOVA which showed a significant main effect of diagnosis on the overall size of this structure (controlling for age and TBV). We recently submitted this paper and just received a request from a reviewer that asked that we run a subfield analysis on these data to better understand the regions driving this overall effect. What I'd like to know is: would the subfield approach *not* be recommended on this dataset considering that artifacts necessitated a good deal of manual intervention for the entire region? Second, if it a subfield approach *is* okay to run on these data, how can I feed in my manually edited volumes to ensure that the corrected segmentations of the entire hippocampus is used during subfield creation? thanks very much in advance! Lara Lara Foland-Ross, Ph.D. Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

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Group Analysis Covariates
by Hua, Jessica 13 Jun '18

13 Jun '18

External Email - Use Caution Dear Freesurfer Experts: I analyzed my data following the guidelines on the FSL Tutorial/Group Analysis page . I am trying to plot the adjusted values (covariates: age, sex, and ICV) for the significant clusters for each of my participants. I set up the contrast to test group differences. So testing whether there is a difference between groups regressing out the effects of sex, age, and ICV. Contrasts created were [1 -1 0 0 0 0 0 0] and [-1 1 0 0 0 0 0 0]. I then extracted values from this file (cache.th20.abs.sig.y.ocn.dat; i.e., the average value of each subject in each cluster) into my dataset. I believe these are the unadjusted values, correct? I calculated total volume and total surface area by multiplying these values by the total number of vertices in each cluster. To adjust for covariates, I ran a regression with the ExtractedClusterValues as the DV and Group, Sex, Age, and ICV as predictors. Looking at the output, there was no significant effect of group (p = .769; whereas in FreeSurfer the cluster-wise p < .001). Also when I plotted the predicted values adjusting for covariates, the means between the groups were very similar. Why am I getting a p = .769 when I adjust for covariates, but FreeSurfer has a cluster-wise p < .001? Or is there a way to calculate adjusted values in FreeSurfer? Best, Jessica

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