Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Ubuntu VM Developer Password request?
by Dean, Owen 12 Mar '22

12 Mar '22

External Email - Use Caution Dear the Freesurfer Team, I am writing to request the Ubuntu VM Developer password for the Freesurfer version? Thank you! Sincerely, Owen Owen Dean University of Rochester School of Medicine and Dentistry he, him, his

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Research Assistant Position Available at the Ohio State University Department of Psychology (MINDSET Lab)
by Shell, Abby 11 Mar '22

11 Mar '22

External Email - Use Caution Research Assistant Position Available at the Ohio State University Department of Psychology. Looking for someone with prior experience in MRI. Familiar with structural preprocessing and/or other modalities. Comfortable with coding. More details below and at the following link: https://secure-web.cisco.com/1Ew4JKXvwVU2ux2rMVVo8xQZAYM4_HBG8Cs5i1y-L-yuc_… The MINDSET lab Department of Psychology, within the College of Arts and Sciences, seeks a Research Assistant 1-Social to join our team. The College of Arts and Sciences is the largest college and the academic heart of the university. The College hosts 81 majors. With 38 departments, 20+ world-class research centers, and more than 2,000 faculty and staff members, students have the unique opportunity to study with the best artists, scholars, and scientists in their field. The College values diversity and offers a supportive, open, and inclusive community. The MINDSET lab is directed by Dr. Jasmeet Hayes. The MINDSET lab studies relationships among physical and psychological trauma, cognition and the brain [using Magnetic Resonance Imaging (MRI) metrics]. We also examine neural correlates of memory in healthy and clinical populations. The Research Assistant 1 assists in the general coordination and conduct of research in the MINDSET lab, including administration of neuropsychological tests and/or questionnaires to young and older adults; recruits, screens, and schedules human subjects, including coordination of subject appointments (cognitive, MRI, and physical fitness assessments), subject payments, and submission of IRB amendments; assists with participant recruitment efforts between the laboratory and community partners; assists with research lab purchases and maintains lab supplies; assists with cognitive, MRI, and medical history data collection, including obtaining informed consent, cognitive testing (computer and paper and pencil based testing), MRI data acquisition, and record keeping; assists with cognitive and MRI data processing and analyses, including analyses of behavioral data and MRI data using openly available software like FSL, AFNI, or SPM and/or UNIX or MATLAB; supervises undergraduate research assistants. Position available for one year with the possibility of extension for additional years based on satisfactory performance and availability of funds. Required Education Bachelor's degree in psychology or related field or an equivalent combination of education and experience. [The Ohio State University] Abby Shell Research Assistant The MINDSET Lab Department of Psychology 1835 Neil Avenue, Columbus, OH 43210 6149497868 Office shell.73(a)buckeyemail.osu.edu<mailto:shell.73@osu.edu> / osu.edu<http://secure-web.cisco.com/17n3otLadud0JP4E4Ze6BBYSds4smQaxEvWETdy8i1BIt6g…> Pronouns: she/her/hers

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Re: [Freesurfer] SAMSEG Lesion images not written
by Cerri, Stefano 11 Mar '22

11 Mar '22

Hi Randy, "seg.mgz" is the "hard segmentation", with lesion labeled as 99. You have all the volumes in "samseg.stats". If you want segmentation maps (values between 0 and 1), you should add the flag --save-posteriors to run_samseg. They will be saved in the samseg output directory under the "posteriors" folder. You can get a lesion segmentation mask by binarizing the lesion probability map with mri_binarize. Best, Stefano Dear experts I was able to get SAMSEG --lesion to work on WSL (did not crash once I used float images instead of 16bit usign), but all that's being written out are listed below: Folder: D:\0007_Subjects-FS\T1T2-lesion-float\ Files: cost.txt gaussians.rescaled.txt mode01_bias_corrected.mgz mode01_bias_field.mgz mode01_scaling.txt mode02_bias_corrected.mgz mode02_bias_field.mgz mode02_scaling.txt samseg.stats samseg.talairach.lta sbtiv.stats seg.mgz template.lta template_coregistered.mgz template_transforms.mat Since this is the first time got --lesion to run, I have no idea what the output "should" be.? Shouldn't some sort "lesion mask" be written out? Thanks in advance for any insights/comments you might have -Randy XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX SNIPPET FROM THE END OF THE "SUCCESSFUL" SAMSEG --lesion run XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX run_samseg -o $SUBJECTS_DIR/T1T2-lesion-float -i o_ADNI_002_S_4654__MRI-m072_float.nii rT1_o_ADNI_002_S_4654__MRI-m072_FLAIR_float.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --threshold 0.7 .................................... .................................... Sample 44 times Sample 45 times Sample 46 times Sample 47 times Sample 48 times Sample 49 times Sample 50 times thresholding posterior of? Lesions with threshold: 0.7 Constructing image-to-world transform from header information (o_ADNI_002_S_4654__MRI-m072_float.nii) Read image: o_ADNI_002_S_4654__MRI-m072_float.nii using default intracranial structures to compute sbtiv measure run_samseg complete: 0:34:36.159030 daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$ .................................... YAY! .................................... XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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SAMSEG Lesion images not written
by daedalus39＠aol.com 10 Mar '22

10 Mar '22

External Email - Use Caution Dear experts I was able to get SAMSEG --lesion to work on WSL (did not crash once I used float images instead of 16bit usign), but all that's being written out are listed below: Folder: D:\0007_Subjects-FS\T1T2-lesion-float\ Files: cost.txt gaussians.rescaled.txt mode01_bias_corrected.mgz mode01_bias_field.mgz mode01_scaling.txt mode02_bias_corrected.mgz mode02_bias_field.mgz mode02_scaling.txt samseg.stats samseg.talairach.lta sbtiv.stats seg.mgz template.lta template_coregistered.mgz template_transforms.mat Since this is the first time got --lesion to run, I have no idea what the output "should" be. Shouldn't some sort "lesion mask" be written out? Thanks in advance for any insights/comments you might have -Randy XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX SNIPPET FROM THE END OF THE "SUCCESSFUL" SAMSEG --lesion run XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX run_samseg -o $SUBJECTS_DIR/T1T2-lesion-float -i o_ADNI_002_S_4654__MRI-m072_float.nii rT1_o_ADNI_002_S_4654__MRI-m072_FLAIR_float.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --threshold 0.7 .................................... .................................... Sample 44 times Sample 45 times Sample 46 times Sample 47 times Sample 48 times Sample 49 times Sample 50 times thresholding posterior of Lesions with threshold: 0.7 Constructing image-to-world transform from header information (o_ADNI_002_S_4654__MRI-m072_float.nii) Read image: o_ADNI_002_S_4654__MRI-m072_float.nii using default intracranial structures to compute sbtiv measure run_samseg complete: 0:34:36.159030 daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$ .................................... YAY! .................................... XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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SAMSEG Lesion images not written
by daedalus39＠aol.com 10 Mar '22

10 Mar '22

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Re: [Freesurfer] MACBOOK PRO M1 Monterey
by fsbuild 10 Mar '22

10 Mar '22

External Email - Use Caution Hello Zaenab, The package you highlighted, freesurfer-darwin-macOS-dev.pkg, is the one to install on the Mac to use the development build with the latest updates.  If you’ve run other Mac package installers, then the steps should be familiar to you when you install it.  I think you could also run the more stable 7.2.0 Freesurfer (with an installer named freesurfer-darwin-7.2.0-dev.pkg) if you are not using a 2nd monitor to display graphics with an M1 machine running MacOS Monterey. - R. On Mar 10, 2022, at 15:58, Dhari, Zaenab S <zaenab.dhari(a)gmail.com> wrote:       External Email - Use Caution        Hello,For downloading the development version of FS which package of theones available you recommend (attached screen shot), Since the newcomputer I have is Macbook Pro M1 Monterey ( brand new with no otherOS installed other than its built in MacOS), I am not sure howcompatible it with these Linux/Centos OS. I just have been readingpeople posts on random tech websites and it seems a bit tricky, anysuggestions will be much appreciated.Thanks<screen shot of versions.PNG>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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MACBOOK PRO M1 Monterey
by Dhari, Zaenab S 10 Mar '22

10 Mar '22

External Email - Use Caution Hello, For downloading the development version of FS which package of the ones available you recommend (attached screen shot), Since the new computer I have is Macbook Pro M1 Monterey ( brand new with no other OS installed other than its built in MacOS), I am not sure how compatible it with these Linux/Centos OS. I just have been reading people posts on random tech websites and it seems a bit tricky, any suggestions will be much appreciated. Thanks

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mri_glmfit error: MatrixMultiplyD(): m2 is null
by 정현우 10 Mar '22

10 Mar '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare cortical surface area among three groups while controlling for estimated total intracranial volume (eTIV), as described on the Surface Based Group Analysis tutorial ( https://secure-web.cisco.com/1A0QSPCwnovVVVsFNKDP8OXxiBFqZ78jELzRvCgQt7us3r… I ran the following command: mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir --eres-save Then I got the following error: gdfRead(): reading three_group_comparison.area.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 eTIV 1.53351e+06 139455 Class Size and Means of each Continuous Variable 1 0 42 1566070.5417 2 1 34 1515147.1360 3 2 15 1483959.5000 INFO: gd2mtx_method is dods Reading source surface /media/sjkim/hd2/subject_data/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65417.000000 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 7.2.0 cwd /media/sjkim/hd2/subject_data/glm cmdline mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir --eres-save sysname Linux hostname sjkim-System-Product-Name machine x86_64 user sjkim FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh logyflag 0 usedti 0 FSGD three_group_comparison.area.fsgd labelmask /media/sjkim/hd2/subject_data/fsaverage/label/lh.cortex.label maskinv 0 glmdir three_group_comparison.area.lh.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory three_group_comparison.area.lh.glmdir Loading y from /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to three_group_comparison.area.lh.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 833.575 Matrix condition is 1e+08 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 149953 voxels in mask Saving mask to three_group_comparison.area.lh.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74612.059149 DOF = 85 Starting fit and test Fit completed in 0.0373833 minutes Computing spatial AR1 on surface Residual: ar1mn=0.997826, ar1std=0.000886, gstd=8.674183, fwhm=20.426140 Writing results three_group_comparison.area maxvox sig=3.0263 F=7.57212 at index 107440 0 0 seed=1645215319 error: No such file or directory error: MatrixMultiplyD(): m2 is null break /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596 I used FreeSurfer version 7.2.0 and Ubuntu 20.04. I've searched the mail archives and similar errors have been reported in qdec, but I could not find any specific solution for this problem. Do you have any suggestions to solve this problem? Thank you in advance, Hyunwoo Jeong

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Re: [Freesurfer] recon-all permissions problems
by fsbuild 09 Mar '22

09 Mar '22

External Email - Use Caution Hello Giuseppe, Try the same command (with lowercase w) or use a+w and then enter your password, $ sudo chmod -R  a+w  $SUBJECTS_DIRPassword: … then test to see if it works to create a file there, i.e., it should not report permission denied ... $ touch $SUBJECTS_DIR/foo … then see if you can remove the file … $  rm  $SUBJECTS_DIR/foo If that works you should be OK. - R. On Mar 6, 2022, at 11:46, giuseppe messina <giusmex(a)gmail.com> wrote:        External Email - Use Caution        hi i am a neurosurgeon, and i am a newbie in freesurfer, nut i thin i installed it appropriately and the licence txt file is oki have a macbookpro 16 last generation with 32 gb of memorymy freesurfer version is 7.2.0the problem is that when i run recon-all ( in correct syntax) , permission issues appear; it seems that i dont have permissions to go ahead with the freesurfer.i also used ( as indicated in one of your tutorial ) the sudo chmod -R a+W $SUBJECTS_DIR command, but if i do so, a password is requested in the terminal.really, i dont know hot to solve this problem, please help me GiuseppeThank you again-- Giuseppe MessinaDept NeurosurgeryIstituto Nazionale Neurologico "Carlo Besta", MilanE-mail  giusmex@gmail.com_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Oracle VM - SSH
by fsbuild 09 Mar '22

09 Mar '22

External Email - Use Caution Hello Zoe, The VM is not setup out of the box with an IP address you can use to remotely login to from an outside machine.  It uses (or piggy-backs off) the existing network connection from the host machine.   This enables the VM to boot w/o needing to negotiate for a non-local IP address and it is also for security.  We don't know the policy for someone connecting a new (virtual or real physical) machine to the network the host machine is already using.  If you can remotely VNC into your host machine and see/use the desktop, then you can use the VM running on the desktop as just another application. There’s information available online about how setup a VirtualBox VM to be accessible from the outside, e.g., via ssh.   If you have IT support, you could ask them for help.  But it’s not really practical for us to support users configuring a machine to run on their local network. On Mar 9, 2022, at 14:44, Zoe O'Brien-Moran <zobrienmoran(a)cubresa.com> wrote:        External Email - Use Caution        Hello FS expertsI'm using freesurfer with the oracle VM and I need to SSH in from my host machine, I see that openSSH is installed on the VM, but haven't been able to get in. Does anyone have experience with/ advice for this?Thanks in advance Zoë_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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