Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

problem with mri_surfcluster
by Barletta, Valeria 21 May '19

21 May '19

Dear Freesurfers, I am trying to obtain clusters of vertices whit a certain value over a threshold inside a lesion mask projected to the surface, with the command: mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask lh.surf_magn_CL02_fwhm1.mgh --thmax 49.95807 --thmin 1 --sign pos --minarea 0.01 --sum summary.txt But I obtain this result saying there are no vertices in my mask. thsign = pos, id = 1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = lh srcid = /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/CME_all/lh.MS075_R01_07_R1year.subjspace.mgh srcsubjid = MS075_R01_07_R1year srcsurf = lh.pial srcframe = 0 thsign = pos thmin = 1 thmax = 49.9581 fdr = -1 minarea = 0.01 xfmfile = talairach.xfm nth = -1 sumfile = /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/SINGLE_LESION/MS075_R01_07_R1year/summary.txt subjectsdir = /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3 FixMNI = 1 Found 0 vertices in mask Can you help me figure out why? Thanks, Vale

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Mri glmfit sim error
by Amrita Bedi 21 May '19

21 May '19

External Email - Use Caution ---------- Forwarded message ---------- From: *abedi000(a)citymail.cuny.edu <abedi000(a)citymail.cuny.edu>* < abedi000(a)citymail.cuny.edu> Date: Tuesday, May 21, 2019 Subject: To: "amibedi273(a)gmail.com" <amibedi273(a)gmail.com> Hi Freesurfer developers, While running the mri glmfit sim command for a smoothing of 30 FWHM, I got the following error- Original mri_glmfit command line: cmdline mri_glmfit.bin --y lh.BINGE15.g2v1.30B.mgh --fsgd BINGE15.g2v1.txt dods --C BINGE.g2v1.group-x-LDH_age.mtx --surf fsaverage lh --cortex --glmdir lh.BINGE15_g2v1.group-x-LDH_age.30B.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 53.156463 ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/ cortex/fwhm53/abs/th13/mc-z.csd I researched on the Freesurfer wiki page and found Dr Greve answered a similar question saying-"When running mri_glmfit-sim, add --cache-dir /path/to/mult-comp-cor" but I dont understand. What is this path? Thank You! Best, Amrita

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Postdoctoral fellowship in cognitive neuroscience at UCSF
by Maria Luisa Mandelli 21 May '19

21 May '19

External Email - Use Caution The ALBA Language Neurobiology laboratory or the UCSF Memory and Aging Center has an open postdoctoral position in cognitive neuroscience. Directed by Dr. Maria Luisa Gorno Tempini, the ALBA lab conducts cutting-edge research on the cognitive and neural correlates of language and related cognitive functions across the life span. In particular, neurodegenerative as well as neurodevelopmental disorders, including frontotemporal dementia, primary progressive aphasia, and dyslexia, are used as clinical models. The postdoctoral fellow will contribute to ongoing experiments and pursue self-directed projects within the lab’s area of investigation. Working closely with the current members of the team, he/she will contribute to our empirical efforts to further our understanding of the neurobiology of language. The ideal candidate will have expertise in either cognitive neuroscience or neuroimaging (in particular understanding of, and experience with, fMRI data analysis). Excellent English (oral and written) and good communication skills are necessary. Strong computational and programming skills are preferred. Appropriate areas of doctoral training include, but are not limited to, cognitive neuroscience, psychology, and computer science. The successful candidate would join the multidisciplinary team of world-class neurologists, neuropsychologists, speech-language pathologists, engineers, and cognitive scientists working at the UCSF - Memory and Aging Center, the largest cognitive and behavioral neurology center in the United States. Cognitive neuroscience research will integrate our rich, multidisciplinary datasets to study the cognitive, clinical, anatomical, and neuropathological correlates of disease. To apply, please send a cover letter, a CV, and 3 names of potential references to elizabeth.weis(a)ucsf.edu Informal inquiries are most welcome. -- Maria Luisa Mandelli, PhD Associate Professional Researcher UCSF Department of Neurology 675 Nelson Rising Lane Mission Bay Campus San Francisco, CA 94158 phone (415) 353-9420 -- Maria Luisa Mandelli, PhD Associate Professional Researcher UCSF Department of Neurology 675 Nelson Rising Lane Mission Bay Campus San Francisco, CA 94158 phone (415) 353-9420

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Reminder: OHBM 2019 Brain-Art Competition is open for submissions! {Disarmed}
by Maria Luisa Mandelli 21 May '19

21 May '19

External Email - Use Caution The OHBM Brain-Art SIG <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.humanbrainmapping.…> 2019 Brain-Art Competition is open for submissions! This competition aims at fostering the dialog between art and science. We believe that the exchange of ideas and tools between these two disciplines encourages the development of novel approaches to scientific data visualization, and promotes the exploration of different perspectives on human brain structures and functions. Everyone is encouraged to submit original work(s)! There is no limit to the number of submissions per participant, and both team and single-person entries are welcome. All submitted pieces will be exhibited during the OHBM 2019 Annual Meeting in Rome <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.humanbrainmapping.…>. This year submissions will be accepted to the following categories *1. Erato: **2D *i.e., digital images such as drawings, photos, paintings. *2. Clio: **3D *i.e., sculptures and installations. Note that any 3D submission should be entered as a photo then shipped/brought to Rome. Please reach out to us should this be impossible. *3. Calliope: **1D *i.e., short texts (one-page maximum) with or without illustrations such as short fiction or poetry. *4. Terpsichore: real-time performance *i.e., any performative act (e.g. singing, dancing, live sketching, etc…). Please note that a one-page max description should be entered at time of submission, then the act should be performed during the conference. *5. Melpomene*: *failed attempt / bug / artifact* Key information: - Submission Deadline: *Friday, May 31st, 2019, midnight eastern time* - Award Notificaiton: Monday, June 10th, 2019 - Submission portal: https://www.neurobureau.org/brainart/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.neurobureau.org_br…> -- Maria Luisa Mandelli, PhD Associate Professional Researcher UCSF Department of Neurology 675 Nelson Rising Lane Mission Bay Campus San Francisco, CA 94158 phone (415) 353-9420

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Fixing of Morphometry Stats and Global Measure of Volume: Longitudinal analysis
by Diana Tordesillas-Gutiérrez 21 May '19

21 May '19

External Email - Use Caution Dear Freesurfer experts, I have a question about the bug in FreeSurfer v.6 in the global metrics computation: I have run my data through the longitudinal pipeline. I would like to know if my analysis have been affected (3T, voxel size 0.94) and I have to rerun the whole analysis in case they have. Thank you! Diana -- -------------------------------------------------------- Diana Tordesillas Gutiérrez, PhD Neuroimaging Unit IDIVAL IDIVAL Building Avda. Cardenal Herrera Oria s/n 39011 Santander Spain Tel. +34 942202677 diana.tordesillas(a)idival.org diana.tordesillas(a)gmail.com CIBERSAM G26 ----------------------------------------------------------

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Moving data files
by Mingzhu Hou 20 May '19

20 May '19

External Email - Use Caution Dear Freesurfer team / community, This is a very basic and general question. I am currently setting up for a team in our lab to use the Freesurfer automated pipeline for thickness / volumetric measures on hundreds of adult brains. As there will be around 7 people working on these data (each working on different subsets of the data), I am planning to set up different working directories for each researcher’s subset of subjects to avoid possible confusion / overwriting etc. for the initial recon, manual editing and re-recon. Once happy with the re-recon, I plan for all individual S folders to be moved to one general data folder for further analysis. I am just concerned that moving S folders between initial individual processing/analysis and further group analyses will cause problems if, say, there is directory information embedded within any of the files during initial processing. Does anyone know if moving these files in this way might cause problems at some point, or is it advised to keep individual S folders in the same directory throughout? Thanks in advance for your help. Best, Mingzhu

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Re: [Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6
by fsbuild 20 May '19

20 May '19

External Email - Use Caution Hello Caspar, So are you saying that if you run directly from the terminal in bash (or maybe in csh with % sign as prompt) $ mri_convert -i inputvolume.mgz --out_orientation LPS -iis .5 -ijs .5 -iks .5 -vs 1.2 1.2 1.2 - that the command works, but it does not work when run from within a csh script ? If you are getting different results from running commands in the terminal environment/shell compared to when the same command runs in a script, there must be something different between the terminal and the script shell environment, e.g. LD_LIBRARY_PATRH, PATH, or something getting set differently. I would try and reproduce the shell environment variable settings that work from the terminal in the csh script. You could try explicitly running the csh script with -xf as arguments (prints out what is getting executed and bypasses any startup settings) to see if it works differently.   You can replace foo.csh with your script name below. $ csh -xf  foo.csh Another useful thing to do is to look at all the environment variables getting set in the terminal window where the command works, via $ env | sort - and compare that with what you see the csh script sets in the output of “csh -xf foo.csh”.  You can put an “env | sort” command in the csh script just before the mri_convert command runs to see the environment (and then compare it to the output of :”env | sort” in the terminal window where the command works).  - R.         External Email - Use CautionHi!Unfortunately, it turns out that downgrading glibc does not solve this issue, neither with .14 nor with .15 versions.Doug, we are calling mri_convert from a csh script, with the following options:mri_convert -i inputvolume.mgz \-o outputvolume.nii.gz \--out_orientation LPS \-iis .5 -ijs .5 -iks .5 \-vs 1.2 1.2 1.2We then simply get segmentation fault (core dumped).It seems to work when we run the same command directly in the terminal.CasparAm Do., 16. Mai 2019 um 23:10 Uhr schrieb Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>:   Can you send the command line and full terminal output?   On 5/16/19 5:17 AM, Caspar M. Schwiedrzik wrote:        External Email - Use CautionHi!We are getting segmentation fault (core dumped) error when trying torun mri_convert on NIFTI files. This is running Freesurfer v5.3 onCentos6, specifically v1.179.2.7 of mri_convert.I suspect that this has to do with libcrypt incompatibilitiesdescribed for other operating systems , e.g., here:   https://urldefense.proofpoint.com/v2/url?u=https-3A_… in the known issues list of v5.3. here   https://urldefense.proofpoint.com/v2/url?u=https-3A__… have libcrypt version 2.17 installed and do not have access tolibcrypt-2.14.1.so <http://libcrypt-2..14.1.so>   <https://urldefense.proofpoint.com/v2/url?u=http-3A__libcrypt-2D2.14.1.so&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s&s=oWqfVu5YGSWScZMw3Ypfdy53osHoNywLPtAffB75oR8&e=>.Is there a way to get libcrypt-2.14.1.so   <http://libcrypt-2.14.1.so> … you or is there another known workaround (other then   updating toFreesurfer 6)?Thank you very much! Caspar_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu   <mailto:Freesurfer@nmr.mgh.harvard.edu>   https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s&s=HKE_BsPSCQQGF6or1qTbQw7OmHSzKd1zDxWDvkVFR6k&e=   _______________________________________________   Freesurfer mailing list   Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>   https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s&s=HKE_BsPSCQQGF6or1qTbQw7OmHSzKd1zDxWDvkVFR6k&e=<Attached Message Part.txt>

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mris_label2annot empty Annot
by Michal Tanzer 20 May '19

20 May '19

External Email - Use Caution Dear Freesurfer experts, I am having some difficulties in creating annot file for specific ROIs using the 2009atlas. When I am using this command, it saves the annot but I am getting empty files. Using the same command with the aparc.annot file and different ROIs seems fine, so I am not sure what is the problem. mris_label2annot --s fsaverage --h lh --ctab label/aparc.annot.a2009s.ctab --a myaprac--l dir/lh.G_insular_short.label --l dir/lh.G_Ins_lg&S_cent_ins.label --debug Thank you for your help, Kind regards, Michal -- Michal Tanzer, PhD Postdoctoral fellow; Clinical Psychologist. Research Department of Clinical, Educational and Health Psychology, University College London, United Kingdom

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mkanalysis-sess refeventdur
by Nasiriavanaki, Zahra 20 May '19

20 May '19

Hi Freesurfer experts I am making an analysis in Freesurfer version 6 and I have a question about the "refeventdur" in mkanalysis-sess command. My stimulus duration is 16 seconds, but for a specific analysis, I only want to include half of the stimulus duration (ex: the first 8 seconds only OR the last 8 seconds only). I was wondering if I can do this, by setting the "refeventdur" to 8 seconds. Will that work? and if it does, is it including the first 8 seconds or the last 8 seconds? Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Question about recon-all.v6.hires
by Zeng,Victor (BIDMC - Psychiatry) 20 May '19

20 May '19

Hi all, I am running 7T scans through FS6, and I have been recommended to install the tools in ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/ . So I ran the new recon-all.v6.hires, specifically with the command "recon-all.hires.v6 -s subj -conf2hires -all" For the most part, it ran, but I while QCing, it couldn't seem to load the surfs files. Recon-all seemed to have generated files called ?h.white.H and ?h.white.K, but apparently skipped the steps for ?h.white? I don't think I can load the surfs files without it, and I don't know if this is intentional. Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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