Freesurfer May 2019

freesurfer@nmr.mgh.harvard.edu

95 participants
141 discussions

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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MP-RAGE protocol
by mustafa amin 20 May '19

20 May '19

External Email - Use Caution Dear Freesurfer experts, I need advice, the MRI operator need to confirm whether she had done the right protocol of MP-RAGE. I have attached the picture that has been taken by her. Please share some thoughts. Thank you in advance. Yours faithfully, Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara

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Postdoctoral position in multimodal neuroimaging on frontotemporal dementia
by Erik Lindberg 20 May '19

20 May '19

External Email - Use Caution Dear all, We are looking for a post-doc student for our lab at Karolinska institute in Stockholm. We are doing structural and functional MRI research on dementia. In current project we are acquiring multimodal MRI on frontotemporal dementia patients. We are also running an experimental fMRI paradigm on these patients. We are looking for a person that is well familiar with doing analysis of multimodal MRIs, to relate findings to other variables such as CSF-data, neuropsychology etc. See further: https://ki.mynetworkglobal.com/what:job/jobID:254449/

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mri_convert segmentation fault (core dumped) in v5.3 on centos6
by Caspar M. Schwiedrzik 20 May '19

20 May '19

External Email - Use Caution Hi! We are getting segmentation fault (core dumped) error when trying to run mri_convert on NIFTI files. This is running Freesurfer v5.3 on Centos6, specifically v1.179.2.7 of mri_convert. I suspect that this has to do with libcrypt incompatibilities described for other operating systems , e.g., here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/04052… and in the known issues list of v5.3. here https://surfer.nmr.mgh.harvard.edu/fswiki/PreviousReleaseNotes. We have libcrypt version 2.17 installed and do not have access to libcrypt-2.14.1.so. Is there a way to get libcrypt-2.14.1.so from you or is there another known workaround (other then updating to Freesurfer 6)? Thank you very much! Caspar

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statistical map in matlab
by Worker, Amanda 19 May '19

19 May '19

External Email - Use Caution Hi, I am working with cortical thickness data in matlab and I have a t-statistic map that I'd like to firstly write to .mgh/mgz format so that I can overlay it in freeview. And secondly, convert it to MNI space and write it out as a volume (preferably nifti). I think that save_mgh might be what I need but I don't understand what M is and how I would get that info for a statistical map in fsaverage space. Any ideas would be much appreciated. Thanks in advance, Amanda

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PetSurfer gtmpvc
by Boris Rauchmann 17 May '19

17 May '19

External Email - Use Caution Hi all, is there a way to easily get the volume stats for all regions after pvc correction using mri_gtmpvc ? I think its not included in gtm.stats.dat. Thanks, Boris

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Postdoctoral position in object and face recognition at NYU Abu Dhabi
by Olivia Cheung 17 May '19

17 May '19

External Email - Use Caution *Postdoctoral position in object and face recognition at NYU Abu Dhabi* A postdoctoral research position is open at the Objects and Knowledge Laboratory, headed by Dr. Olivia Cheung, at New York University Abu Dhabi ( http://www.oliviacheunglab.org/) The postdoctoral researcher will carry out behavioral and fMRI experiments on human object, face, letter, and/or scene recognition. Potential research projects include, but are not limited to, investigations of the influences of experience and conceptual knowledge on recognition processes. Applicants must have a Ph.D. in Psychology, Cognitive Neuroscience, or a related field, and should possess strong programming skills (e.g., Matlab). Prior experience with neuroimaging and psychophysical techniques is highly preferred. Initial appointment is for up to two years. Starting date is flexible, preferably between August/September 2019. The Objects and Knowledge Laboratory is part of the rapidly growing Psychology division at New York University Abu Dhabi. The lab is located in the campus on Saadiyat Island (Abu Dhabi’s cultural hub), and has access to the state-of-the-art neuroimaging and behavioral facilities (including MRI, MEG, eyetracking). Apart from a generous salary, the postdoctoral researcher will receive housing and other benefits. More information about living in Abu Dhabi can be found here: http://nyuad.nyu.edu/en/campus-life/residential-education-and-housing/livin… New York University has established itself as a Global Network University, a multi-site, organically connected network encompassing key global cities and idea capitals. The network has three foundational degree-granting campuses: New York, Abu Dhabi, and Shanghai, complimented by a network of eleven research and study-away sites across five continents. Faculty and students circulate within this global network in pursuit of common research interests and the promotion of cross-cultural and interdisciplinary solutions for problems both local and global. Informal inquiries regarding the position, university, or area, are encouraged. To apply, individuals should email a curriculum vita, a brief statement of research interests, the expected date of availability, and contact information of two referees. All correspondence should be sent to Olivia Cheung (olivia.cheung(a)nyu.edu) **Olivia Cheung is at the Vision Sciences Society (VSS) conference this week and will be happy to meet with any individuals who are interested in learning more about the position.**

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Freesurfer May 2019