Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

recon-all not parcellating
by Carlos Estévez Fraga 10 Mar '23

10 Mar '23

External Email - Use Caution Dear Freesurfer team, I am trying to run recon-all -all in the cluster but unfortunately I am unable to obtain the parcellated images (exact command is recon-all -parallel -openmp $NSLOTS -s ${j} -i ${j}_corrected.nii.gz -all -cw256) I have run the script different times with different subjects and it just stops abruptly always in the same point, after WM segmentation, see below the recon-all-status.log for one subject (same in all of them, it stops after WM segmentation) I tried it on my laptop and in my desktop computer and it works, but not in the cluster... Any chance you know why this may be happening? Best regards, Carlos #@# MotionCor Tue Mar 7 22:10:08 GMT 2023 #@# Talairach Tue Mar 7 22:10:18 GMT 2023 #@# Talairach Failure Detection Tue Mar 7 22:13:37 GMT 2023 #@# Nu Intensity Correction Tue Mar 7 22:13:37 GMT 2023 #@# Intensity Normalization Tue Mar 7 22:16:54 GMT 2023 #@# Skull Stripping Tue Mar 7 22:18:15 GMT 2023 #@# EM Registration Tue Mar 7 22:20:49 GMT 2023 #@# CA Normalize Tue Mar 7 22:22:45 GMT 2023 #@# CA Reg Tue Mar 7 22:23:44 GMT 2023 #@# SubCort Seg Tue Mar 7 23:07:13 GMT 2023 #@# CC Seg Wed Mar 8 00:00:24 GMT 2023 #@# Merge ASeg Wed Mar 8 00:03:01 GMT 2023 #@# Intensity Normalization2 Wed Mar 8 00:03:01 GMT 2023 #@# Mask BFS Wed Mar 8 00:04:47 GMT 2023 #@# WM Segmentation Wed Mar 8 00:04:48 GMT 2023 #@# Fill Wed Mar 8 00:07:28 GMT 2023 -- *Dr Carlos Estevez-Fraga, MD, PhD* Senior Clinical Research Fellow Department of Neurodegenerative Diseases UCL Queen Square Institute of Neurology London, UK *Mail:* c.fraga(a)ucl.ac.uk *Phone*: +44 7788 926 982

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acces to virtual machine archive
by Free Surfer 10 Mar '23

10 Mar '23

External Email - Use Caution Hello, I have just downloaded the virtual machine and ubuntu package. Could you send me a password for unpack archive with virtual machine image, and for ubuntu account? Thanks so much in advance!

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Request: Password VirtualBox Vm Images
by Fislage, Marinus 09 Mar '23

09 Mar '23

External Email - Use Caution Dear all, I would like to kindly ask for the password related to the VM zip archive: https://secure-web.cisco.com/1f7WVlIuUEn_Vllgaj670_9Zm1yN5Kl0O5jr8VA3slmuHC… Thank you very much! Kindest regards, Marinus

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Re: [Freesurfer] Segmentation fault (core dumped)
by fsbuild 09 Mar '23

09 Mar '23

External Email - Use Caution As Yujing said, the 5.1.0 release is quite old (dating back to CentOS4) and binary backwards compatibility cannot be expected to work indefinitely going forwards to newer versions of the OS.  I ran a simple mri_surf2surf command from 5.1.0 on CentOS7 and it crashed immediately.    I then tried the same command using the freesurfer 5.3.0 release built for CentOS6 and it worked on CentOS7. You can download freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz from https://secure-web.cisco.com/1S9OGgcf17zFMWWXjC8lPSf7mq4hk6Ou69iX…, or see the direct link  https://secure-web.cisco.com/1O5P1_jnLPrOGdYkXFNDEb2y-k3m7evHo5fe2uNzyoNAaKSkB3Nt1_wXhgDLemrYevJFPQsp5tpz_wdWUjWhVTD9p6CNaNieHzYFY7XvcOkTsvaaxQ14203xL-zEAR2Eav2sKtvuxzucTJqIFKJcJxwO4tU1LWxZbL8HSzpbAx4gHo4SUez6Lwz1bZarwjhy7YEdn5NslhRbXzeF8MIl4YiwsVYH1XGmK-teHPP1FTJiVcnLV6oEDyz9jwP0uUf5tP9RGIWsdKBnItP4JbrHc-fZumOroSi_i6GuKCOsp-IouIjFOvOowWaI6ldL4IOMcIeaqNW-BG-wO4CN5ByZFrg/https%3A%2F%2Fftp.nmr..mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.3.0%2Ffreesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz%26nbsp;  The 5.3.0 release notes are here, https://secure-web.cisco.com/19Gm_LLMuws0ked03zCf5tnQ6jPznJWqxPj… Please be aware we post this caveat on our download page saying that numeric/floating point results can differ when you switch to a different freesurfer release or newer version of the OS, Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). I would expect the above to be true if you switch from the 5.1.0 release to the 5.3.0 release. So if you must continue to run 5.1.0, then I would try to run it on the (same) version of the OS you used where it previously worked.  One way to do that is with a virtual machine (VM) hosting the (old) OS.   It looks like we have a virtual machine image with freesurfer 5.1.0 installed available from under https://secure-web.cisco.com/11VzvQh0Sbki3c91H_Wr1_Sbun-1WBJp0X7…;  That virtual disk image file (..vdi), https://secure-web.cisco.com/1f9gnsQF3U_bgE7wRs0_PPUaeSlPgrJxG-afglho7qOnEI6IK3x6Q74lVczCqUz814qnE3gT4GO-FHPsn6fv4NwsG7SMQykR-ghIZUMdjGSmckggj6M5NAUe9S37AMJzV215rTC59h7VmVa-paqybjKPfVK-VAtQ2oUwks-053E4KC89mt53wvYjRuyAhnLrA0JFdOGOuMo-8KrX_ENyyGH2zzQJtiTEGmBnnMpKIGFw9QCAfWRqmgMi_BDHy7lmAxYnWCVd_XdH1VJ1HqLhBIonwjm5X2caNf1OTebriIZfm2h5IupSjvLGZMRF43ej87-9ybXcYkIZ6L_qBDq_D-A/https%3A%2F%2Fftp.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.1.0%2Ffreesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi,  should still run in virtual box on your CentOS7 machine.   My guess would be it is a CentOS4 VM image with freesurfer 5.1.0 installed but I don’t know how that matches up to any previous version of the OS you used to successfully run freesurfer 5.1.0. - R. On Mar 9, 2023, at 20:17, Huang, Yujing <YHUANG43(a)mgh.harvard.edu> wrote:Hi Tracy, I looked at your recon-all.log.  There are total of 19 runs.  The first 4 runs from 2015 and 2016 finished without errors. They were all run on hippocampus.umd.edu. The later failed ones with segmentation fault were run a different machine - seahorse.umd.edu. Since you are using Freesurfer 5.1 built for centos4, I’m wondering if there are some compatibility issues. Can you try running it on hippocampus.umd.edu? I did notice that you tried 6.0.0 and 7.1.1 but those runs reported a different error. Best, Yujing From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Tracy RigginsSent: Thursday, March 9, 2023 6:26 PMTo: freesurfer@nmr.mgh.harvard.edu; Allard, Tamara Lynn <tallard@terpmail.it-prod-webhosting.aws.umd.edu>Subject: [Freesurfer] Fwd: Segmentation fault (core dumped)         External Email - Use Caution        YujingAny insight on this?Thanks,Tracy---------- Forwarded message ---------From: Tracy Riggins <riggins(a)umd.edu>Date: Mon, Mar 6, 2023, 10:44 PMSubject: Re: Segmentation fault (core dumped)To: <freesurfer(a)nmr.mgh.harvard.edu> Yujing Yes, we have run this successfully with other participants (although it was a while ago).Attached is the recon-all.logthanks for your help!Tracy On Sun, Mar 5, 2023 at 1:21 PM Tracy Riggins <riggins(a)umd.edu> wrote:Greetings FS experts: We are trying to run recon-all -s -qcache on a handful of brains processed in freesurfer v5.1.0.   (it's an old dataset...5.1 makes the most sense for our purpose.) The error is below: <image001.png> --------------------------------------#@# 1/1 HMN080 Fri Mar  3 12:14:44 EST 2023 -------------------------------------mri_surf2surf --srcsubject HMN080 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.51930/HMN080.1.mgh --sval /export/data/seahorse_ncdl/HMN/data/HMN080/surf/lh.thickness --sfmt curv --noreshape --no-cortexSegmentation fault (core dumped)Linux seahorse.umd.edu 3.10.0-1160.80.1.el7.x86_64 #1 SMP Sat Oct 8 18:13:21 UTC 2022 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s HMN080 exited with ERRORS at Fri Mar  3 12:14:48 EST 2023 Can you assist?  OR perhaps tell us where to find the core dump file, which may have more information?-- Tracy Riggins, Ph.D.Pronouns: she/her/hersAssociate Professor of Psychology4094 Campus Drive, Biology/Psychology Building 2147JUniversity of Maryland, College Park, MD 20742Zoom Meeting ID: 6751666548*****************************************************Research info:  MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/16uU9Voo_CziLp-ng0Dkh27qT2SP4MKOfHHDUkD… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1OFC1dVVEqctiVCBhWLVpuWAqvx-VAFmj5QcsN… lives matter in academiaLGBTQIA+ Ally _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Segmentation fault (core dumped)
by Tracy Riggins 09 Mar '23

09 Mar '23

External Email - Use Caution Greetings FS experts: We are trying to run recon-all -s -qcache on a handful of brains processed in freesurfer v5.1.0. (it's an old dataset...5.1 makes the most sense for our purpose.) The error is below: [image: image.png] -------------------------------------- #@# 1/1 HMN080 Fri Mar 3 12:14:44 EST 2023 -------------- ----------------------- mri_surf2surf --srcsubject HMN080 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.51930/HMN080.1.mgh --sval /export/data/seahorse_ncdl/HMN/data/HMN080/surf/lh.thickness --sfmt curv --noreshape --no-cortex Segmentation fault (core dumped) Linux seahorse.umd.edu 3.10.0-1160.80.1.el7.x86_64 #1 SMP Sat Oct 8 18:13:21 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux recon-all -s HMN080 exited with ERRORS at Fri Mar 3 12:14:48 EST 2023 Can you assist? OR perhaps tell us where to find the core dump file, which may have more information? -- Tracy Riggins, Ph.D. Pronouns <https://secure-web.cisco.com/1WTjrK6XJwG7-24mUYPAFcId6puqiKxHmofCChPCQb4mC-…>: she/her/hers Associate Professor of Psychology 4094 Campus Drive, Biology/Psychology Building 2147J University of Maryland, College Park, MD 20742 Zoom Meeting ID: 6751666548 <https://secure-web.cisco.com/1hviwkViTW16JTEvWH-47gs1rSV1H4pi6BZD9e1QCPEJ2V…> ***************************************************** Research info: http://secure-web.cisco.com/1JWrYfqglbLMQuNvUkCI3__mdHJZE-j2I4GZAMwxbYavfuR… and https://secure-web.cisco.com/1gMMoT_3zpTn_EJwufCskhV5rA9d3a3dfl-3blyeCnoRvf… Black lives matter in academia <https://secure-web.cisco.com/1J1h-u95rDMtqm8NNRIKxQgXcKxqK0HepLClZ-LZRNQ_s5…> LGBTQIA+ Ally <https://secure-web.cisco.com/1gzE6oBTSI-WE3shKwya1t2cvYue63e9MW9Tseqcx37Bos…>

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Substantia nigra segmentation status
by Christian Owen 09 Mar '23

09 Mar '23

External Email - Use Caution Hi, The latest post I could find about substantia nigra segmentation in FreeSurfer is from May 2020 <https://secure-web.cisco.com/1kbKgUj7tgWerg-kNskO0E4pbYddAh99-3abcyl688pSr5…>. As of that post, it was not possible. Is it still not possible? If that's the case: - is substantia nigra segmentation on the roadmap? - is there anything a software engineer could do to help make it happen? I cannot promise any resources atm, but there's a chance we could help out (if it turns out to be enough of a priority). Best, Christian

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freesurfer could not parse freeview-loadable surface label
by Yigu Zhou 09 Mar '23

09 Mar '23

External Email - Use Caution Hello Freesurfer community I am trying to transform a label file obtained in subject native surface space to subject native volume space. This label file was obtained through binarizing the subject lh.sulc morphological data through the function write.fs.label from R package freesurferformats, in the left hemisphere, resulting in a binary label for all sulci in the subject. Visual quality control of the label file through Freeview was adequate: I can load the surface label file with any surface of the subject. Now, I would like to map the corresponding voxels that belong to sulci in the left hemisphere of this subject. I tried to convert the label to volume using mri_label2vol first, but got the following error message could not parse 48510th line '1e+05 -37.5524826049805 -5.55967617034912 18.56817436218261' in label file I then tried to first convert the file to annot format using mris_label2annot and then convert to volume using mri_aseg2aparc. Similarly, mris_label2annot threw the error could not parse 48510th line '1e+05 -37.5524826049805 -5.55967617034912 18.56817436218261' in label file The list described similar errors but no obvious solution that I can access right now e.g. having a developer inspect the label file. I would love to get any pointer as to why the label file may have been unparse-able to Freesurfer tools. Sincerely Yigu

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password to unzip virtual machine
by Pierpaolo Croce 09 Mar '23

09 Mar '23

External Email - Use Caution I would like the password to unzip the virtual machine installation -- Ing. Pierpaolo Croce, PhD. Institute for Advanced Biomedical Technologies - ITAB and Department of Neuroscience and Imaging University of Chieti "G. D'Annunzio" Via dei Vestini, 33 66013 Chieti, Italy

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Re: [Freesurfer] SynthSeg with CT images.
by Gonzalo Rojas Costa 08 Mar '23

08 Mar '23

External Email - Use Caution Hi Benjamin: I tested with the clipping, and it works ok with a CT image. Sincerely Gonzalo Rojas Costa El mié, 8 de mar de 2023, 14:39, Benjamin Billot <bbillot(a)mit.edu> escribió: > Yes, agreed. > > Gonzalo: Also, if SynthSeg still gives you a bad result after clipping, > you might want to check that the image header is not corrupted. > > Best > > Benjamin > ------------------------------ > *From:* Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > *Sent:* 08 March 2023 12:25 > *To:* Gonzalo Rojas Costa; freesurfer(a)nmr.mgh.harvard.edu > *Cc:* Benjamin Billot > *Subject:* Re: SynthSeg with CT images. > > > Dear Gonzalo, > > Can you please try clipping the input to Hounsfield between 0 and 80? That > should do the trick. If you have trouble with this, feel free to send me > scan so I can take a look. > > Benjamin: maybe we should add this as a flag, as we do in SynthSR… > > Cheers, > > /E > > > > -- > > Juan Eugenio Iglesias > > http://secure-web.cisco.com/1oY_Ta7QUv3TybD8UgzuVG9Dc0uElb0r5sAAb2tL8RYcVO1… > > > > *From: *Gonzalo Rojas Costa <gonzalo.rojas.costa(a)gmail.com> > *Date: *Wednesday, March 8, 2023 at 12:04 > *To: *"freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Cc: *"Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > *Subject: *SynthSeg with CT images. > > > > * External Email - Use Caution * > > Hi: > > > > I tried SynthSeg using CT images, but I got very bad results... CT > images must have some specific characteristics? I tried with axial > acquisition and volumetric one.... > > > > Sincerely, > > > > > > Gonzalo Rojas Costa > > Department of Radiology > Clínica las Condes > Lo Fontecilla 441, Las Condes, Santiago, Chile. > Tel: 56-2-2105170 > Cel: 56-9-97771785 > > https://secure-web.cisco.com/1dx-ON0IVqdFsAlkwbnFP-5CWyzUsWOqcXmV2sh2Kowfhn… > <https://secure-web.cisco.com/1X4JTWBblTD8tld8oBtoX_hRATMKAHXt1kz8xQ7YPlXYPC…> > https://secure-web.cisco.com/1WfM5q5JiWue1joAWuZpJ-2gnXIfCTH4jF5i5mncbvG8VT… > <https://secure-web.cisco.com/1jIR1VD1EGr6FdxqTGgScWCn_mHW5DPrMZAjfRggLiGtOa…> > > https://secure-web.cisco.com/18CztnN9siLRgJ0-UmgEchKrQq1yBr_pJu3oqRmA8vMLAA… > <https://secure-web.cisco.com/1yA9l7ISJLI6AsyMtjg6tqVLF4b_n1UlUVhia2mXbDUAX5…> > http://secure-web.cisco.com/1wJM_skjI0l0zygtqAs442I6qKn4WaYZxNrNXu6J9to22-8… > <http://secure-web.cisco.com/1WbHoWnrfeHvPRvJjfNf_577rSGYT1ApJAnQKa2Hbt1Jxqb…> > https://secure-web.cisco.com/1cCGpAkoZIpj8dp3v1C-VWfKKTjUqACatHALHubNHZqPhL… > <https://secure-web.cisco.com/1ZasoGFuD7Kwh5m95aUJSJ7Cq9E3amXs01l9LmTC_TxXWG…> > > 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 Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1Mc_8xJ_hTrW0ec0dAEqEMWEeqF1_jDIzgw0QhAg6eBMmS… . > > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. >

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Clinical Research Coordinator position at Penn FTD Center, Univ. of Pennsylvania, Philadelphia
by Jeff Phillips 08 Mar '23

08 Mar '23

External Email - Use Caution Dear colleagues, The Penn Frontotemporal Degeneration Center is seeking a Clinical Research Coordinator to manage our ongoing NIA-funded PET and MRI studies of atypical, early-onset Alzheimer's disease and frontotemporal dementia patients. This position is ideal for aspiring researchers looking to gain experience with neuroimaging, Alzheimer's disease and related dementias, and clinical trial management. Please share this link with your talented trainees or colleagues--I'm happy to respond to direct inquiries: https://secure-web.cisco.com/12wO4MVCs84118ysL8fy6xvbYNtL9LzfpZBTronQnSEbQR… Thanks so much, Jeff Phillips Research Assistant Professor of Neurology Penn Frontotemporal Degeneration Center Philadelphia, PA

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