Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Opening for research engineer position based in Tours (Loire Valley, France)
by briend 31 Jan '23

31 Jan '23

External Email - Use Caution Dear colleagues, Apologies for double posting, The INSERM-U1253 & University of Tours research unit based in Tours (Loire Valley, France) invites applications for a research engineer position to begin as soon as possible on cognitive neuroscience methodologies. A good command of written and spoken French is requested of all applicants. Prospective candidates should also contact directly Marie Gomot (marie.gomot(a)univ-tours.fr) Please include the following documents in your application (as a single PDF-file): Cover letter and curriculum vitae. For more information, and to apply: Follow this link* Frederic Briend * https://secure-web.cisco.com/1f7AdKWFpC1jtfmp6TJI2MWV2Ug2R8yxHmHoVS5EM8BAOv…

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Re: [Freesurfer] Skull stripping with external brainmask
by Iglesias Gonzalez, Juan E. 30 Jan '23

30 Jan '23

Dear Narlon, I believe you can add -xmask [mask_volume_file] to your recon-all command. To generate such external mask, maybe you could use mri_synthseg with the --robust flag and binarize the output? Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Boa Sorte Silva, Narlon" <narlon.silva(a)ubc.ca> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, January 30, 2023 at 01:14 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Skull stripping with external brainmask External Email - Use Caution Hi there, I just wanted to follow-up on this. Thanks! Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon On Jan 18, 2023, at 7:33 PM, Boa Sorte Silva, Narlon <narlon.silva(a)ubc.ca> wrote: Dear FreeSurfer experts, I dealing with some issues regarding skull stripping in FreeSurfer (v7.1.1). It seems like the conventional approaches (e.g., adjusting -wsthresh) doesn’t seem to help. As well, applying these preprocessing steps to the raw T1w BEFORE processing in FreeSurfer doesn’t seem to help either. I have tried: intensity truncation, N4 bias field correction, data normalization (with different combinations). Considering that we’re analyzing data from a large dataset (>500 scans * multiple timepoints), manual editing may not feasible. Therefore, to address poor skull stripping, I was wondering if it is possible to use a brain mask created outside FreeSurfer for the same subject to help with skull stripping. I saw in previous emails in the Archive that the steps below could work. Can someone confirm if this is still true and would work for v7.1.1? 1. run recon-all (as one normally would) 2. apply mri_mask to mask the T1.mgz with external brain mask volume (in native space) 3. name the output “brainmask.mgz” and move it to "subjid/mri/“ 3. re-run recon-all starting from -autorecon2 -autorecon3 Thanks for your help! Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon

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A doubt regarding autorecon after watershedding
by Rakshathi Basavaraju 30 Jan '23

30 Jan '23

External Email - Use Caution Dear FS, I intend to examine cortical thickness correlates of negative symptoms in my schizophrenia sample. I ran recon-all and corrected a few brainmasks which were excessively stripped by watershedding with different h values (ran autorecon-pial for those watershedded). I am attaching a few screenshots of scans where the segmentation is erroneous and the aseg omits the right temporal and parietal or cerebellar regions. How do I set this right? [image: Screenshot 2023-01-27 at 3.37.46 PM.png] [image: Screenshot 2023-01-27 at 3.29.47 PM.png][image: Screenshot 2023-01-27 at 3.26.29 PM.png][image: Screenshot 2023-01-27 at 3.32.08 PM.png] Dr. Rakshathi Basavaraju (M.D. Psychiatry) Assistant Professor (Department of Health Research-sponsored return-home research fellowship) Principal Investigator - OPCINSS Department of Psychiatry National Institute of Mental Health and Neurosciences (NIMHANS) Bengaluru, Karnataka, India-560029 Phone: +91-9480829898/+91-80-26972156/+91-80-26995320

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Fw: error: Numerical argument out of domain; error: MRIhistogramLabelRegion: constant image\00
by adriana.jorge＠unibe.ch 30 Jan '23

30 Jan '23

External Email - Use Caution Here follows my previous email, with the logs. Best, Adriana ________________________________ From: Jorge, Adriana (ARTORG) Sent: Tuesday, January 10, 2023 2:31 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: error: Numerical argument out of domain; error: MRIhistogramLabelRegion: constant image\00 Hi FreeSurfer Developers, I'm trying to obtain brain parcellations/segmentations of a subject's brain, using T1 and T2 images, but when I execute the recon-all command, I get the following error message: error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image Segmentation fault Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux recon-all -s Test_withT2 exited with ERRORS at Tue Jan 10 13:17:00 CET 2023 The FreeSurfer version I'm currently using is the freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275, but I have also tried the exact same process (same command and same data) in the freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 version and got the exact same error message. When I tried running the recon-all again with the freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b version, no error was reported and the recon-all outputs were correct. Recon-all works for versions reesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 and freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 if I use only the T1 image. The recon-all logs for the 2 failed and the 1 successful attempts are attached here. Can you help me figure out what the issue is? Why can't I run the recon-all using both T1 and T2 in the latest versions? Best, Adriana Jorge

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What if FS fails
by Rakshathi Basavaraju 30 Jan '23

30 Jan '23

External Email - Use Caution What is to be done if we get such an error message for recon-all: (copied from recon-allstatus log) status file for recon-all Tue Jan 3 22:43:36 IST 2023 #@# MotionCor Tue Jan 3 22:43:41 IST 2023 #@# Talairach Tue Jan 3 22:43:53 IST 2023 #@# Talairach Failure Detection Tue Jan 3 22:47:14 IST 2023 #@# Talairach Tue Jan 3 22:47:15 IST 2023 #@# Talairach Failure Detection Tue Jan 3 22:50:31 IST 2023 #@# Talairach Tue Jan 3 22:50:32 IST 2023 #@# Talairach Failure Detection Tue Jan 3 22:53:29 IST 2023 Darwin JAGADISHAs-Mac-mini.local 21.2.0 Darwin Kernel Version 21.2.0: Sun Nov 28 20:29:10 PST 2021; root:xnu-8019.61.5~1/RELEASE_ARM64_T8101 x86_64 recon-all -s subj39_anat exited with ERRORS at Tue Jan 3 22:53:30 IST 2023 Dr. Rakshathi Basavaraju (M.D. Psychiatry) Assistant Professor (Department of Health Research-sponsored return-home research fellowship) Principal Investigator - OPCINSS Department of Psychiatry National Institute of Mental Health and Neurosciences (NIMHANS) Bengaluru, Karnataka, India-560029 Phone: +91-9480829898/+91-80-26972156/+91-80-26995320

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Re: [Freesurfer] Fw: error: Numerical argument out of domain; error: MRIhistogramLabelRegion: constant image\00
by adriana.jorge＠unibe.ch 30 Jan '23

30 Jan '23

External Email - Use Caution Hello, I'm just checking to see if you have received the images and if you are still working on my issue? I don't think I got any more replies from you and just want to make sure if you're still working on it. Best, Adriana ________________________________ From: Jorge, Adriana (ARTORG) Sent: Friday, January 13, 2023 12:16:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] Fw: error: Numerical argument out of domain; error: MRIhistogramLabelRegion: constant image\00 Hello, Yes, of course. I trust you won't share the images, please. Best, Adriana ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43(a)MGH.HARVARD.EDU> Sent: Wednesday, January 11, 2023 3:50:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] Fw: error: Numerical argument out of domain; error: MRIhistogramLabelRegion: constant image\00 Hi Adriana, Is it possible for you to share the T1 and T2 images so we can debug it? Best, Yujing From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of adriana.jorge(a)unibe.ch Sent: Tuesday, January 10, 2023 8:53 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Fw: error: Numerical argument out of domain; error: MRIhistogramLabelRegion: constant image\00 External Email - Use Caution Hi FreeSurfer Developers, I'm trying to obtain brain parcellations/segmentations of a subject's brain, using T1 and T2 images, but when I execute the recon-all command, I get the following error message: error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image Segmentation fault Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux recon-all -s Test_withT2 exited with ERRORS at Tue Jan 10 13:17:00 CET 2023 The FreeSurfer version I'm currently using is the freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275, but I have also tried the exact same process (same command and same data) in the freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 version and got the exact same error message. When I tried running the recon-all again with the freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b version, no error was reported and the recon-all outputs were correct. Recon-all works for versions reesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 and freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 if I use only the T1 image. The recon-all logs for the 2 failed and the 1 successful attempts are attached here. Can you help me figure out what the issue is? Why can't I run the recon-all using both T1 and T2 in the latest versions? Best, Adriana Jorge

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password to extract FS_7_2_0_ubuntu_18_04_06.ova.7z
by Balish 28 Jan '23

28 Jan '23

External Email - Use Caution Hi, I am requesting the password to extract the image named "FS_7_2_0_ubuntu_18_04_06.ova.7z" ThanksMBalish

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VirtualBox ubuntu failed to start
by Casper Cappelen 28 Jan '23

28 Jan '23

External Email - Use Caution Hi, I am currently following the tutorial within your wiki at https://secure-web.cisco.com/1FhH_mVr-gZRnmOt8bSFGdT80u9kDmY3jmw7_fkHsGRV8q… I am reading the pdf-file Vbox_load_image.pdf at page 10, where I am attempting to boot up ubuntu. When pressing the Start button and choosing *ubuntu I get the screen shown below. How do I fix this, thanks. Best regards, Casper Cappelen [image: bilde.png]

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Request for password for extraction of .ova.7z file
by Casper Cappelen 27 Jan '23

27 Jan '23

External Email - Use Caution Hi, I am requesting the password to extract the image named "FS_7_2_0_ubuntu_18_04_06.ova.7z" Thank you, best regards, Casper Cappelen

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Re: [Freesurfer] Problem with quantifyHAsubregions.sh
by Georgina Angelopoulou 26 Jan '23

26 Jan '23

External Email - Use Caution Dear Eugenio, Thank you for your kindly reply. Actually, I tried both options and neither worked. When I renamed one subject and ran the following command, an error occurred. Please see below: Georginas-MacBook-Pro:ALBION georginaangelopoulou$ quantifyHAsubregions.sh hippoSf T1 -4393 testhippo.txt Gathering results from subjects in: testhippo.txt Using the prefix name: hippoSf Using the suffix name: T1 And writing them to: -4393 /Applications/freesurfer/7.3.2/bin/quantifyHAsubregions.sh: line 8: cd: testhippo.txt: No such file or directory failed to do cd testhippo.txt and then when I tried the following, another error occured: Georginas-MacBook-Pro:ALBION georginaangelopoulou$ quantifyHAsubregions.sh hippoSf T1 testhippo.txt -4393 Gathering results from subjects in: -4393 Using the prefix name: hippoSf Using the suffix name: T1 And writing them to: testhippo.txt /Applications/freesurfer/7.3.2/bin/quantifyHAsubregions.sh: line 8: cd: -4: invalid option cd: usage: cd [-L|-P] [dir] failed to do cd -4393 The second option with the script you sent me, did not provide any error, yet no output appeared. Could you please help me with that? Is there any possibility that this has to do with the version I used (7.3.2), using the following command: segment_subregions hippo-amygdala --cross 6608 Moreover, when compared this analysis with a previous version of Freesurfer, using the same subject, I noticed that all subfields’ indices are very similar except from three (Whole_hippocampus, Whole_hippocampal_body and Whole_hippocampal_head) for which all values were doubled compared to the previous version of FS. Could you please tell me why did this happened and which version should I trust? Apologies for such a long email. Thank you in advance. Best, Georgina

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