Freesurfer

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nu_correct: Command not found
by Ian Hardingham 29 Mar '19

29 Mar '19

External Email - Use Caution Hello all. I am attempting to run recon-all in a docker container. I have a set of commands to set up the system, and on my local machine (Ubuntu) it works fine. However on the docker container (also Ubuntu) I get nu_correct: Command not found. I imagine there is some software that is required that I haven't installed on the container image - does anyone have any idea what it might be? 1. I have run these commands: source /usr/local/freesurfer/SetUpFreeSurfer.sh export PATH=/usr/local/freesurfer/bin:PATH=/usr/local/freesurfer/mni/bin:$PATH 2. I have set FREESURFER_HOME Attached at the end is some output from both failing and successful runs. 3. nu_correct exists in freesurfer/mni/bin 4. Perl is present and correct on both systems. Thank you in advance, Ian FAILING OUTPUT: #-------------------------------------------- #@# Talairach Thu Mar 28 14:12:31 UTC 2019 /subjects/FS_subj_001/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /subjects/FS_subj_001/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 40ed7e79aa5d 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 GNU/Linux Thu Mar 28 14:12:32 UTC 2019 nu_correct: Command not found. SUCCESSFUL OUTPUT: #-------------------------------------------- #@# Talairach Thu Mar 28 14:33:45 GMT 2019 /home/ian/subjects/FS_subj_001/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/ian/subjects/FS_subj_001/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux ian-Sabre-17WV8 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thu Mar 28 14:33:45 GMT 2019 Program nu_correct, built from: -- Ian Hardingham

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Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: [WARNING: UNSCANNABLE EXTRACTION FAILED]talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***
by Bruce Fischl 28 Mar '19

28 Mar '19

Hi Chhavi can you post this type of question to the FS list (which I'll cc on my response)? You only need to give recon-all a single dicom slice that is from the correct series. If the rest of the dicoms are in the same dir we will find them and properly assemble the volume from them. cheers Bruce On Mon, 25 Mar 2019, Chhavi Yadav wrote: > > External Email - Use Caution > > Hi Bruce, is there a way I can do recon-all -autorecon1 for all the slices for a subject without > using the -i flag? I mean I do not want to mention every single slice's name in the command. > > On Mon, Mar 25, 2019 at 12:59 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > On Mon, 25 Mar 2019, Chhavi Yadav wrote: > > > > > External Email - Use Caution > > > > Okay got it. So I will still writerecon-all -autorecon1 -i new.dcm -s outnew > > Just that new.dcm should be in the folder with the other slices. Is that correct? > > > > Also some of my slices are noisy, just ears or completely black. > > Sorry for sending to the list. > > > > Thanks for your help.. > > Chhavi > > > > > > On Mon, Mar 25, 2019 at 12:44 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > Hi Chhavi > > > > if you look in the recon-all.log file you will see the volume dimensions > > as: > > > > Image information > > RunNo 4 > > SeriesNo 5 > > ImageNo 56 > > NImageRows 256 > > NImageCols 240 > > NFrames 1 > > SliceArraylSize 1 > > IsMosaic 0 > > ImgPos 36.2753 164.5335 99.2486 > > VolRes 1.0000 1.0000 1.2000 > > VolDim 240 256 1 > > Vc -0.0000 -1.0000 0.0000 > > Vr -0.0000 -0.0000 -1.0000 > > Vs -1.0000 -0.0000 0.0000 > > VolCenter 35.6753 44.5335 -28.7514 > > TransferSyntaxUID 1.2.840.10008.1.2.1 > > > > > > so it is only a single slice. You need to have the entire dicom series in > > the same directory so that we can find the other slices > > cheers > > Bruce > > > > > > On Mon, 25 Mar 2019, > > Chhavi Yadav wrote: > > > > > > > > External Email - Use Caution > > > > > > attached is a sample on which it fails.I just do recon-all -autorecon1 -i > new.dcm -s outnew > > > > > > Is this okay? Also attached is the log. > > > I haven't tried all. > > > > > > On Mon, Mar 25, 2019 at 12:26 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > > > did all of them fail? That seems unlikely. Our failure rates are usually > > > pretty low (less than a couple of percent). If they are all failing > > > something else is wrong > > > > > > > > > On Mon, 25 Mar 2019, Chhavi Yadav wrote: > > > > > > > > > > > External Email - Use Caution > > > > > > > > HI Bruce,Thanks for your email. > > > > I actually have 3500 files. So cant do transform on them manually. Any > other way? > > Like > > > downloading the > > > > previous version of freesurfer? > > > > Chhavi > > > > > > > > On Mon, Mar 25, 2019 at 10:56 AM Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: > > > > Hi Chhavi > > > > > > > > the automated Talairach transform creation can sometimes fail, > > > > particularly in the presence of very large ventricles or lots of > > > > damaged white matter or > > > > both. We have a tutorial on checking and correcting it here: > > > > > > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard… > l_Tala > > ir > > > > > > >ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKb > HktL7Q > > rJ > > > > > > > JELPuLToS-_5lkY&s=LpBDOkEFGzHx0owj2xszaOGP5m2RG6gsMN9vq30fOBU&e= > > > > > > > > cheers > > > > Bruce > > > > > > > > On > > > > Mon, 25 Mar 2019, Chhavi Yadav wrote: > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > Hi,I am a beginner to freesurfer. Never used it before. > > > > > Currently I am working on some dicoms from ADNI that I want to > preprocess. > > > > > But I am getting this 'talairach_afd: Talairach Transform: > > transforms/talairach.xfm > > > > ***FAILED*** ' error. > > > > > I am attaching the error log and other files for your > reference. Please > > help me > > > out. > > > > > > > > > > Regards, > > > > > Chhavi > > > > > > > > > >_______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… > reesur > > fe > > > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJJELPu > LToS-_ > > 5l > > > > > > > kY&s=bKPWvTI6mhmqTDXPcjuZiBrd9LczeJVcqb47rKN8Lvg&e= > > > > > > > > > > > >_______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… > eesurfe > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQWvKqc6fZyhUQKNa911LU20WsF_ > c8g2VP7 > > > > > LM&s=DgN0IsA48XVzgAFsDxvg5H2euo0dyxsaX8Y4v0koRB0&e= > > > > > > > > >_______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… > surfe > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=0en6N_H-HDM_3l0J3ZVznuaBX1sw-F8kv1S2 > TCg3F > > G0&s=9Qp6YLWJpuHPgkqfW-Sv0N-cNqEect_0FX7_G-R_V10&e= > > > > > > > > >

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Special image protocol
by mustafa amin 28 Mar '19

28 Mar '19

External Email - Use Caution Dear member, I am really new with this freesurfer, just need to ask 1 question. Is there a special image protocol before running the MRI and then upload it to freesurfer? Please share your thoughts. Thank you for your kind attention and cooperation. Yours faithfully, Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara

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Protocol for MRI
by mustafa amin 28 Mar '19

28 Mar '19

External Email - Use Caution Hi Bruce/ Doug, This is the picture I got from the MRI operator. She needed to know that she had done the right thing about the MP-RAGE sequence. Is this the right protocol? Please share some thoughts. Thank you for your kind attention and cooperation. Yours faithfully, Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara

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tract all prep error mv: cannot stat ?/project/3015068.01/sub030/dmri/dwi_orig_las.nii.gz?: No such file or directory
by Camerino, .I.L. (Ileana) 28 Mar '19

28 Mar '19

External Email - Use Caution Hallo, I wrote to the mailing list last Monday because after running tract-all prep I got the following error: segmentation fault (core dumped). I tried to run tract-all prep with more gb (50 gb). Now, I do not get anymore the tract-all.e file containing the message: segmentation fault (core dumped) but I get another error (see attachment). The tract-all.e is empty and the tract-all.o and .log give a more clear error. It says: "mv: cannot stat ?/project/3015068.01/ilecam/RUNDMC_dwi_2015/subset_declined_constant/test_tracula/freesurfer/tracula_out/sub030/sub030/dmri/dwi_orig_las.nii.gz?: No such file or directory Linux dccn-c029.dccn.nl 4.4.121-1.el7.elrepo.x86_64 #1 SMP Sun Mar 11 14:33:50 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at wo mrt 27 18:26:20 CET 2019" A bit earlier in the tract-all o file, it seems looking for this file but it also says: "INFO: input image orientation is LAS INFO: input image determinant is -15.625 than it will try to tranform dwi_orig.nii in LAS" It seems odd to me that the program is trying to tranform the dwi.nii in LAS orientation when it says that the file is already in LAS orientation. Maybe the first issue was insufficient memory. Now it cannot find this dwi_orig_file. Please, do you have any idea/suggestion about how to solve this error? Thank you in advance Cheers Ileana

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Symposium on Advances in High-Field MRI in Montreal, right after ISMRM (fwd)
by Bruce Fischl 27 Mar '19

27 Mar '19

FYI ---------- Forwarded message ---------- Date: Thu, 28 Mar 2019 01:53:47 +0000 From: "Amir Shmuel, Dr." <amir.shmuel(a)mcgill.ca> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Symposium on Advances in High-Field MRI in Montreal, right after ISMRM External Email - Use Caution Hi Bruce, I’d appreciate it if you could forward this message to the Free-Surfer email list. Thanks! Amir. From: Amir Shmuel, Dr. Subject: Symposium on Advances in High-Field MRI in Montreal, right after ISMRM Symposium Advances in High-Field Brain Imaging – celebrating the arrival of McGill’s 7T MRI May 17, 2019 The Neuro (MNI), Montreal, QC, Canada Program Co-Chairs: Richard Hoge, Amir Shmuel, Julien Doyon The McConnell Brain Imaging Centre will host a one-day scientific symposium to celebrate the arrival of our 7T MRI scanner. This symposium follows the ISMRM meeting in Montreal. Speakers Julien Cohen-Adad, University of Montreal, Canada Laurentius Huber, Maastricht University, The Netherlands Seong-Gi Kim, Sungkyunkwan University, Korea Silvia Mangia, University of Minnesota, USA Ravi Menon, The University of Western Ontario, Canada Karla Miller, University of Oxford, UK Bruce Pike, University of Calgary, Canada Jonathan Polimeni, Massachusetts General Hospital and Harvard Medical School, USA Amir Shmuel, McGill University, Canada Christina Triantafyllou, Siemens, Canada Kamil Ugurbil, University of Minnesota, USA Larry Wald, Massachusetts General Hospital and Harvard Medical School, USA Nikolaus Weiskopf, Max Planck Institute for Human Cognitive and Brain Sciences, Germany For more information: https://www.mcgill.ca/neuro/events/advances-high-field-brain-imaging-sympos… Student promo code for registration: https://www.mcgill.ca/neuro/events/advances-high-field-brain-imaging-sympos… Contact: Deborah Rashcovsky, Events Officer, 514 398-6047 deborah.rashcovsky(a)mcgill.ca cid:image006.jpg@01D3A4D6.9D165740

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Questions regarding Hippocampal Subfields And Nuclei Of Amygdala module
by Jessica Bourgin 27 Mar '19

27 Mar '19

External Email - Use Caution Hi, I am interested in the Hippocampal Subfields And Nuclei Of Amygdala module and have a few questions regarding its functionalities. Regarding the segmentation of amygdala nuclei, you say that currently, "volumes of the nuclei must be interpreted with caution". What does it mean exactly ? Can these volumes be used for comparison between patients and controls, or must we wait for further test ? I would like to create masks from this module and use these masks in functional connectivity analysis (Conn toolbox). Is it possible and if so, how can I do that ? You mention that the freesurfer command "recon-all" must be used before the segmentation of the nuclei is performed. I tried this and recon-all took about 7 hours to compute on one subject. I plan to use this module on 150 subjects, so do you know if there is a way to speed up data processing ? Thanks in advance for your help. Best regards, Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France

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*.dcm to *.mgz
by Z Hessam 27 Mar '19

27 Mar '19

External Email - Use Caution Hello FreeSurfer Developers, I,m attempting to convert my dicom files to *.mgz, with command line in below: $ recon-all -i /data/14ZOGOO/1.dcm -autorecon1 -subjid d14zogoo but it exits with error and the recon-all.log file is attached. why this error occur and what should I do to solve it?

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mri_binarize --replace
by Song, Da-Yea 27 Mar '19

27 Mar '19

External Email - Use Caution Hello, I have a set of binary mask files that I'm trying to assign different values to. Currently I'm doing: mri_binarize --i sub001.nii.gz --o final_sub001.nii.gz --replace -117 2 mri_binarize --I sub002.nii.gz --o final_sub002.nii.gz --replace -128 2 The problem I'm having is that the values (V1) for each binary mask is not constant. For example, for one participant the values may be -117 whereas the values are -128 for another participant. Is there a way to set a range for the --replace option so that I can loop it through the subjects rather than having to do this command for each one separately? Any suggestions would be greatly appreciated! Thank you, Da-Yea ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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exact time of data acquisition per run
by Nasiriavanaki, Zahra 27 Mar '19

27 Mar '19

Dear Freesurfer experts Hi I am trying to extract the time of data acquisition for each run from the functional data and compare it with my paradigm files. I thought the numbers in DICOM file names (ie, MR.1.3.12.2.1107.5.2.43.67026.2019011316475911712728505 ) are correspondent with the date and time of data acquisition. But they don not exactly match with my paradigm files. Do these numbers represent the exact time of data collection for each run? 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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