Freesurfer May 2022

freesurfer@nmr.mgh.harvard.edu

86 participants
124 discussions

Re: [Freesurfer] Recon-all
by fsbuild 06 May '22

06 May '22

External Email - Use Caution Hello Krystally, Try putting the directory Sub-132 under your userid’s home directory, i.e., /home/developer/Sub-132, and then set SUBJECTS_DIR in the environment to point to it.  With the directory Sub-132 specified on your command line, you could then try,$ export SUBJECTS_DIR=/home/developer - R. On May 5, 2022, at 21:53, krystaly <krystaly(a)hku.hk> wrote:        External Email - Use Caution        Dear Freesurfer experts, I am new to FS 7.2.0 (Window 10), and trying to run the Recon-all command as demonstrated on the website (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://andysbrainbook.readthedocs.io/en/latest/FreeSurfer/FS_ShortCourse/FS_03_ReconAll.html). Before running the command, I have converted DICOM files into NIFTI files.  I, then, moved the nii files to Desktop at FS.  They are in the folder named “Sub-132”.  However, I got the following errors: developer@developer-VirtualBox:~/Desktop/Sub-132$ recon-all -s Sub-132 -i Sub-132_SAG_T1_MPRAGE_(INC_UPPER_CX_AS_MUCH)__2.nii -allbash: syntax error near unexpected token `(' To make another attempt, I tried to process with another T1 image, and I got the following error: developer@developer-VirtualBox:~/Desktop/Sub-132$ recon-all -s Sub-132 -i Sub-132_T1_COR_5_0.5__250_i00002.nii -allmkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission deniedmkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission deniedmkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission deniedcp: cannot create regular file '/usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt': No such file or directorycat: /usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt: No such file or directoryINFO: FreeSurfer build stamps do not matchSubject Stamp: Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b/usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/patchdir.txt: No such file or directory. I reckoned that the T1 images could not be processed with only 1 plane.  Would you please kindly advise on merging 3-plane T1 images into one comprehensive T1-weighter image for further processing? Or would you please let me know what went wrong in this case? Thanks. Best regards, Krystal  _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail..nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Passcode VM
by fsbuild 05 May '22

05 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 5, 2022, at 16:36, Marius Zeinhofer <mariusz(a)simula.no> wrote:        External Email - Use Caution        Hi,I am interested in the passcode for the VM as explained on the Freesurfer website.Thank you very much.Best,Marius_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Library Error
by fsbuild 05 May '22

05 May '22

External Email - Use Caution Hello Jabeur, Please check your setup.  When the VM is first setup and run, there should be no library errors from freeview.  You can test this with the following commands. developer@developer-VirtualBox:~$ cd $HOMEdeveloper@developer-VirtualBox:~$ pwd/home/developerdeveloper@developer-VirtualBox:~$ which freeview/usr/local/freesurfer/7.2.0/bin/freeviewdeveloper@developer-VirtualBox:~$ ldd `which freeview` | grep "not found"developer@developer-VirtualBox:~$ If you still see a library reported as not found then something happened with your environment and/or how freesurfer is now setup to cause the error.  In that case, I recommend you delete the current FS_7_2_0_ubuntu_18_04_06 virtual machine from the VirtualBox client (choose to delete the files), setup the VM again, and when you first login check freeview again with the above commands. When you want to process your own subject data we recommend you create a new directory in your home directory and set the environment variable SUBJECTS_DIR to point to it.  The install of freesurfer including the provided subject data is meant for reference and the files are in a protected system directory.  So it’s preferable to not modify and/or write files to where SUBJECTS_DIR points to out of the box.  Instead, just create a new directory for processing subjects with, e.g., developer@developer-VirtualBox:~$ cd $HOMEdeveloper@developer-VirtualBox:~$ mkdir my_subjectsdeveloper@developer-VirtualBox:~$ export SUBJECTS_DIR=$HOME/my_subjects - and put your subject data to process in $HOME/my_subjects - R. On May 5, 2022, at 19:14, Jabeur Mouna <jabeurmouna(a)gmail.com> wrote:        External Email - Use Caution        <image.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Library Error
by Jabeur Mouna 05 May '22

05 May '22

External Email - Use Caution [image: image.png]

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Curvature data question
by Samuel Paré 05 May '22

05 May '22

External Email - Use Caution Hello, We are looking at some of our data acquired on a 7T magnet. We ran recon-all with the “highres” flag. The obtained results for cortical thickness and cortical volume are very comparable to data that we obtain when using 3 T brain images. However, the results for cortical curvature are significantly different from what we get by our 3 T data. I attach the output of mean cortical curvature values using the Destrieux atlas for a 3T and 7T dataset on healthy controls. As you can notice, they differ roughly by a factor of 2. Any explanation for what may cause this large difference? Thanks, Samuel [image: image.png] -- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal

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Passcode VM
by Marius Zeinhofer 05 May '22

05 May '22

External Email - Use Caution Hi, I am interested in the passcode for the VM as explained on the Freesurfer website. Thank you very much. Best, Marius

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recon-all -long error (the third step of the longitudinal pipeline)
by FONG, manson CM [CBS] 05 May '22

05 May '22

External Email - Use Caution Hello Experts, I'm attempting to run the longitudinal pipeline, as described in this tutorial page (https://secure-web.cisco.com/1Ixk7gG7cuuWHkljgthBFn12YPhnTaeVaFK7XUh0r8RABW…) I've tried the pipeline on 13 subjects (from the Alzheimer Disease Neuroimaging Initiative), each with varying number of time points. For all of them, I succeeded in the first two steps ( [CROSS] & [BASE] ), but recon-all threw an error for all subjects & for all time-points midway through the third step ( [LONG] ). For example, for the subject 128_S_4832, I've run the cross-sectional step for all time points, resulting in corresponding folders called $SUBJECTS_DIR/128_S_4832_Ses01 and so on, and a template in the folder $SUBJECTS_DIR/128_S_4832 (from the [BASE] step). The exact command that exited with ERRORS was: recon-all -long 128_S_4832_Ses01 128_S_4832 -all -parallel -openmp 16 Like in the first two step, I was using parallel computing with 16 cores. From recon-all.log in the folder $SUBJECTS_DIR/128_S_4832_Ses01.long.128_S_4832/scripts, it appears that the last command that reported no issue was: mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated After this step, recon-all threw an error. The last four lines in my log file are: Usage: reconbatchjobs logfile cmdfile1 [cmdfile2 ...] See recon-all script for examples. Linux ubda-d050 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 128_S_4832_Ses01.long.128_S_4832 exited with ERRORS at Sat Apr 30 22:10:07 HKT 2022 I've searched the list and no similar errors have been reported. 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b 2) Platform: CentOS Linux 7 (Core) 3) recon-all.log & recon-all.error: see attached Many thanks for your advice in advance! Best regards, Manson Fong [https://secure-web.cisco.com/1RCpfhD31IvrvhPAqouiPEccsev2Meg7QPUJ7MSltmEQqz…] Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.

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segmentHA_T1, mri_segstats: How can I get the PVC uptake for amygdalar nuclei?
by Tun, Samantha 05 May '22

05 May '22

External Email - Use Caution Hello Freesurfer Devs! I am attempting to extract the tau uptake in the amygdalar segmentations. I ran this command: mri_segstats --seg rh.hippoAmygLabels-T1.v21.FS60.FSvoxelSpace.mgz --i anat_resliced.mgz --sum rHA_stats.dat to try and calculate the tau uptake. I was able to get an output, but I am unsure how to proceed from here. I basically want to get the pvc uptake of the amygdalar and hippocampal subfields scaled to the pons. I don't think I can run the mri_gtmpvc command, so if you had any insight on how to calculate the scaled uptake of tau in the subfields, let me know! Best, Samantha

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Scalable recon workflow
by Horn, Mitchell Jacob 05 May '22

05 May '22

Hi Experts, If I have 100s of subjects to recon and have access to an HPC with both GPU and CPU options what is the recommended flags to maximize speed performance? Is … -parallel -openmp 4 … still the best approach? And if so, is 2GB memory/core best (keeping it 8GB memory/subject) or is there some better arrangement? Best, Mitch

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"B0 distortion correction with reverse-polarity DWIs"
by Gonzalo Rojas Costa 04 May '22

04 May '22

External Email - Use Caution Hi: I tried to process a tractography with TRACULA. I got the error "ERROR: for B0 distortion correction with reverse-polarity DWIs. ERROR: or for model-based eddy-current distortion correction, ERROR: must specify PE direction". What does it mean? I read the webpage https://secure-web.cisco.com/1guG1MnfZf84DwQHfWaHHLuw6SMY7Z-tutMOyUkvQB8sNK…, but It was not clear to me how to solve the problem. 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 http://secure-web.cisco.com/12GtciP9OUiW5DkspMfrRVy3WsQH7lo4AsKjg0Sj8uml6hm… https://secure-web.cisco.com/1MqLKS1F46RbplHUM6h_KNyjN0BiKcyL58vxd1gCfQMyaz… https://secure-web.cisco.com/1VYyKt8bpinu3O6RicUYTbOJmllqjZD8fa4vMdxnypEQay… https://secure-web.cisco.com/1cDJNj5GQNOJNQJmRBcgfx71cRT_O6MgqP1ftnJlfUY5Nu… http://secure-web.cisco.com/1FaAL_RhtLAORTKofMH0umP03Sz7z4fz1ix6_BxtTBFSkxZ… https://secure-web.cisco.com/1Chz4Nd2Gs4bv5UU_W7XXxgXJhQCBYB_9QHiTrY3XemPxP…

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Freesurfer May 2022