Freesurfer August 2021

freesurfer@nmr.mgh.harvard.edu

73 participants
101 discussions

bilateral seed to whole brain connectivity analysis
by Nasiriavanaki, Zahra,M.D. 10 Aug '21

10 Aug '21

Dear Experts, I have functional ROIs on the left and right hemispheres, and I’m trying to do a bilateral seed to whole brain connectivity analysis. My question is: in order to make a bilateral seed, shall I manually average the .dat files (output of fcseed-sess) from left hemi and right hemi to make a bilateral seed (see below)? fcseed-config -segid 1 -seg lh.mgz -fcname lh.dat -fsd rest -rlf restruns -mean -cfg lh.config fcseed-sess -s . -d . -cfg lh.config fcseed-config -segid 1 -seg rh.mgz -fcname rh.dat -fsd rest -rlf restruns -mean -cfg rh.config fcseed-sess -s . -d . -cfg rh.config bilateral.dat= (lh.dat+rh.dat)/2 OR should I use the left and right ROIs in fcseed-config at the same time, so the out put of fcseed-sess be the bilateral seed? Please see below commands: fcseed-config -segid 1 -seg lh.mgz -segid 1 -seg rh.mgz -fcname bi.dat -fsd rest -rlf restruns -mean -cfg bi.config fcseed-sess -s . -d . -cfg bi.config I appreciate your responses. Thanks, Mona Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

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Fwd: [Neuroimaging] [Nibabel] Discourse category for Surface API discussions
by Satrajit Ghosh 09 Aug '21

09 Aug '21

External Email - Use Caution fyi ---------- Forwarded message --------- From: Christopher Markiewicz <markiewicz(a)stanford.edu> Date: Mon, Aug 9, 2021 at 5:01 PM Subject: [Neuroimaging] [Nibabel] Discourse category for Surface API discussions To: neuroimaging(a)python.org <neuroimaging(a)python.org> Hi all, I'm starting to work on the Surface API portion of the Nibabel grant. I've created a category on the Discourse here: https://secure-web.cisco.com/1fZyTqmwozZU5Qoa2utEX0kDdW_8B7XIMEFga96aHR-Yct… And I've started some initial notes here mostly laying out the problem: https://secure-web.cisco.com/1qQtCe4EJSW0O7Z_CBMnNittP03bU4FYzr1xy2YZOTw_oa… The next steps are going to be to identify use cases for people working with surface data, which will also involve finding people who I may not know about, so please forward this on to people who might be interested in joining the discussion. -- Christopher J. Markiewicz, PhD Center for Reproducible Neuroscience Stanford University _______________________________________________ Neuroimaging mailing list Neuroimaging(a)python.org https://secure-web.cisco.com/1Zrv7RS4PEvZfb7azKaQbWoX5ysGPT8TngX38S6Ud5LMDA…

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Announcement for Neurodevelopmental Special Issue in Brain Sciences
by Picci, Giorgia 09 Aug '21

09 Aug '21

External Email - Use Caution Dear all, It is our pleasure to invite manuscript submissions for publication in our special issue entitled "Neurodevelopmental Correlates of Substance Use and Abuse in Adolescence" in Brain Sciences (IF: 3.33; ISSN 2076-3425; CODEN: BSRCCS). For this special issue, we are soliciting original research papers, brief reports, reviews, perspectives, and meta-analyses regarding the neural antecedents and consequences of adolescent substance use. We particularly encourage submissions that focus on cutting-edge methodological approaches and imaging methods (e.g., brain-predicted age, multimodal approaches, leveraging large datasets, dynamic/brain state & functional connectivity). Manuscripts are due November 25th, 2021 and will be peer-reviewed and published online as they are accepted. Further details regarding this special issue can be found here<https://secure-web.cisco.com/1gLIbySUMZ9_BPqko-w2QqJO5OhNNe2MASV8liqYOJ4ySQ…>. If you have any questions, please feel free to reach out to the guest editors or managing editor (Emma Paintain, emma.paintain(a)mdpi.com<mailto:emma.paintain@mdpi.com>). Kind regards, Dr. Emma Rose (Penn State University) Dr. Giorgia Picci (Boys Town National Research Hospital & PSU) ______________________________________ Giorgia Picci, PhD (she/her) Postdoctoral Research Fellow * DICoN Lab<https://secure-web.cisco.com/1x2Ljh6i4aAkfI4hxBBOh8XoGqaNEM2kgNwjnks9OV8A-R…> Institute for Human Neuroscience Boys Town National Research Hospital

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dwi_orig_las issue trac-all -prep in FS 7.2
by juergen.haenggi＠upd.unibe.ch 09 Aug '21

09 Aug '21

External Email - Use Caution Dear TRACULA experts I use the newest version of TRACULA (FS 7.2, official release) and face the same problem as already reported by another user https://secure-web.cisco.com/1X5AHUcHXClyJtmxIDuq0cEQ7oR9Y81XGrojDN0ZsSnvYn… As suggested by the answer to the above link, this other user did not use an official release of FS, and no explicit solution was mentioned in this link. I used an official version, but got the same error. BTW, if using TRACULA in FS 7.1.1, this error did not occur. The error that occurs is the following (log and config file attached): error: niiRead(): error opening file /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/01_TRACULA_Results_NIFTI_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz As described by the other user, the file is initially created, but then renamed to dwi.nii.gz and therefore not present in the dmri directory. BTW, my data is already in LAS orientation. The error only occurs if using NIFTI files but not if using the DICOM files. Actually, I could use DICOMs, but I faced the problem that dTE could not be found in the DICOM header and/or b0info.dat file, respectively, (see error below) because only one TE is present in the DICOM header of the phase image as suggested by the meta data in the OSIRIX DICOM viewer, and therefore I would rather use NIFTI files and define dTE in the config file as it has been suggested that this is possible in TRACULA in FS 7.2. writing to /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0pha.nii.gz... mri_probedicom --i /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm > /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0info.dat ERROR: Need dTE for field map /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm However, if I try to use DICOM files and "set dTE = 2.46“ in the config file, the same error occurred as when not setting dTE in the config file. Thanks in advance for any advice Best regards Jürgen

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Ubuntu image developer password
by John Hayes 07 Aug '21

07 Aug '21

External Email - Use Caution Hi, I installed the Ubuntu image in virtual box to run free surfer on windows, but it is requiring a password to log into the developer user. Is it possible to get this password? Thanks, John

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Diffusion MRI postdoc position
by Corinna Bauer 06 Aug '21

06 Aug '21

External Email - Use Caution We are seeking a full-time postdoctoral fellow with experience in diffusion analysis with an emphasis on network-based approaches, NODDI, DKI, and tract-specific analysis. The NIH-funded project employs structural, diffusion, and relaxometry based MRI methods to target thalamo-cortical changes in morphometry, neural networks, and MRI-based markers of myelin in youths with perinatal brain injury. We are seeking a candidate with the following qualifications: • Doctoral degree in computer science, neuroscience, or related field • Advanced skills in the processing and analysis of diffusion (including connectivity, DKI, and NODDI approaches) data, particularly focusing on network-based approaches are required • Strong coding skills in python, MATLAB, bash, etc. • Experience with fMRI design and analysis is a plus Interested candidates should send a cover letter including, a brief summary of their research interests and career goals, their C.V., and the names and phone numbers of three references to Corinna Bauer ( Corinna_Bauer(a)meei.harvard.edu) Additional details can be found at: https://secure-web.cisco.com/1PRcDuRd4mfRf2yIwKkDZ9B-oKmLA-2p68m-jCGxuMCJA8…

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Re: [Freesurfer] recon-all exited with ERRORS
by fsbuild 05 Aug '21

05 Aug '21

External Email - Use Caution If you are running Virtualbox to host linux on a windows machine sharing a folder from a windows NTFS file system, then it may not work to create soft links in linux on the mounted share w/o setting some things on the Windows side.  I’m not up on what current versions of VirtualBox support for creating soft links in a linux file system on top of the (different) NTFS file system, but here is some info from ~2 years ago, https://secure-web.cisco.com/1FAdsc9WBYl3JetwHMp2nc_AR2rQlI8PlEU1… - R. On Aug 5, 2021, at 10:20, Kiyotaka Nemoto <kiyotaka(a)nemotos.net> wrote:        External Email - Use Caution        Hi,I think the problem is caused because Zhaoguang uses a VirtualBox share folder.The path "/media/sf_T1/" indicates the path is a shared folder of VirtualBox.Symbolic links can be used on some certain conditions.Source: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1SzkQ16diCzjzLRbWT9fZxbUN_qVihhNUAbkqh… think there are two workaround options..1. Avoid using shared folders    If you copy your T1 image from shared folder to somewhere on your Linux guest, recon-all should go well.2. Change "ln -s" to "cp" in recon-all    I tweak recon-all a little bit so that recon-all works well with files on VirtualBox shared folders.    The commands below makes backup of recon-all first, then substitute "ln -s" with "cp" or "cp -r"=====cd $FREESURFER_HOME/binsudo cp recon-all recon-all.origsudo sed -i 's/ln -s \$hemi/cp \$hemi/' recon-allsudo sed -i 's/ln -s \$FREESURFER_HOME\/subjects\/fsaverage/cp -r \$FREESURFER_HOME\/subjects\/fsaverage \$SUBJECTS_DIR/' recon-allsudo sed -i 's/ln -s \$FREESURFER_HOME\/subjects\/\${hemi}.EC_average/cp -r \$FREESURFER_HOME\/subjects\/\${hemi}.EC_average \$SUBJECTS_DIR/' recon-all=====Hope this helps,KiyotakaOn Thu, Aug 5, 2021 at 10:42 PM Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote:Look in /media/sf_T1/recon/demo3/surfDoes lh.white.preaparc.H exist?If so, does lh.white.H exist?If not, what happens when you runln -s lh.white.preaparc.H lh.white.Hin that folder?On 8/5/2021 1:41 AM, guang wrote:        External Email - Use Caution        Hello FreeSurfer Developers,I'm attempting to preprocess my nii.gz files with FreeSurfer, But some errors occurred  when I  recon-all the data. I've attached the batch script and  recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0..0-2beb96c2) Platform: CentOS release 6.10 (Final)3) uname -a: Linux bogon 2.6.32-754.2.1.el6.x86_64 #1 SMP Fri Jul 13 12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux4) recon-all.log: see attached5) batch .sh file:see attachedThank you  for any reply.zhaoguang  _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1qXkHhWjbbX7kqhyJvxsVIR9MtQArotd4VbtHCKRYOGOQ0… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1II6DOs_uxItsRQUh3upLmjq_rgOJnRtQnqFDe… 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/16Inw7HJ6kpX4IG1P-lnhb3mwA7tevjm5pPEH7e…;. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.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. --Kiyotaka Nemoto, M.D., Ph.D.Associate ProfessorDepartment of PsychiatryDivision of Clinical Medicine, Faculty of MedicineUniversity of Tsukuba1-1-1 Tennodai Tsukuba, Ibaraki 305-8575, JapanE-mail: kiyotaka@nemotos.net_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Creating an Freesurfer .annot file from an MNI coordinate region of interest
by Paul Dhami 05 Aug '21

05 Aug '21

External Email - Use Caution Dear FS community, My ultimate goal is to do a seed of interest connectivity analysis. Accordingly, I have MNI coordinates for a seed (e.g., left DLPFC). However, for the softwares I am using (CONN toolbox and Brainstorm), I need a .annot file which has the surface region of interest label I want to use as the seed. My problem is I do not know how to create an .annot file from MNI coordinates of my seed/region of interest. Can I create an .annot or label file with Freesurfer centered around an MNI coordinate, or would I first need to create a volume ROI using another software? Any directions as to how I can do this would be greatly appreciated. Best Wishes, Paul

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recon-all exited with ERRORS
by guang 05 Aug '21

05 Aug '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to preprocess my nii.gz files with FreeSurfer, But some errors occurred when I recon-all the data. I've attached the batch script and recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: CentOS release 6.10 (Final) 3) uname -a: Linux bogon 2.6.32-754.2.1.el6.x86_64 #1 SMP Fri Jul 13 12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached 5) batch .sh file:see attached Thank you for any reply. zhaoguang

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How to join certain segmentation with T1.mgz and save them in one file with nifti format
by Ammar Shujaa 05 Aug '21

05 Aug '21

External Email - Use Caution Hello FreeSurfur Developers, I have used binary mask and got the segmentations: right and left-hypocampus.mgz. I just want to know how to join these segmentations with T1.mgz so that I can get one file containing T1 image with the two segmentations. I also want to save the T1 image with the the segmentions in nifti format. Thanks in advance. Ammar

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Freesurfer August 2021