Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

Re: [Freesurfer] help
by Sarah Lavelle 01 Nov '22

01 Nov '22

External Email - Use Caution Hi Bruce, Thank you for your response, I really appreciate it. I am trying to understand the *mris_flatten* code so I can *quantify distortions* from inflated surface to flatmap for *parcelated regions*. There is a value printed of "total metric distortion ..%". I'm wondering how this is calculated because I can't find it anywhere on github. I would like to get this distortion value for a region of interest. Do you have any advice on how this could be done? Also, has there been any work on *automating the cuts*? Thanks, Sarah Hi Sarah Sorry, I?m not sure we have much to add. We don?t flatten much any longer, and the cuts are kind of ad hoc ? the one around the medial wall to get rid of non-cortical stuff, then the radial ones from there to remove particularly the curvature from the 3 poles. Mostly we just follow what Anders and Marty started doing way back when Bruce On Tue, 25 Oct 2022 at 17:02, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://secure-web.cisco.com/1kKhwjU99c5iofRTZoE0kIx6UgoX3fbPqapKpqVjol5sRm… > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Fail to install FreeSurfer 7 from the *.deb package (fsbuild) > 2. Re: FreeSurfer Mac crash (fsbuild) > 3. help (Sarah Lavelle) > 4. Re: help (Fischl, Bruce R.,PHD) > 5. MRI recon-all failed at talairach (Jonany, Vincent Joe) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 25 Oct 2022 06:14:54 +0200 > From: fsbuild <fsbuild(a)contbay.com> > Subject: Re: [Freesurfer] Fail to install FreeSurfer 7 from the *.deb > package > To: freesurfer(a)nmr.mgh.harvard.edu > Cc: liangqunjun(a)foxmail.com > Message-ID: <9e9ccbd9762dc3fe12a584cc5905b258(a)trashmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > This error in the log reports the file is likely corrupted and so could > not be unpacked and installed, > > > > dpkg-deb (subprocess): decompressing archive member: lzma error: > compressed data > >  is corrupt > > The md5 checksum of the file > downloaded to your machine needs to match the MD5 sum column > for the file as listed on the download page.  Check you see the > output listed below before trying to install the .pkg file (and re-download > if necessary). > > - R. > > > $ md5sum  freesurfer_ubuntu20-7.3.2_amd64.deb > b2d0f8e6285f4a8da72d008a6390a7fe  freesurfer_ubuntu20-7.3.2_amd64.deb > > > >

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Re: [Freesurfer] Issues Loading files from a Network Drive
by fsbuild 31 Oct '22

31 Oct '22

External Email - Use Caution Hello M, If you scroll down on this pagehttps://surfer.nmr.mgh.harvard.edu/fswiki/VM_67to the link for,Vbox_Windows_mount_external_drive - you will see an example of mounting an external SSD that has been formatted in the old exFAT file system.  I think that just works as is in the current VM w/o installing anything extra. If your NAS is formatted using Windows NTFS, then I think you will need to install some additional software in the VM in order to try mounting it.   I would first check about how your NAS is setup.   If it is NTFS formatted, you can try following this post to install the fuse software in the Linux VM and then try adding read only or read/write mount points to it inside the VM.   You might first try mounting things read only. https://secure-web.cisco.com/1sX6e0mzHWcMONw_UNzeH9a8TmqsfHaKzi8_FTDxExAK9I… - R. On Oct 31, 2022, at 19:40, Marielena Mendoza <marie.mendoza017(a)gmail.com> wrote:        External Email - Use Caution        Hello,I am having issues accessing files using "load volume."  The files I am trying to load are from a Network Attached Storage server. I can access the files fine through files explorer, but the entire directory does not appear when trying to select volume files. I installed Free Surfer on my Windows 11 laptop using Ubuntu 18. I also tried changing my directory for Subjects and received the following error WARNING: /mnt/network-drive/file path/... does not exist. Has anyone encountered this issue and have suggestions on how to fix this?Best,M_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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About recon-all -i option
by Ryosuke Hayashi 31 Oct '22

31 Oct '22

External Email - Use Caution Dear All, Hi. I have a question about the -i option for "recon-all". According to the explanation on the following page, the -i option specifies DICOM and NIfTI files, but is it OK to specify a mgz file with the -i option? https://secure-web.cisco.com/1UYHLpktzY4BG51M3Fy6Hmuwp2mf6dniSilXbYvOmS82Wj… I want to create a generic script file that calls NIfTI and mgz files as follows. recon-all -subject $SUBJECTS_ID -i $IMAGE_FILE -all Thank you, ryo

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Issues Loading files from a Network Drive
by Marielena Mendoza 31 Oct '22

31 Oct '22

External Email - Use Caution Hello, I am having issues accessing files using "load volume." The files I am trying to load are from a Network Attached Storage server. I can access the files fine through files explorer, but the entire directory does not appear when trying to select volume files. I installed Free Surfer on my Windows 11 laptop using Ubuntu 18. I also tried changing my directory for Subjects and received the following error WARNING: /mnt/network-drive/file path/... does not exist. Has anyone encountered this issue and have suggestions on how to fix this? Best, M

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Password Virtual Image file
by Brammie15 31 Oct '22

31 Oct '22

External Email - Use Caution Dear Freesurfer Team, I downloaded the Virtual Box image provided for windows computers. But was unable to extract the 7zip file. I read that I needed to send an e mail to this group. Can anybody help? Thank you Bart

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Neuroimaging Data Analyst Position Available at the Memory and Aging Program at Butler Hospital
by Elizabeth Sharp 28 Oct '22

28 Oct '22

External Email - Use Caution The Memory and Aging Program (MAP) at Butler Hospital is seeking a Neuroimaging Data Analyst to join the Neuroimaging Core Team (Director, Dr. Hwamee Oh) in the MAP. The MAP, one of the leading clinical research centers for Alzheimer’s disease (AD) in the United States, is conducting landmark studies that focus on preclinical and early AD such as ADNI, DIAN, LEADS, development of tau PET, tau-based treatments, deep brain stimulation and primary and secondary prevention trials for autosomal dominant and sporadic AD. The program performs extensive evaluations of study participants across the stages of AD from preclinical to dementia. The Neuroimaging Data Analyst will implement neuroimaging analysis pipelines of amyloid and tau PET as well as structural and functional MRI scans for ongoing studies. They will assist with neuroimaging data management, statistical analysis of imaging data, and preparing image data measures to be shared with MAP investigators as well as external collaborators. They will work closely with MAP investigators, 7-8 post-doctoral fellows, 5-7 undergraduate students and 3-5 research assistants. This position will also be responsible for providing supervision to trainees and research assistants. *Requirements:* Bachelor’s Degree in Computer Science, Bioinformatics, Biomedical Engineering, Electrical Engineering or related fields. A minimum of 3-5years of experience in neuroimaging data management or analysis, preferably of large dataset and clinical and brain imaging data and/or equivalent combination of skills and experience. Programming experience and proficiency in programming in Python (preferred) or Matlab. Demonstrable brain imaging data analysis skills (ideally PET and MRI) and solid working knowledge of Linux, MATLAB, python based neuroimaging analysis packages, and similar systems are required. Experience preprocessing and analyzing amyloid and tau PET and MRI imaging data using a variety of statistical packages, including SPM, FSL, and FreeSurfer are preferred. Must possess excellent communication and strong organizational skills. Must demonstrate an analytical mindset, excellent ability to attend to detail, superb problem-solving skills, and the ability to work independently as well as in a team setting. Knowledge in statistical analysis of neuroimaging data and experience using statistical packages e.g., R, SAS, SPSS.Possesses a willingness and ability to support a diverse and inclusive campus community. Applications can be submitted through this website: http://secure-web.cisco.com/1p9dusbzXfhud_haws8TdVK6yMNypE9bIi3p3TNwH7Qt9yH… opening.php?req=2195751&&cust_sort1=-1&cust_sort2=-1&cust_sort3=-1nohd&&internal=3932&nohd#job Schedule: Full Time -Days 40/wk -- Elizabeth Sharp Research Assistant Oh Lab Brown University

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Tracula path outputs quality checking
by Shanika Jayakody 28 Oct '22

28 Oct '22

External Email - Use Caution Dear FreeSurfer TRACULA team I have processed subjects using TRACULA on FS6.0 and 7.2. With both pipelines all the steps are completed without errors but for most subjects when I checked the pathstats.overall.txt file volume of the tract is almost equal to the length average. (unlike the example in Freesufer Wiki) I have attached pathstats for two people with (ID30720) and without (ID 30018) that problem (also attached one of my configuration files). Does this mean the tracts are not fully constructed? I was referring tracula freesurfer page and the following paper https://secure-web.cisco.com/1dIfxly6kRVrrbDgNkmQxrmTgb-DRd5cF1t7FkABP7tQos… I have done re-initializing of the tracts too without any luck of improving Even in freeview the tracts for 30720 looks like thin lines. I have been having this problem for a while and any suggestion to correct it will be much appreciated! Regrards Shanika

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conversion of .stats to .csv
by priya padma 27 Oct '22

27 Oct '22

External Email - Use Caution Dear Team, I would like to convert the .stats files that are being generated in the stats folder as an output from recon-all to csv file or excel file. Is there any way to convert .stats to .csv or .excel format? any help on this would be much appreciated. Thank you -- Best Regards Padma Priya *AI Developer * *PhenoMx, Inc.* *priya(a)phenomx.ai <priya(a)phenomx.ai> | (+82)10-5405-2685*

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Trac-all -prep error with interreg
by Ashwati Vipin (Dr) 27 Oct '22

27 Oct '22

External Email - Use Caution Hello, I’ve been trying to run the first step of DTI processing for my subjects. In the config file I left the “interreg” option default as “5” but it gives me a “set variable name” error and prematurely stops the processing. When I set “interreg = 4” it gives “trctrain : at least one mean and/or Gaussian curvature file is missing (.H, .K)” error. I’m not sure if this is a problem with the ANTs installation which is why “interreg=5” doesn’t work but “interreg = 4” doesn’t work either. So I’m really not sure what’s happening. I’ve attached the log file and config file. For the ANTs installation I ran the following before running the trac-all command: export ANTSPATH=/Volumes/Macintosh\ HD/Applications/freesurfer/7.2.0/ants-2.4.1/bin/ export PATH=${ANTSPATH}:$PATH echo $ANTSPATH Could someone please help? Best, Ashwati -- Ashwati Vipin (PhD) Research Fellow – Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore http://secure-web.cisco.com/1OSlDvqPJhl51Sc40lK71VUoqHNLymDzVOO62XWii17W08V…<http://secure-web.cisco.com/1OSlDvqPJhl51Sc40lK71VUoqHNLymDzVOO62XWii17W08V…> [signature_2362934844] ________________________________ CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you.

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overlay_threshold is ignored when using custom overlay
by Maya Yablonski 26 Oct '22

26 Oct '22

External Email - Use Caution Hello, I'm trying to use a custom colormap for an overlay in Freeview and I can't get the threshold option to work. Specifically, I want to display positive values with specific colors, and negative values with different colors, similarly to using the threshold with the default Heat colorscale ('Hot' for positive and 'cold' for negative, values outside the threshold do not appear at all). This is the code I've been using, and it seems to ignore the values provided by overlay_threshold: freeview -f <MYPATH>/sub-01/surf/lh.inflated:overlay=<MYPATH>tmap.curv:overlay_custom=-3,45,0,130,-9,220,210,250,3,255,70,0,9,255,255,0:overlay_threshold=3,9:overlay_color='clearlower','clearhigher' -colorscale This uses the right colors, but creates a continuous colorscale that spans -9 to 9, including the range [-3 3] which I want to threshold out of the map. I tried toggling the overlay_color='clearlower' and 'clearhigher', but couldn't find a combination that thresholded the low values around zero and not the extreme values (<-9 and >9). I also tested different values and seems like overlay_threshold is being completely ignored when overlay_custom is used. I couldn't get the right settings even when using the Freeview GUI. I tested this on Freesurfer versions 7.1.1 and 7.3.2 on MacOS Catalina (10.15.7). I'd appreciate any leads on this! Thanks, Maya

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