Freesurfer April 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
170 discussions

Question about LGI
by 肖伏龙 28 Apr '20

28 Apr '20

External Email - Use Caution Hi all Now I have file called lh.pial which comes from recon-all, but I want to obtain the local gyrification index (LGI), which should be lh.pial_lgi, so how to get this file from the lh.pial? what is the command line? And how long does it take?

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3dt1 contrast enhanced mri
by bar gen 28 Apr '20

28 Apr '20

External Email - Use Caution Hi everyone; Can I use 3dt1 contrast enhanced mri for thalamic, hippocampus and amygdala parcellation ?

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convert MNI152 coordinates into vertex index
by Marina Fernández 28 Apr '20

28 Apr '20

External Email - Use Caution Dear Freesurfer experts, I would like to convert the x, y, z MNI152 coordinates into the vertex index of the fsaverage5. I would like to do it with a function that can give me the vertex index as output, because I would like to use this information in a matlab script that continues with more calculations. Is there any function that can give me the vertex index (which corresponds to certain coordinates) as output? Thank you very much for your attention. Best wishes, Marina

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Re: [Freesurfer] Dev7bet1 links don't work
by fsbuild 28 Apr '20

28 Apr '20

External Email - Use Caution Hello Liz, The dev7 beta 1 links have been taken down in preparation for the 7.0.0 release.   There will be an announcement when the 7.0.0 release is available for download. - R. On Apr 28, 2020, at 02:39, Elizabeth Haris <e.haris(a)unsw.edu.au> wrote:        External Email - Use Caution        Hi all,I was trying to download the dev7bet1 version of FS but the page cannot be found (complete message below). I was trying to download it for Mac, but tested the other links too – they all show the same error.Many thanks, Liz Not FoundThe requested URL /pub/dist/freesurfer/7.0.0-beta/TBD was not found on this server.Apache/2.2.15 (CentOS) Server at surfer.nmr.mgh.harvard.edu Port 443 _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Dear professor
by 肖伏龙 28 Apr '20

28 Apr '20

External Email - Use Caution for example, here is the lh.gyrification.gii file from CAT calculation. I want a mgh file called lh.gyrification.mgh. My mris_convert command line is as followings: mris_convert lh.gyrification.gii lh.gyrification.mgh But this mgh file seemed failed. I do not know whether my command line is right or not. You should use mris_convert. What is your command line and terminal output? On 4/27/2020 11:05 AM, 肖伏龙 wrote: External Email - Use Caution Dear professor: I have a question to consult you. I have used the software CAT loaded in matlab to calculate the local gyrification index (LGI) and obtain a .gii file. But I want to use DODS model in freesurfer to statistics the LGI, so now I have to convert the .gii file into .mgh file. I have tried the mris_convert in freesurfer to carry out this but it seemed failed, so would you kind to show or tell me how to convert the .gii file to .mgh file? Thank you very much! I am looking forwards to hear from you. Sincerely, Fulong Xiao

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Dev7bet1 links don't work
by Elizabeth Haris 28 Apr '20

28 Apr '20

External Email - Use Caution Hi all, I was trying to download the dev7bet1 version of FS but the page cannot be found (complete message below). I was trying to download it for Mac, but tested the other links too – they all show the same error. Many thanks, Liz Not Found The requested URL /pub/dist/freesurfer/7.0.0-beta/TBD was not found on this server. ________________________________ Apache/2.2.15 (CentOS) Server at surfer.nmr.mgh.harvard.edu Port 443

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total brain volume
by Alexopoulos, Dimitrios 27 Apr '20

27 Apr '20

External Email - Use Caution Along with normalizing for eTIV, we'd like to normalize regional cortical volumes for total brain/tisuse volume (TBV). Is the output BrainSegNotVent in the aseg.sats basically equivalent to TBV? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Changing DOF with preproc-sess
by Wang, Jianbao 27 Apr '20

27 Apr '20

Hi Doug, It's a question follows the previous one about how to change the DOF with preproc-sess (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64033.html) This bug also happens when I only use the bbregister. Have this been fixed in Freesurfer7? If so, how can I add a different option for DOF while using preproc-sess? I don't find the related option in help document. Thanks! Best, Jianbao

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Question about pial surface error
by Giorgia Picci 27 Apr '20

27 Apr '20

External Email - Use Caution Hello, I have an editing question. We have some overlap in WM and pial surfaces, but we're unsure if this is an actual issue that should be edited, and if so, which surface should we be editing? I have attached an image of the issue here. We have circled the areas that we see the issue. It spans multiple slices. All the best, Giorgia [image: image.png] -- *Giorgia Picci, Ph.D.* Postdoctoral Researcher in Developmental Neuroimaging Program for Translational Research on Adversity and Neurodevelopment (P-TRAN) Department of Human Development and Family Studies The Pennsylvania State University 310 Biobehavioral Health Building University Park, PA 16802 814-863-0230

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Tracula error: ERROR: Must specify input table of gradient vectors
by Figueiro Longo, Maria Gabriela 27 Apr '20

27 Apr '20

Hello Dear Freesurfer Developers, I am attempting to run Tracula in the last to subject of my study (I had processed all the other subjects using the same script without problems). However, when I try to run the scrip bellow, I am having the error: " ERROR: Must specify input table of gradient vectors " I am reviewed the associated DICOM images and couldn't find any problem with the images. I reviewed a couple emails in the list, but couldn't find a clear reason for keeping having this error. I am using the Freesurfer Dev version. I really appreciate any help. Thank you, Gabriela # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /autofs/cluster/guptagp/LLLT/fsrecon # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /autofs/cluster/guptagp/gabi/tracula/Output # Subject IDs (one per time point per subject) # set subjlist = ( 3LT050_s1_170715 ) # Longitudinal base template subject IDs (one for each time point above) # set baselist = ( 3LT050 ) # In case you want to analyze only Huey and Louie # Default: Run analysis on all time points and subjects # # set runlist = (1 2 5 6) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /autofs/cluster/guptagp/LLLT/raw_data set dcmlist = ( 3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.20170715092715598296003 ) Gabriela Longo, MD, MSc. Emergency Radiology Clinical Fellow, Emergency Radiology Division Massachusetts General Hospital (MGH) mfigueirolongo(a)mgh.harvard.edu Phone: +1 857 214 0568

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Freesurfer April 2020