Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

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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来自肖伏龙的邮件
by 肖伏龙 27 Apr '20

27 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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Dear professor
by 肖伏龙 27 Apr '20

27 Apr '20

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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correcting fsaverage surface area by eICV
by Paul 27 Apr '20

27 Apr '20

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How is Total cortical gray matter volume calculated
by Ian Hardingham 27 Apr '20

27 Apr '20

External Email - Use Caution Morning Freesurfers. Can you describe how the FS stat Total cortical gray matter volume is calculated from the files in the freesurfer subject directory? Is there an mgz file where each voxel has an estimated percentage grey matter here as the value... or is the volume between the surfaces calculated somehow? Thanks, Ian

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Freeview surface loading error : MRISread failed
by Sezer, Idil 27 Apr '20

27 Apr '20

Hello FreeSurfer developers, I am having an issue viewing a .mgh file I created. Using an output from the fmriprep pipeline, I converted an nii.gz to a .mgh surface : mri_vol2surf --src <participant_ID>_desc-preproc_T1w.nii.gz --<participant_ID> --regheader <participant_ID> --hemi lh I am trying to visualize this surface on an inflated brain using: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=/Users/idilsezer/Desktop/fmriprep_outputs/test/lh.<participant_ID>.mgh I get an error message saying : MRISread(/Users/idilsezer/Desktop/fmriprep_outputs/freesurfer/fsaverage/surf/lh.inflated): could not open file No such file or directory MRISread failed MRISread(/Users/idilsezer/Desktop/fmriprep_outputs/freesurfer/fsaverage/surf/lh.inflated): could not open file And Freeview’s GUI says : Failed to load Surface /Users/idilsezer/Desktop/fmriprep_outputs/freesurfer/fsaverage/surf/lh.inflated I also tried loading it directly from the GUI instead of the command line, it also doesn’t seem to work unfortunately. FreeSurfer version : freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform : mac OS Catalina version 10.15.4 (19E287) Thanks in advance for your help, Best regards, Idil

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Mri_segstats for PET data: Reviewer question
by Shane Schofield 27 Apr '20

27 Apr '20

External Email - Use Caution Hi Freesurfer Team, I have used mri_segstats to get ythe mean PET uptake across all the parcellations in the WMPARC space. These values were calculated in the native PET space (following the DTI tutorial). A reviewer asked what is the grey matter probability of the ROI and I am not sure how to address this. Any help is kindly appreciated. Thanks.

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