Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

Pass code request for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Eduardo Europa 12 Nov '22

12 Nov '22

External Email - Use Caution Hello, This is a request to receive the pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z Thank you, *Eduardo Europa, PhD, CCC-SLP (he/him)* Assistant Professor, Communicative Disorders & Sciences San José State University eduardo.europa(a)sjsu.edu Visit my website: https://secure-web.cisco.com/1bg97TFGS27e-eo0fDqTrd0vj7supBHYYlcL4qEd1DTPLS…

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Virtual Machine zip Password
by Cesare Jenkins 12 Nov '22

12 Nov '22

External Email - Use Caution Could I please obtain the password to unzip the virtual machine zip file (the most recent one, 7.2 I believe)? Thanks, Cesare

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Only extract stats information question
by 蔡嘉鑫 12 Nov '22

12 Nov '22

External Email - Use Caution Dear freesurfer, Greeting! We met a problem need your kind help. What if I only need extract the stats information in freesurfer? You know it will take a long time to run all step. Can I only get the 'stats' information and shorten the running time? Best wishes! Jiaxin Cai

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How to set original orientation for converted images
by Haiyun Chen 11 Nov '22

11 Nov '22

External Email - Use Caution Hello FreeSurfer Experts, I converted the aseg.mgz file to aseg.nii using mri_convert command, the aseg.mgz file is located in the directory below based on your tutorial: tutorial_data_20190918_1558/practice_with_data/Subj001/mri When I open the file aseg.nii in a different application, the original orientation is not sagittal. In the MRI protocol, the original orientation is sagittal. Could you please help to tell how to set the original orientation of output images to be sagittal? Thank you in advance! Best regards Haiyun

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Pass code request
by Lorenzo Civilla 11 Nov '22

11 Nov '22

External Email - Use Caution Dear Freesurfer team, thank you for the great software you're developing, it is extremely nice! I am writing to ask you for a pass code to open the 7z archive I downloaded from the following page: https://secure-web.cisco.com/1a_Lk7dJKn84XrIID0fEz1mmFgsz5S6WNCBj4IDEm0i7Kd… I would like to use Freesurfer for research purposes in Neurosurgery, in particular in neurovascular. My best regards, Lorenzo Civilla, MSc -------------------- Senior Scientist at Medical University of Vienna lorenzo.civilla(a)meduniwien.ac.at

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Segmentation of hippocampus(left), grey and white matter regions.
by PRASAD D 10 Nov '22

10 Nov '22

External Email - Use Caution Hello everyone. I’m new to FREESURFER I would like to segment the sMRI images. I have extracted(skull stripped) the brain region from the sMRI image using BET. but i'm interested in hippocampus(left), grey and white matter regions. Can you please guide me how to segment those specific regions automatically. Thanks in advance. -- *Yours sincerely* *D.PRASAD* *Full Time Research Scholar(QIP)* *Dept. of ECE, PTU.*

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[Freesetfer] Requesting Password for VM soft
by Андрей Калиниченко 10 Nov '22

10 Nov '22

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Re: [Freesurfer] Preproc-sess crashed - 3dvolreg.afni error
by fsbuild 10 Nov '22

10 Nov '22

External Email - Use Caution On MacOS I would try running the fs_install_mcr script with, $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh <... output showing SUBJECTS_DIR and other environment variables> $ cd  $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2014b That script should setup the environment to find the libmwm* libraries it installs in the freesurfer tree under $FREESURFER_HOME/MCRv84/bin/glnxa64. But If your shell environment (e.g., via $HOME/.cshrc or $HOME/.bashrc) somehow sets LD_LIBRARY_PATH to point to a different matlab installation, then you may not pick up the matlab distribution from the freesurfer tree. - R.

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volumes/surfaces FS6.0 vs FS7.2/3.2
by Alexopoulos, Dimitrios 09 Nov '22

09 Nov '22

External Email - Use Caution We have processed a large pediatric cohort (9-10 y.o. subjects) acquired with 1 mm isotopic voxels using FS 6.0. We are now beginning to rescan the same cohort at 15-16 y.o. using the exact same imaging protocol and scanner (3T, Prizma). If we process with FS 7.2/7.3.2, can we analyze the surface/volume measures/outputs with the earlier FS.6.0. structural outputs? We'd like to look at volume changes and cortical expansion analysis between the 2 timepoints. Is this reasonable or should we run the new cohort using 6.0 as well? Or rerun the earlier cohort at 7.2/7.3.2. Any suggestions as to the best approach. 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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FS-FAST preprocessing of rs-fMRI data and extracting timeseries from Yeo's Networks
by stdp82＠virgilio.it 09 Nov '22

09 Nov '22

External Email - Use Caution I aim at FS-FAST preprocessing of rs-fMRI data and extracting timeseries from Yeo's Networks. 1 - I won’t perform a seed based analysis. 2 - I want to exclude the five sets of nuisance variables in mkanalysis-sess. Please could you check whether the command lines listed below are corrected for this aim? mkanalysis-sess -analysis fc.noseed.surf.lh -surface fsaverage lh -fwhm 0 -notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten -force mkanalysis-sess -analysis fc.noseed.surf.rh -surface fsaverage rh -fwhm 0 -notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten -force selxavg3-sess -s subj_folder_name -a fc.noseed.surf.lh -overwrite -no-con-ok selxavg3-sess -s subj_folder_name -a fc.noseed.surf.rh -overwrite -no-con-ok 3 - I want to extract the timecourse, subject-by-subject, from each spitted Yeo's component. The feature of produced "fc.noseed.surf" files are: type: nii dimensions: 163842 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 I have tried to use mri_segstats --slabel ${1} lh subj/label/Xcomponent --i ${1}/rest/fc.noseed.surf.lh/meanfunc.nii.gz --sum /Xcomponent.sum.txt --avgwf Xcomponent.wav.txt But an error of dimension mismatch between input volume and seg occurs. input 163842 1 1 seg 116809 1 1 The input should be in fsaverage. Which is the correct average of set? And what do I do to run correctly at this step? Thanks Stefano

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