Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

Error Opening File
by Rachel Wagner 28 Jun '22

28 Jun '22

External Email - Use Caution Hello, I am getting the following error when trying to convert a file on my desktop: developer@developer-VirtualBox:~$ mri_convert home/developer/desktop/brain.mgz brain.nii mri_convert home/developer/desktop/brain.mgz brain.nii reading from home/developer/desktop/brain.mgz... error: mghRead(home/developer/desktop/brain.mgz, -1): could not open file developer@developer-VirtualBox:~$ Am I doing something incorrectly? Thanks! Rachel

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Converting File Type
by Rachel Wagner 28 Jun '22

28 Jun '22

External Email - Use Caution Hello, I have an img and an mgz file I would like to convert to a nii file. How can I do so? Thanks! Rachel

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passcord for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Ryo Kitada 28 Jun '22

28 Jun '22

External Email - Use Caution Dear FreeSurfer developer teams, Could you send me the passcode for FS_7_2_0_Ubuntu_18_04_06.ova.7z? Cheers, Ryo.

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7Zip Password
by Richard Ronayne 27 Jun '22

27 Jun '22

External Email - Use Caution Hi there, I am trying to unzip FS_7_2_0_ubuntu_18_04_06.ova.7z to run in VirtualBox. Could you please reply to this email with the password for the 7Zip file? Thank you for your time. Kind regards, Richard

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Pass Code for the Virtual Image with FreeSurfer
by Hyun Song 27 Jun '22

27 Jun '22

External Email - Use Caution Hello FreeSurfer developers, I am attempting to set up and run the Freesurfer 7.2.0 release with the virtual image as described in https://secure-web.cisco.com/12fbDRySJWvFNE95kfnxYyknT6iNKMuI4NW2jBTJerlb-r… <https://secure-web.cisco.com/1Yywe94avXxYd05IrWZqd84sqbEs04TfWQqAXcGEXEEWs6…>. Would you please send me the pass code to expand the 7zip file? Thanks much, Best, Hyun

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mri_label2vol fill-ribbon segmentation fault
by Benjamin Deck 27 Jun '22

27 Jun '22

External Email - Use Caution Hi there, Having issues with the following command: mri_label2vol --annot lh.yeo_2011.annot --temp /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz produces the following error: Number of labels: 0 Annot File: lh.yeo_2011.annot Template Volume: /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz Outut Volume: lh.sub-DAEK_annot_nat.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 Template RAS-to-Vox: -------- -1.25000 -0.00000 -0.00000 160.00000; -0.00000 -0.00000 -1.25000 160.00000; -0.00000 1.25000 -0.00000 160.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 0.512 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- -1.25000 0.00000 0.00000 160.00000; 0.00000 0.00000 -1.25000 160.00000; 0.00000 1.25000 0.00000 160.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from lh.yeo_2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault But when I run the same command without fill-ribbon the process runs to completion. Not sure if this is a memory issue or something else. Ben -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1iKwJbETCAUSlHWE3gbz9IWJ4YvkeL0JhP2fGTP_IRLe0Y…> Virus-free. http://secure-web.cisco.com/1sIn3vnwCXrSMS_IlIv6nc9WGBmrAG1JrUsifsa6xR7SIRw… <https://secure-web.cisco.com/1lKwnHJD_3HKNZFq3yBeIxnL1wagOdiYUAdM7xFJLwCTPp…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Fwd: Pass code request for 7z
by Lesly Manresa 27 Jun '22

27 Jun '22

External Email - Use Caution Hi, I am writing to request the pass code to unzip the FS_7_2_0_Ubuntu_18_04_06.ova.7z file. Thanks, Lesly

1 0

MeanItensities- PET
by Bouchra Guelib 27 Jun '22

27 Jun '22

External Email - Use Caution Hi, I wonder if someone can help me to do something similar to that: " the mean intensity of each FreeSurfer region (ROI) for the 45 subcortical and the 68 cortical regions were assessed the mean intensity of each FreeSurfer region (ROI) for the 45 subcortical and the 68 cortical regions were assessed to obtain SVU". Also, I found an article that mentioned that " the estimated total intracranial volume (eTIV) is calculated, which is used later for normalization of the volumetric measures". My questions are: 1) In " gtm.stats.dat" not all subcortical regions are mentioned, why? 2) I applied "mri_getmpc" to obtain the mean intensity, however, I could not figure out what I should do after this step to obtain the mean intensity and compute SVU. 3) why do they use eTIV, should I use it, and if yes how! best regards. -- *GUELIB Bouchra: *Ph.D. student *Lire *Laboratory University: Constantine 2-Abdelhamid Mehri- *Algeria * Alternative email: Guelibbouchra(a)gmail.com

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segmentation fornix with mri_cc
by Mostafa Fakhri 27 Jun '22

27 Jun '22

External Email - Use Caution Hello to all of you I ran recon-all: $ recon-all -sd /share/users/mfakhri/FS/subjects -subject 102109 -i T1w.nii.gz -all Then I tried segmentation fornix and I used -f on the mri_cc command: $ mri_cc -f -force -sdir /share/users/mfakhri/FS/subjects 102109 including fornix in segmentation processing regardless of existence of cc in input volume using /share/users/mfakhri/freeSurfer-analys/subjects as SUBJECTS_DIR... reading aseg from /share/users/mfakhri/freeSurfer-analys/subjects/102109/mri/aseg.mgz reading norm from /share/users/mfakhri/freeSurfer-analys/subjects/102109/mri/norm.mgz 128569 voxels in left wm, 173189 in right wm, xrange [111, 140] MRIprincipleComponents: unsupported input type 1 searching rotation angles z=[-7 7], y=[-7 7] searching scale 1 Z rot 5.8 global minimum found at slice 128.0, rotations (-0.50, -1.00) final transformation (x=128.0, yr=-0.500, zr=-1.000): 0.99981 0.01745 -0.00873 0.02437; -0.01745 0.99985 0.00015 130.23384; 0.00873 -0.00000 0.99996 126.88302; 0.00000 0.00000 0.00000 1.00000; mri_cc: no WM voxels found with norm > 40 -- check skull stripping There was no fornix.mgz in mri directory and this error file has been created: $ cat error.log MRIprincipleComponents: unsupported input type 1 I used an HCP 3T preprocess image. Thanks for the help! Mostafa

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selxavg3-sess out of memory error
by Caspar M. Schwiedrzik 27 Jun '22

27 Jun '22

External Email - Use Caution Hi! I am running large single subject GLMs with selxavg3-sess and I run into a Matlab "out of memory" error. I was wondering whether you had any advice on how to get around that. I have 40-50 runs per subject, and the analyses are whole brain. The GLM per subject runs through fine, but the error occurs once selxavg3-sess starts computing contrasts. The problem occurs with v5.3 and v7.2. This is a Centos 7 system with 320 GB of memory, and 7 GB of swap memory. Any advice would be appreciated! Caspar

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