Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30085 discussions

password for VirtualBox
by Miguel Hornero 14 Dec '20

14 Dec '20

External Email - Use Caution Hi!I wanted to try out FreeSurfer and followed the install guide from the FreeSurfer webpage with the linkedUbuntu 18 virtual disk image (FStutorial_clone_2.7z, downloaded 2020-12-14).However, upon startup of the virtual machine, the Ubuntu installation asks me for my user credentials with a preselected "developer" user (seescreenshot attached). According to the install guide, the virtual machine should just boot up to Desktop without requiring a password.Is there a default password I am supposed to use (I tried leaving the password field blank, "freesurfer", "FreeSurfer", "developer" but none of those worked) Thank you in advance, Miguel

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Multiple Frames Error
by Hsieh, Stephanie 14 Dec '20

14 Dec '20

Hi FreeSurfer Developers, I am trying to process a few MPRAGE sequences (different sessions), so I can edit the scans. And I am having trouble reconning the .mgz files. I have looked into why my job terminated early and I have attached the message below. The error states that ‘input(s) cannot have multiple frames’. And I then looked into the mri_info, which I have also attached below, and based off of some similar questions I found in the archive, my dimensions seem to be incorrect for freesurfer to process. My dimensions are 240 x 256 x 176 x 2, and I believe they should be 240 x 256 x 176 in order for it to work. How do I go about fixing my dimensions? Does it have to do with how I unpacked the DICOMS? I have not run into this issue before so I would love to learn what caused this error. Thanks in advance, Stephanie Early termination error: Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /autofs/cluster/brutha/FS6 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Linux compute-0-85.nmr.mgh.harvard.edu<http://compute-0-85.nmr.mgh.harvard.edu/>3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux '/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/recon-all' -> '/autofs/cluster/brutha/FS6/SCD_021_BL/scripts/recon-all.local-copy' /autofs/cluster/brutha/FS6/SCD_021_BL mri_convert /autofs/cluster/brutha/FS6/SCD_021_BL-1.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz mri_convert.bin /autofs/cluster/brutha/FS6/SCD_021_BL-1.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/brutha/FS6/SCD_021_BL-1.mgz... TR=2300.00, TE=2.95, TI=900.00, flip angle=9.00 i_ras = (0.108201, -0.990984, 0.079018) j_ras = (0.0145467, -0.0778978, -0.996855) k_ras = (-0.994023, -0.10901, -0.00598659) writing to /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz... /autofs/cluster/brutha/FS6/SCD_021_BL mri_convert /autofs/cluster/brutha/FS6/SCD_021_BL-2.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz mri_convert.bin /autofs/cluster/brutha/FS6/SCD_021_BL-2.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/brutha/FS6/SCD_021_BL-2.mgz... TR=2300.00, TE=2.95, TI=900.00, flip angle=9.00 i_ras = (0.108201, -0.990984, 0.079018) j_ras = (0.0145467, -0.0778978, -0.996855) k_ras = (-0.994023, -0.10901, -0.00598659) writing to /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz... #-------------------------------------------- #@# MotionCor Thu Dec 10 21:00:24 EST 2020 Found 2 runs /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz has 2 frames Linux compute-0-85.nmr.mgh.harvard.edu<http://compute-0-85.nmr.mgh.harvard.edu/>3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SCD_021_BL exited with ERRORS at Thu Dec 10 21:00:25 EST 2020 mri_info on the session I am trying to run: Volume information for SCD_021_BL-1.mgz type: MGH dimensions: 240 x 256 x 176 x 2 voxel sizes: 1.054688, 1.054688, 1.200000 type: SHORT (4) fov: 270.000 dof: 0 xstart: -126.6, xend: 126.6 ystart: -135.0, yend: 135.0 zstart: -105.6, zend: 105.6 TR: 2300.00 msec, TE: 2.95 msec, TI: 900.00 msec, flip angle: 9.00 degrees nframes: 2 PhEncDir: ROW FieldStrength: 3.000000 ras xform present xform info: x_r = 0.1082, y_r = 0.0145, z_r = -0.9940, c_r = 9.2070 : x_a = -0.9910, y_a = -0.0779, z_a = -0.1090, c_a = 36.6058 : x_s = 0.0790, y_s = -0.9969, z_s = -0.0060, c_s = -29.9521 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: 0.1141 0.0153 -1.1928 98.5179 -1.0452 -0.0822 -0.1308 184.0548<tel:184.0548> 0.0833 -1.0514 -0.0072 95.2548 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1.33484 ras to voxel transform: 0.1026 -0.9396 0.0749 155.6942<tel:155.6942> 0.0138 -0.0739 -0.9452 102.2669<tel:102.2669> -0.8284 -0.0908 -0.0050 98.8026 -0.0000 -0.0000 -0.0000 1.0000 Volume information for SCD_021_BL-2.mgz type: MGH dimensions: 240 x 256 x 176 x 2 voxel sizes: 1.054688, 1.054688, 1.200000 type: SHORT (4) fov: 270.000 dof: 0 xstart: -126.6, xend: 126.6 ystart: -135.0, yend: 135.0 zstart: -105.6, zend: 105.6 TR: 2300.00 msec, TE: 2.95 msec, TI: 900.00 msec, flip angle: 9.00 degrees nframes: 2 PhEncDir: ROW FieldStrength: 3.000000 ras xform present xform info: x_r = 0.1082, y_r = 0.0145, z_r = -0.9940, c_r = 9.2070 : x_a = -0.9910, y_a = -0.0779, z_a = -0.1090, c_a = 36.6058 : x_s = 0.0790, y_s = -0.9969, z_s = -0.0060, c_s = -29.9521 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: 0.1141 0.0153 -1.1928 98.5179 -1.0452 -0.0822 -0.1308 184.0548<tel:184.0548> 0.0833 -1.0514 -0.0072 95.2548 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1.33484 ras to voxel transform: 0.1026 -0.9396 0.0749 155.6942<tel:155.6942> 0.0138 -0.0739 -0.9452 102.2669<tel:102.2669> -0.8284 -0.0908 -0.0050 98.8026 -0.0000 -0.0000 -0.0000 1.0000

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Fwd: Password for Virtual Machine {Disarmed}
by Miguel Hornero 14 Dec '20

14 Dec '20

External Email - Use Caution ---------- Forwarded message --------- De: Miguel Hornero <miguelhornero28(a)gmail.com> Date: lun, 14 dic 2020 a las 14:08 Subject: Password for Virtual Machine To: <freesurfer(a)nmr.mgh.harvard.edu> Hi!I wanted to try out FreeSurfer and followed the install guide from https://secure-web.cisco.com/1aVjrKMkEJV_BmsbE4Zk5EdoFrDeZFRXS4LAWnl9PPwS1h… with the linkedUbuntu 18 virtual disk image (FStutorial_clone_2.7z, downloaded 2020-12-14).However, upon startup of the virtual machine, the Ubuntu installation asks me for my user credentials with a preselected "developer" user (seescreenshot attached). According to the install guide, the virtual machine should just boot up to Desktop without requiring a password.Is there a default password I am supposed to use (I tried leaving the password field blank, "freesurfer", "FreeSurfer", "developer" but none of those worked) Thank you in advance, Miguel

1 0

labels in the surface
by Alberto Del Cerro Leon 14 Dec '20

14 Dec '20

External Email - Use Caution Hello Freesurfer team With your help i obtained a AAL atlas on the surface and 1 label for each region. However, when I load the label into the inflate image, I obtain something like the one submitted in this e-mail. I expected a solid ROI on the surface to obtain the volume, curvature, etc of the entire region. It's something wrong? I am loading the label in an incorrect way? The image represent the label of the anterior cingulate into the inflated image

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Question about scaling intensities
by Hye Min Shin 13 Dec '20

13 Dec '20

External Email - Use Caution Hello, I was wondering if there was a way to scale intensities of normalized T1 images. For instance, I wanted to rescale intensities of white matter from [0,110] to [-1, 1] and intensities gray matter from [0, 80] to [-1, 1]. I wanted to rescale intensities to get consistent normalization levels across all T1 images for neural networks. Best, Julia Shin

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Computing thickness from woT2.pial surfaces
by Antonín Škoch 13 Dec '20

13 Dec '20

External Email - Use Caution Dear experts, I have processed my data with -T2pial option. I would like now to also compute thickness from woT2.pial surfaces (i.e. surfaces created by T1 only). Is here a comannd which does the trick, without running recon-all -pial (which rewrites current .pial and .thickness files generatedy by -T2pial? I am using freeSurfer version 6.0. Thank you in advance, Antonin Skoch

3 2

Does segmentation depend on input orientation {Disarmed}
by Nederpelt, D. van (David) 13 Dec '20

13 Dec '20

External Email - Use Caution Hi, I ran recon-all twice, once on a T1w image (nifti) with RAS orientation, and once on this image converted to LAS orientation I would expect the output (especially in volume) to be equal, because freesurfer reconverts it to its own orientation if I understood correctly. However, I found that the segmentation and output volumes differed depending on the input orientation. So while in fact both images are actually the same, the output differs. What would be the reason for this difference in output? Any help would be much appreciated Kind regards, [cid:image002.png@01D40E30.3E299A80] David van Nederpelt, MSc. | PhD Candidate Radiology and Nuclear Medicine Amsterdam UMC, Location VUmc | PK -1 X 004 | De Boelelaan 1118, 1081 HZ Amsterdam, the Netherlands E: d.vannederpelt(a)amsterdamumc.nl<mailto:d.vannederpelt@amsterdamumc.nl> http://secure-web.cisco.com/1yrDXcY3eqFuC9AUoZEDMJuZ0ojaLvbgGcFJ6eX6d_5r-mV…<http://secure-web.cisco.com/19L5zWn8iSh3B8KxDO60RgDjt3gGMMF3QPQVn6IQE8toN2A…> | http://secure-web.cisco.com/1yZ-GMAcIXR2JVaYlHW4MkWh3pH3uqqnFtkndplOESePIIi…<http://secure-web.cisco.com/1iEODCCa6CXtMd9bQZjIQntIRXNo8vPN3sVVSIFZ5bZfflE…> / http://secure-web.cisco.com/1WysKpLXmYNNaIkdkI_HIp4gMvxMuUUMRBYKfxhbUgZoyKo…<http://secure-web.cisco.com/1AZmq9gaNj_RNBv07qct3dKWqN9IDFqy7xUHiAIz_0p7qYt…> ______________________________________________________ ______________________________________________________ VUmc disclaimer : http://secure-web.cisco.com/1Ai9BHY5QjRrNjsey9Ku_Ls90P8m7yD1J3X1ZEtstl9pbp9… AMC disclaimer : http://secure-web.cisco.com/1SIW7YiOGJ67yQ9iSniK8HIFxe7Ww4tUic1RZXHUlvGbSzN…

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question about PVC of PETSurfer
by 蒋袁芳 13 Dec '20

13 Dec '20

External Email - Use Caution Hello Freesurfer, We know that the freesurfer7 has given a new module to separate hippocampal subfields in MRI image, but we encoumter problems in registering the PET image with MRI image. We find that the resolution radio of PET image is not enough, it made the SUVr of hippocampal subfield we get is not accurate. So we want to use the PVC function of PETSurfer. Whether the PETsurfer output the result of PET image after PVC ? so that we can use it directly to registering with MRI image. If it doesn't output the result, can we save it in some ways? Thank you for your guidance.

2 3

Correct for sulcuses & ventricles size
by John Anderson 13 Dec '20

13 Dec '20

External Email - Use Caution Dear Freesurfer experts, I have two groups of subjects (healthy and patients). The patients have different degrees of atrophy. Looking into the individual scans, the subjects are largely different in the space between the sulcuses and the size of ventricles. My questions are: 1. Is there any way to correct for these differences in the surface based analysis? 2. Including eTIV covariate does it help in this case? 3. Does the resampling to "fsaverage" overcome the challenge of these differences between the subjects? I appreciate any advice, John

3 5

inflated surface with holes
by Jie Zhao 13 Dec '20

13 Dec '20

External Email - Use Caution Hello Freesurfer Team I have some questions about the inflated surface. As is shown in the attached pictures, there are one big hole and three small hole on the right hemisphere, one big hole on the left hemisphere. Could anyone give me some suggestions to handle it. If you need any files, please let me know. Thanks in advance! Jie Zhao

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