Freesurfer December 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
131 discussions

Hippocampus left out in longitudinal study
by Albulena Shaqiri 17 Dec '20

17 Dec '20

External Email - Use Caution Dear all, I am new to freesurfer and this might be an evident question, if so, I am sorry. We have a longitudinal study with t0 and t1 scans. I followed the procedure and did the 3 steps. 1. Cross (with the following command: recon-all -subject 01_t0 -i /subjectfiles/t0/sanlm_13.nii -all -qcache -notal-check) 2. Base (recon-all -base 01_t0t1template -tp 01_t0 -tp 01_t1 -all) 3. Long (recon-all -long 01_t0 01_t0t1template -all) The problem is once I am inspecting the data, I see that the hippocampus is left out in all the cases (4 different subjects are attached in the screen captures).I used this command: freeview -v 01_t0/mri/norm.mgz \ -f 01_t0/surf/lh.pial:edgecolor=red \ 01_t0/surf/rh.pial:edgecolor=red \ 01_t0/surf/lh.white:edgecolor=blue \ 01_t0/surf/rh.white:edgecolor=blue) Also, you should know that we used for T1 MP2RAGE instead of MPRAGE. Is there anything I can do without having to re-do all the corrections by hand point by point and without having to restart over all my data pre-processing? I have to specify that we are interested in the hippocampus, so this is a major point in our study. Thanks in advance for your help, Alba [image: Screen Shot 2020-12-09 at 15.45.30.png] [image: Screen Shot 2020-12-09 at 15.45.38.png] [image: Screen Shot 2020-12-09 at 15.45.45.png] [image: Screen Shot 2020-12-09 at 15.45.55.png]

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MP2RAGE pial surface edit error
by Elisa Rehbein 17 Dec '20

17 Dec '20

External Email - Use Caution Dear Freesurfer experts, we are currently running recon-all for our MP2RAGE images, using Freesurfer 7. However, when trying to edit pial surface errors and re-running (recon-all -autorecon-pial -subjid) it does not adjust the surface for some participants and leaves a black space (see picture attached). For denoising the salt and pepper noise in the background we used the script provided by (Marcques et al. 2010). We are very confused as to why this may be happening for some subjects, as the background noise seems to be removed equally for all subjects. Do you maybe have suggestions for us on how to solve this problem? Many thanks in advance! Kind regards, Elisa

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(no subject)
by Laura f 17 Dec '20

17 Dec '20

Dear Sir or Madam, I am not longer working with FreeSurfer so I would like to remove my subscription to the mailing list. Thank you, Laura External Email - Use Caution

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1 PostDoc and 1 PhD Position available at University Hospital Cologne - Germany {Disarmed}
by Merle Hönig 17 Dec '20

17 Dec '20

External Email - Use Caution The Multimodal Neuroimaging Group at the University Hospital Cologne (visit us on https://secure-web.cisco.com/19Wxvgr1d6Wzl6rJWybWxBosnfgQu9HN-Ju0G9UAxz0P3Y…) currently looks for two highly motivated and qualified scientists (1 PostDoc and 1 PhD position) with a background in neuroscience or related fields. The positions are available as early as possible. The candidates will mainly work on a project focusing on the impact of striatal dopamine loss on vigor, planning, and motivation of movements as well as the role of motor reserve in patients with prodromal and clinical Parkinson’s disease. In this project, we will apply a unique combination of behavioral and computational phenotyping and state-of-the-art molecular, functional, and structural neuroimaging technologies (e.g. 7T MRI, dopamine transporter imaging). The successful candidates will be involved in the preparation and conduct of the study and the analysis and publication of newly acquired and already existing datasets. The positions provide the excellent opportunity to work in an interdisciplinary environment as part of the recently awarded Collaborative Research Center “SFB 1451: Key mechanisms of motor control in health and disease” with an integrated Research Training Group. For more details please see the official advertisement or attachment: https://secure-web.cisco.com/1lXwa1UK7Y5Mh6M-4mWn2QFc9BCdVXUsLlQ_KkbRm--4eB… We are looking forward to your application! Best regards, Merle Hoenig

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Re: [Freesurfer] Recon-all error: MatrixMultiply: m1 is null!
by Hoopes, Andrew 16 Dec '20

16 Dec '20

Hi Nárlon, Unfortunately, this is a known bug with parallel processing in FS 7.1.1. A fix will make it into the next v7 patch. As you mentioned, this error occurs at random, so in the meantime, you can mitigate this by either: - Rerunning recons until they don’t fail (not recommended) - Rerunning these failing recons without the parallel flag enabled - Patching your version of recon-all by commenting out or removing the following (line 4217) from $FREESURFER_HOME/bin/recon-all: if($OMP_NUM_THREADS > 1) set cmd = ($cmd --parallel) Hope that helps, Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Boa Sorte Silva, Narlon" <narlon.silva(a)ubc.ca> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, December 14, 2020 at 7:31 PM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Recon-all error: MatrixMultiply: m1 is null! External Email - Use Caution Hi there, Hope this finds you well I have noticed the following error for some of my runs: @# Cortical ribbon mask Mon Dec 14 15:43:24 PST 2020 /Applications/freesurfer/7.1.1/subjects/BT_long/BT_055_base/mri \n mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --parallel BT_055_base \n SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects/BT_long loading input data... Running hemis in parallel Processing left hemi Processing right hemi computing distance to right white surface computing distance to left white surface error: MatrixMultiply: m1 is null! Darwin PHTH-CDM-NBOASORT 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64 recon-all -s BT_055_base exited with ERRORS at Mon Dec 14 15:43:27 PST 2020 Here are details of the computer and FS version I am using: * OS: macOS Mojave (10.14.4) * FS: 7.1.1 It seems to happen at random, whenever I run recon-all on the same subject again, the error doesn’t occur. This is true for cross-sectional, base, and long processing steps in my machine. I have seen an email relating to this issue before, but I wasn’t able to access the attachment file which would fix the problem. I was wondering if you guys would be able to help? Thank you Nárlon Cássio Nárlon Cássio Boa Sorte Silva, PhD CIHR/MSFHR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health University of British Columbia Twitter: @BoaNarlon

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Re: [Freesurfer] password for VirtualBox
by fsbuild 14 Dec '20

14 Dec '20

External Email - Use Caution Hello Miguel, I am sending the password to your private email. - R. On Dec 14, 2020, at 11:40, Miguel Hornero <miguelhornero28(a)gmail.com> wrote:        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_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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

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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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Freesurfer December 2020