Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

Re: [Freesurfer] Freesurfer Digest, Vol 202, Issue 30 {Disarmed}
by vittal korann 17 Dec '20

17 Dec '20

External Email - Use Caution Hi Douglas, Thanks a lot for your kind explanation! With regards Vittal On Thu, Dec 17, 2020 at 8:12 PM <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://secure-web.cisco.com/1d5gSB-rqVInM6onHMLDbLhUREGgzCvmI5zHvbuwq-S_PJ… > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: HCP_1200 parcellation problems (Greve, Douglas N.,Ph.D.) > 2. Re: need assistance to decode QDEC results > (Greve, Douglas N.,Ph.D.) > 3. Re: Cortical thickness volume ROI to surface {Disarmed} > (Greve, Douglas N.,Ph.D.) > 4. Re: Error in selxavg3-sess (Greve, Douglas N.,Ph.D.) > 5. Re: cannot find freesurfer/average/RB_all_2008-03-26.gca with > -use-gpu in v5.3 (Greve, Douglas N.,Ph.D.) > 6. Re: cannot find freesurfer/average/RB_all_2008-03-26.gca with > -use-gpu in v5.3 {Disarmed} (Caspar M. Schwiedrzik) > 7. Re: group analyses {Disarmed} (Greve, Douglas N.,Ph.D.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Dec 2020 14:28:37 +0000 > From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] HCP_1200 parcellation problems > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <786b64c3-2d99-06ed-2fe3-812225238514(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Sorry, I can't tell from your email what the problem is. Can you elaborate? > > On 12/9/2020 2:30 PM, najme soleimani wrote: > > External Email - Use Caution > > Dear FreeSurfer Developers, > I downloaded the HCP_1200 subjects' structural extended data. I am > attempting to have equal sized parcellation on scale 100, so I used > parcellation results of Desikan atlas and increased the parcels from 68 to > 100. > after obtaining split file, I run the following commands on FreeSurfer: > mris_divide_parcellation subj lh aparc.annot splitfile Desikan100 > mris_divide_parcellation subj rh aparc.annot splitfile Desikan100 > mri_aparc2aseg --s subj --annot Desikan100 --old-ribbon --o > $SUBJECTS_DIR/subj/mri/Desikan100.subj.mgz > The interesting part is that after running this command some > disconnectivity were seen in the parcels as it is shown in the picture. In > 3D view, also, when the parcels were loaded on dsi studio, there were some > holes on the parcels which caused disconnected parcels. > I will appreciate if you help me to solve this problem. > > > kind regards, > Najme > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1d5gSB-rqVInM6onHMLDbLhUREGgzCvmI5zHvbuwq-S_PJ… > >

1 0

cannot find freesurfer/average/RB_all_2008-03-26.gca with -use-gpu in v5.3
by Caspar M. Schwiedrzik 17 Dec '20

17 Dec '20

External Email - Use Caution Hi! I am trying to run recon-all in version 5.3 with the -use-gpu flag. I am getting a strange error that I would love to get your input on: cannot find freesurfer/average/RB_all_2008-03-26.gca Neither the file nor the path exist. This is the entire input and output: recon-all -s hum_14600_parallel -i /neuro_tools/freesurfer/subjects/hum_14600/mri/011/mp2rage.nii -all -use-gpu Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 10.0 Runtime : 5.0 Acquiring CUDA device Using default device CUDA device: Tesla K40m ======= NUMBER OF OPENMP THREADS = 1 ======= stable5 NVIDIA driver version info: NVRM version: NVIDIA UNIX x86_64 Kernel Module 410.79 Thu Nov 15 10:41:04 CST 2018 ERROR: cannot find /neuro_tools/freesurfer/average/RB_all_2008-03-26.gca Is there some documentation on how to set up the environment beyond LD_LIBRARY_PATH? Could that be the issue? Everything works fine without the -use-gpu flag. Thank you! Caspar

2 2

Cortical thickness volume ROI to surface {Disarmed}
by Alina Rojas 17 Dec '20

17 Dec '20

External Email - Use Caution Hello Freesurfer experts, I am attempting to register a ROI (.nii) to the surface of fsaverage to get the statistical output on the cortical thickness. I followed your instructions on https://secure-web.cisco.com/1vMR3HBqveQVdV1izVoGaJ5VcRtbR7HBn6ADoe1ai7ok5u… <https://secure-web.cisco.com/1vMR3HBqveQVdV1izVoGaJ5VcRtbR7HBn6ADoe1ai7ok5u…> but after mri_vol2surf I get this message, I can’t visualize the ROI on the surface. I I’m using Freesurfer 7.0.1. How can I solve this? Thank you, Alina Rojas. srcvol = M1_L.nii.gz srcreg = tmp.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = 0.5 reshape = 0 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 INFO: using NIfTI-1 qform Done loading volume INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. Input reg is register.dat -------- original matrix ----------- 1.00000 0.00000 0.00000 2.49380; 0.00000 0.00000 1.00000 -22.50500; 0.00000 -1.00000 0.00000 -9.53872; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Reading surface /fsaverage/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 1 using old 2 0.1 0 1 using old 3 0.2 0 1 using old 4 0.3 0 1 using old 5 0.4 0 1 using old 6 0.5 0 1 using old 7 0.6 0 1 using old 8 0.7 0 1 using old 9 0.8 0 1 using old 10 0.9 0 1 using old Done mapping volume to surface Number of source voxels hit = 75073 Writing to lh.fsaverage.M1_L.mgh Dim: 163842 1 1 surfcolor: Subscript out of range.

3 5

need assistance to decode QDEC results
by vittal korann 17 Dec '20

17 Dec '20

External Email - Use Caution Dear FreeSurfer experts, I was running group interaction (for diagnosis and birthplace) in QDEC with gyrification as a dependent variable and age, gender as nuisance factors. In diagnosis, we have 2 groups: i) schizophrenic patients ii) healthy volunteers. Similarly, birthplace has 2 groups: i) urban ii) rural birth For the above-said design, I got reddish yellow color results in the display tab of Qdec. So, my query is that do results indicate that patients who were born in urban have a higher gyrification index than healthy volunteers who born in urban or something else? Do I sound correct in decoding the interaction results? If not please let me know the exact meaning of the results. Looking forward to hearing from you. Thanks, Vittal

2 2

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]

2 1

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

2 1

(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

2 1

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

1 0

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

2 1

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

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer