Freesurfer April 2018

freesurfer@nmr.mgh.harvard.edu

118 participants
177 discussions

Running Linear Mixed Effects (LME) Model
by Kaushal, Mayank 13 Apr '18

13 Apr '18

Dear Freesurfer Community, Running lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex); gives the following error, Starting parallel pool (parpool) using the 'local' profile ... Error using parpool (line 104) You requested a minimum of 8 workers, but the cluster "local" has the NumWorkers property set to allow a maximum of 2 workers. To run a communicating job on more workers than this (up to a maximum of 512 for the Local cluster), increase the value of the NumWorkers property for the cluster. The default value of NumWorkers for a Local cluster is the number of cores on the local machine. Error in lme_mass_fit (line 137) parpool(prs); Error in lme_mass_fit_vw (line 73) [stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e); I am running Matlab on a personal MacBook Pro, 2.4 GHz Intel Core i5, 8 GB 1600 MHz DDR3. I have researched the forum on how to stop the function from trying to initiate parallel processing but so far haven’t been able figure out how to overcome this. Any help would be much appreciated. Mayank Kaushal MD MBA Postdoctoral Fellow Department of Neurosurgery Medical College of Wisconsin

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mri_vol2surf: issue with registration
by srishti goel 13 Apr '18

13 Apr '18

Hi , I am facing an issue when I try to compare two network-based maps, one of which has been registered on a surface while the other one has not. If anyone has tried doing something similar and has any thoughts about it please share your suggestions, I highly appreciate it. I have two sets of network based maps (both generated from meta-analysis), one set is ours' and one set is our collaborators'. We want to compare the two sets of maps. Our collaborators maps are on the surface in freesurfer. We wanted to project our volume based maps on that surface. Our collaborators' maps are: SN_like_cortical_lh.nii SN_like_cortical_rh.nii SN_like_subcortical.nii Our maps are: negative_allsocial_proportion.nii negative_somesocial_proportion.nii Etc. In order to compare their volume map (SN_like_subcortical.nii) to our (negative_allsocial_proportion.nii) we just used the MNI152 template from freesurfer wiki and viewed it in Freeview and it worked fine. The issue is when we try to project our maps on the surface that they used. The gave us the template brain (mni152_subject) folder that had been recon-all already and I just used that with the following steps: mri_vol2surf --src negative_allsocial_proportion.nii --regheader mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 To view it: tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 When I view it, our map doesn't show up on the surface and that is because our map didn't register with --regheader. I checked the registration by using: tkregisterfv --mov negative_allsocial_proportion.nii --reg register.lta --surfs The registration is definitely off, we used bbregister to register our maps on the mni152_subject but that didn't work either. Does anyone has thoughts about this? Thanks!

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Import tract files from other programs
by samanthabaldi145＠gmail.com 13 Apr '18

13 Apr '18

Good morning, For our project, we are studying tracts that from two deep brain nuclei spread to the cortex. Our aim is to find the coordinates of the cortical targets and compare them across individuals to assess the variability of these projections. We used the recon-all command for preprocessing of the T1-weighted anatomical scan and for cortical parcellation. We then switched to the program ExploreDTI, and we registered the DWI images to the brain.mgz file obtained as output of recon-all. We performed brain tractography using ROI masks (from fsl atlases) and obtained tracts files (*.mat, can be converted to *.trk, *.vtk, *.wrl) and tract masks (*.nii). Is it possible to import these tract files in Freesurferview? I would like to obtain one image which shows both the cortical parcellation and the tract of interest, in order to identify the cortical target based on the labeled model obtained from Freesurfer. I first loaded the brain volume brain.mgz (converted to *.nii). Then I selected “File > Load Tract” (converted to *.trk), but I can only visualize the tract separately from the brain volume, meaning that it’s not warped into the subject’s brain. I attach a picture of what I obtain. I wonder whether it is possible to obtain one image as I described above by importing tracts not obtained with Freesurfer? Thanks in advance, Regards Samantha Baldi

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Re: [Freesurfer] Surface Problem
by Vionnet Laetitia 13 Apr '18

13 Apr '18

Dear freesurfer, I saw the issue below online and wondered whether it got solved? I have the “if: Missing file name.” error when testing my installation with recon-all -i sample-002.nii.gz -s bert -all attached my recon-all file. Thank you for your help and best regards, Laeitita -------------------- [Freesurfer] Surface Problem Z K zkaufman at nmr.mgh.harvard.edu <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Surface%20Problem&In-Reply-To=%3C253ef8e4-8ac6-18e9-86f7-f2945cbeba69%40nmr.mgh.harvard.edu%3E> Wed Jun 21 16:28:19 EDT 2017 * Previous message: [Freesurfer] Surface Problem <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/052609.html> * Next message: [Freesurfer] FreeSurfer Boston Course Registration now open! <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/052619.html> * Messages sorted by: [ date ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/date.html#5…> [ thread ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/thread.html…> [ subject ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/subject.htm…> [ author ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/author.html…> Search archives: Can you send me your recon-all script to my email address (not to the list). I suspect it has been modified. On 06/21/2017 02:04 PM, Michael Davies wrote: > Hello, i have been trying to regenerate the surface on one of my > subjects but keep having a problem where the terminal is saying there is > a missing file name. Do you have any suggestions please? > > > Kind regards, Michael > > > bash-4.1$ freesurfer_setup_freeview > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > FSL_DIR /usr/local/fsl > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj5/Subj5 > bash-4.1$ recon-all -autorecon-pial -s Subj5 > if: Missing file name. > bash-4.1$ > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer at nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > * Previous message: [Freesurfer] Surface Problem <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/052609.html> * Next message: [Freesurfer] FreeSurfer Boston Course Registration now open! <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/052619.html> * Messages sorted by: [ date ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/date.html#5…> [ thread ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/thread.html…> [ subject ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/subject.htm…> [ author ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/author.html…> More information about the Freesurfer mailing list<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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Susceptibility artifact
by John Anderson 12 Apr '18

12 Apr '18

Dear Freesurfer experts, I would like t inquire if there is any tool or method in Freesurfer that can help to fix susceptibility artifacts in T1 image like attached Any suggestion is highly appreciated! John

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tksurkfer save error
by Evans, Jennifer (NIH/NIMH) [F] 12 Apr '18

12 Apr '18

Hi, This is a repost as I didn’t get a reply to the one I sent a few weeks ago. This error basically means I can’t automatically generate a webpage of all of the segmentation results. I getting an error when trying to save a tiff file using tksurfer on a linux machine via NoMachine v5.0.47. I’m running the ENIGMA QA pipeline which has a call similar to: tkfsurfer bert lh inflated. Then, trying to save the tiff either from the GUI or using their script doesn’t work and causes the error: pixel read error/resource temporarily unavailable. Is there a way to get this to work or is this a feature of using a virtual desktop? Thanks, Jen

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Data Analyst & Research Assistant Position(s) - Child Mind Institute (New York)
by Ting Xu 12 Apr '18

12 Apr '18

Child Mind Institute is seeking a Data Analyst to join our team. The Data Analyst’s role is to assist and support the acquisition, manipulation, and analysis of data, as well as the reporting results. In particular, our work includes: 1) support the preprocessing of large fMRI dataset in human and non-human primates, 2) maintain databases and imaging processing pipeline 3) test and develop new features (e.g., denoising, segmentation, etc.). 4) implement quality assurance protocols for imaging datasets. Reporting to the Research Scientist of the Center for the Developing Brain, this is an exempt, full-time positions located in our NYC headquarters. Responsibilities: Implementation, execution, and maintenance of fMRI imaging analysis pipelines in human and non-human primate datasets Exploration of novel software packages and problem-solving for issues with current and planned software packages Develop graphs, reports, and presentations of project results Mentoring of junior research staff in data analysis theory and implementation Perform basic statistical analyses for projects and reports Qualifications: Master’s degree or Bachelor’s degree with extensive neuroimaging research experience in neuroscience, computer science, mathematics, statistics or related areas Extensive neuroimaging experience in fMRI analysis and proficiency with one or more packages (e.g. FreeSurfer, AFNI, FSL, Workbench or SPM) Programming experience in one or more languages (e.g., Python, Matlab, R or similar platforms is required) Significant prior neuroimaging experience with more imaging and/or simulation modalities (e.g., DTI, EEG, MEG, TMS etc.) is a plus, but not required A passion for the Child Mind Institute mission To apply: https://workforcenow.adp.com/mdf/recruitment/recruitment.html?cid=371b930b-… -- Ting Xu, PhD Research Scientist Child Mind Institute childmind.org 445 Park Avenue (entrance on 56th Street) New York, NY 10022 Email: ting.xu(a)childmind.org

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Group Analysis Design Matrix
by David S Lee 12 Apr '18

12 Apr '18

Hi FreeSurfer Experts, I have two groups (Male and Female) and two covariates (Age and Weight). I want to test change of cortical thickness with age and weight, after removing effects of Group. In other words, is there an interaction between age and weight, regressing out the effects of groups. How can I set up my Design Matrix to test this? Thank you, -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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tksurkfer save error
by Evans, Jennifer (NIH/NIMH) [F] 12 Apr '18

12 Apr '18

Ok, thanks for the reply. It sounds like the ENIGMA folks need to updage their commands to use freeview. I'll try using ImageMajick's import as a workaround. Jen -------- Message: 11 Date: Thu, 12 Apr 2018 10:59:58 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] tksurkfer save error To: <freesurfer(a)nmr.mgh.harvard.edu>, Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu> Message-ID: <834b362c-841b-5e86-cd3e-74b34ec33b76(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8"; format=flowed We are not really supporting tksurfer anymore. You can use freeview to save a png from the GUI. Ruopeng, is there a way to take a snap shot from the command line? On 04/12/2018 10:29 AM, Evans, Jennifer (NIH/NIMH) [F] wrote: Hi, This is a repost as I didn?t get a reply to the one I sent a few weeks ago.? This error basically means I can?t automatically generate a webpage of all of the segmentation results.? I getting an error when trying to save a tiff file using tksurfer on a linux machine via NoMachine v5.0.47.? I?m running the ENIGMA QA pipeline which has a call similar to: ?tkfsurfer bert lh inflated.? Then, trying to save the tiff either from the GUI or using their script doesn?t work and causes the error: pixel read error/resource temporarily unavailable. ??Is there a way to get this to work or is this a feature of using a virtual desktop? Thanks, Jen

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"preproc-sess" with intermediate volume
by David Sánchez Bestué 12 Apr '18

12 Apr '18

Dear all, I have a problem with the command: "preproc-sess" I wanted to use the Registration option to add an intermediate volume. The only documentation I could find about it was the one that appears with the command: "preproc-sess --help" Registration options -init-fsl : use fsl to initialize bbr registration -init-spm : use spm to initialize bbr registration (needs matlab) -init-header : use geometry to initialize bbr registration -bbr-int ifsd istem : use intermediate volume in sess/ifsd/RRR/istem I used the last flag in my line as follows: preproc-sess -s session_1 -fsd bold -surface self lhrh -mni305 -fwhm 5 -per-run -bbr-int ifsd istem I got this error: ERROR: could not determine file for ifsd/001/istem It seems that the path is not working but I do not why. The relevant paths are this: session_1/bold/001/f.nii session_1/ifsd/001/istem/orig.mgz Any help would be really appreciated! Thank you all Bests, David

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Freesurfer April 2018