Freesurfer November 2012

freesurfer@nmr.mgh.harvard.edu

105 participants
177 discussions

Surface-based normalization, smoothing and averaging
by Shigetoshi Takaya 08 Nov '12

08 Nov '12

Dear Freesurfer experts, I would like to have your help. I have a volume data of a certain parameter on white/grey matter boundary (X.nii). What I want to do are as follows: Step 1: I want to register it onto a standard space using surface-based alignment and smooth it. Step 2: I want to generate the averaged images of several subjects on the standard inflated surface. My questions are follows: Q1) For Step 1, I guess I need to convert the image using mri_vol2surf (X.nii --> X.mgh), then use mri_surf2surf and mris_smooth. If it is the case what should I use for <target subject name> for mri_sur2surf? Q2) How to do Step 2? Thanks in advance, Shige

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Re: [Freesurfer] fs-fast preprocessing resting state
by Douglas N Greve 08 Nov '12

08 Nov '12

Hi Chris, the problem is that you do not have FSLDIR defined. Assuming you have FSL installed, then setenv FSLDIR /place/where/fsl/is/installed doug On 11/06/2012 09:09 PM, Chris McNorgan wrote: > Hi Doug, > > Attached are two plain-text files: fslog2.txt contains the redirected > terminal output after executing: > preproc-sess -s sub00294 -fsd rest -per-run -surface self lhrh -mni305 > -fwhm 0 &> ~/fslog2.txt > > 294files.txt contains the output of `find` for all files in the > project directory related to this participant *after* executing > preproc-sess, in case any clue can be found in this information (I > omitted files in the log/ directory). > > > Thanks, > Chris -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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process exited abnormally
by Varghese Chikku 08 Nov '12

08 Nov '12

Dear all, I am trying to run recon all and FS will either exists with this.... * child process exited abnormally*.......or just a blank window appears with leaving the system to freeze.So i have to power off the VM and start all over again. Does it have to do with the system requirements.I am using VM,. Thanks a lot, chikku

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Rejoindre mon réseau sur LinkedIn
by Barnali Basu via LinkedIn 08 Nov '12

08 Nov '12

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freeview
by Catherine Bois 07 Nov '12

07 Nov '12

Hi, I am trying to use freeview to look at wm/brainmask etc however the command wont work. The command Im suing is freeview -v wm1_edits_before/mri/wm.mgz:colormap=heat:opacity=0.4 wm1_edits_before/mri/brainmask.mgz \ -f wm1_edits_before/surf/lh.white:edgecolor=blue wm1_edits_before/surf/lh.pial:edgecolor=red \ wm1_edits_before/surf/rh.white:edgecolor=blue wm1_edits_before/surf/rh.pial:edgecolor=red (but i am exchanging paths for my own data). However, it keeps saying that operation console failed, and for some reason, even though Ive set the subject directory to where the files are kept it keeps looking in my home directory. I recently attended a course in freesurfer, but this problem was not explained? Grateful for help.

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Re: [Freesurfer] qcache error
by Douglas N Greve 06 Nov '12

06 Nov '12

Do you have write permissions to the output dir? I noticed a perm error in the log. The recon-all.log file has the permission: -rw-rw-r-- 1 guest phd doug On 11/06/2012 03:53 PM, Berg, S.F. van den wrote: > Hi Doug and Bruce > > There is enough disc space. A text file is attached, this file is created with the "recon-all -s 0050 -qcache |& tee mylog.txt" command. I try the "recon-all -s 0050 -qcache" command. The command start to run but finished with errors. > > Have you got any idea of the problem in this case? Also the recon-all.log file is attached (subject 0050). > > Thanks, > > Stan > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: 05 November 2012 19:37 > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] qcache error > > Do run out of disk space? Also, please send terminal output in a text > file rather than as a snapshot. You can do this with > > recon-all ... |& tee mylog.txt > > doug > > On 11/05/2012 10:21 AM, Berg, S.F. van den wrote: >> Dear Freesurfer experts, >> >> I have got a problem with the qcache function. I have already runned >> 150 subjects with the recon-all command. Before i can work with the >> statistical program qdec i have to smooth the subjects. I want to >> smooth them with the command: recon-all -s<subject> -qcache. The >> command start to run but finished with errors. A overview of the >> terminal output is attached to this email in JPEG format. What is the >> problem in this case? >> >> further information about freesurfer version: >> >> recon-all -version: Id: recon-all, v 1.373 2011/03/15 00:43:47 mreuter >> Exp $ >> >> We run FreeSurfer-Linux-centos5_x86_64-dev-201110315 under Debian >> Squeeze. >> >> Thanks a lot, >> >> Stan van den Berg >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] fs-fast preprocessing resting state
by Chris McNorgan 06 Nov '12

06 Nov '12

Hi Doug, Thanks for your help. To be sure of my preproc-sess line, I just ran preproc-sess on my other participant: preproc-sess -s sub00294 -fsd rest -per-run -surface self lhrh -mni305 -fwhm 0 Here's the error output from where it goes south: <SNIP> Tue Nov 6 16:32:30 CST 2012 mc-sess completed SUCCESSFULLY sub00294 To Surface ----------------------------- rawfunc2surf-sess -fwhm 0 -s sub00294 -d /home/chris/resting/func -fsd rest -self -update instem fmcpr outstem fmcpr.sm0.self.hemi ------------------------------ 1/1 sub00294 1/1 sub00294 001 lh --------- Tue Nov 6 16:32:30 CST 2012 ERROR: cannot find /home/chris/resting/func/sub00294/rest/001/register.dof6.dat Try running register-sess with -per-run sub00294 To MNI305 ----------------------------- rawfunc2tal-sess -fwhm 0 -s sub00294 -d /home/chris/resting/func -fsd rest -update -subcort-mask ------------------------------ 1/1 sub00294 1/1 sub00294 001 ---------------- Tue Nov 6 16:32:30 CST 2012 ERROR: cannot find /home/chris/resting/func/sub00294/rest/001/register.dof6.dat Try running register-sess with -per-run ---------------------------------------- Started at Tue Nov 6 16:32:25 CST 2012 Ended at Tue Nov 6 16:32:30 CST 2012 preproc-sess done </SNIP> Date: Mon, 05 Nov 2012 21:44:23 -0500 From: Douglas Greve<greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] fs-fast preprocessing resting state To:freesurfer@nmr.mgh.harvard.edu Message-ID:<50987987.7010308(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Chris, it should have been done with preproc-sess. What was your preproc-sess command line? At some point, I had it set up so that it would go to the bold directory by default unless you used "-fsd rest". Newer versions require you to specify the FSD specifically. doug

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fs-fast preprocessing resting state
by Chris McNorgan 06 Nov '12

06 Nov '12

Hello, I'm getting started with freesurfer. I've played around with some of the tutorial data for fs-fast (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1) and was able to follow along and successfully carry out the preprocessing exercises (which sufficed for my purposes), which also included running register-sess on the "rest" tutorial data for sess01. I've run into a few gotchas with some resting state data, and wanted to know if there are any problems specific to processing resting state data that can be easily avoided? For example, here's the file structure: Project root: /home/chris/resting Anatomical data root ($SUBJECTS_DIR): /home/chris/resting/anat Functional data root ($FUNCTIONALS_DIR): /home/chris/resting/func Subject 1 anatomical directory: $SUBJECTS_DIR/sub00156 (already run through recon-all) Subject 1 functional directory: $FUNCTIONALS_DIR/sub00156 contains: subjectname ("sub00156") and a nii file in a nested subdirectory: $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz Where f.nii.gz is some resting state data (hence no paradigm files) For my inaugural attempt, I've run anatomical data for a participant through recon-all, and was having problems registering $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz to the surface map in $SUBJECTS_DIR/sub00156. After some trial and error and wandering through this mailing list, I found I had to first run mktemplate-sess and then register-sess (the fs-fast tutorial lead me to believe everything was automatically handled by preproc-sess). Are these deviations a foreseeable consequence of working with resting state data? Is there some documentation of important considerations for working with resting state data? Thanks for any help, Chris

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Research engineer – Neuroimaging in Alzheimer’s disease and dementia (ICM, Paris, France)
by Olivier Colliot 06 Nov '12

06 Nov '12

Research engineer – Neuroimaging in Alzheimer’s disease and dementia (ICM, Paris, France) Recruitment date: as soon as possible Type of contract: Limited duration (18 months) Gross salary: 33.000 Euros / year Status / category: Engineer Context: The Brain & Spine Institute (ICM) is a research centre of international dimensions located within the Pitié-Salpêtrière hospital in Paris. Its mission is to develop new strategies to improve the management of neurological diseases. The ICM is localized in the largest European hospital, in a top-level French university (University Pierre and Marie Curie). Its research activity takes place in a unique environment associating core technological facilities, space for industrial partners and a centre for clinical investigations. This position is offered within the IHU A-ICM project, a Foundation of Scientific Cooperation that federates the scientific and medical expertise of four partners from the public sector (Public Hospitals of Paris (AP-HP), National Center for Scientific Research (CNRS), National Institute of Health and Medical Research (INSERM) and Pierre and Marie Curie University-Paris6 (UPMC). Mission and main activities Main mission: Develop brain image analysis projects for the teams of the IHU working on Alzheimer’s disease and related dementias (fronto-temporal dementia, dementia with Lewy bodies, primary progressive aphasias…) Functional links: The recruited engineer will work within the brain image analysis team Cogimage (O. Colliot) of the ICM. He/she will be in close connection with IM2A (Pr B. Dubois), CENIR (Pr S. Lehéricy), the Functional Imaging Laboratory (H. Benali) and the other teams of the IHU working on Alzheimer’s disease and dementia. Activities: Analysis of MRI data (volumetry, morphometry, tractography, resting-state, classifiers) of the projects coordinated by the teams of the IHU working on Alzheimer’s disease and dementia Scientific monitoring and litterature updates on brain image analysis methods applied to dementia Development of new image analysis tools and automatic classifiers for the identification of biomarkers Assistance to the design and set-up of new studies (choice of protocols and imaging markers) Evaluation of the different available methods and choice of the most appropriate ones Management of the interface between researchers in image and signal processing, clinical and neuroscience teams of the IHU and the neuroimaging platform CENIR Profile of the candidate PhD in neuroimaging An experience in development of brain image analysis methods or/and their application to neuroimaging studies in patients Qualities Knowledge of one or several brain image analysis packages (SPM, Freesurfer, BrainVISA or FSL) Knowledge of statistical methods and tools. Knowledge of one or several programming languages (Matlab, Python or C/C++) Mastering oral and written scientific English Autonomy, having initiative, ability to work at the interface between multidisciplinary teams For more information, please contact: Olivier Colliot - olivier.colliot(a)upmc.fr

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mri_cor2label and unassigned vertices
by Mahinda Yogarajah 05 Nov '12

05 Nov '12

Dear Experts, I am trying to "back-normalise" significant clusters identified in a qdec analysis (2 groups, thickness as main variable of interest) back into individual subjects so that I can derive cortical statisitcs. As per previous posts I have been trying to use mri_cor2label but am running into some problems. My processing is as follows: 1) Identify file of interest which contains 3 clusters (labelled 1.000000 to 3.000000 as viewed in tksurfer and on qdec text output following analysis) significant using Monte Carlo correction 0.05 - mc-z.abs.th13.sig.ocn.annot 2) mri_cor2label --i mc-z.abs.th13.sig.ocn.annot --id 2 --l cluster2 This produces a file called cluster2.label but when I try loading it into tksurfer (tksurfer fsaverage lh inflated - followed by loading of label in menu system) I get the following error message which prevents me from double checking the label: % ******************** 0 nonzero vertices found ******************** label stat field identically zero - setting to 1 1890 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... Couldn't assign 1617 vertices. 1617 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... Couldn't assign 1617 vertices. My questions are: 1) Why does this occur ? 2) How can I convert my qdec results (eg. mc-z.abs.th13.sig.ocn.annot to label files which I can then propagate to all subjects using mri_label2label). Thanks. Mahinda

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Freesurfer November 2012