Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

mri_label_volume
by Flavia Niccolini 11 Sep '14

11 Sep '14

Dear Freesurfer expert, I am trying to normalized for ICV subcortical volume (Buckner et al. 2004) using the following:' mri_label_volume [options] <volume> <label 1> <label 2> ...' where options are either '-atlas_icv <fname> <scalefactor> ' or '-eTIV <fname> <scalefactor> '. My version of freesurfer is 5.3.0. But I get this problem: $ mri_label_volume -atlas_icv '/home/fniccoli/freesurfer/subjects/HD/Control_1/mri/transforms/talairach.xfm' 1948 '/home/fniccoli/freesurfer/subjects/HD/Control_1/mri/aseg.mgz' 11 50 ltMNIreadEx:/home/fniccoli/freesurfer/subjects/HD/Control_1/mri/transforms/talairach.xfm does not start as 'MNI Transform File' mri_label_volume: could not open atlas transform file /home/fniccoli/freesurfer/subjects/HD/Control_1/mri/transforms/talairach.xfm $ mri_label_volume -eTIV '/home/fniccoli/freesurfer/subjects/HD/Control_1/mri/transforms/talairach.xfm' 1948 '/home/fniccoli/freesurfer/subjects/HD/Control_1/mri/aseg.mgz' 11 50 ltMNIreadEx:/home/fniccoli/freesurfer/subjects/HD/Control_1/mri/transforms/talairach.xfm does not start as 'MNI Transform File' mri_label_volume: could not open atlas transform file /home/fniccoli/freesurfer/subjects/HD/Control_1/mri/transforms/talairach.xfm Could you please help me?

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lh.BA.annot vs lh.BA.thresh.annot ... generalization question
by Krieger, Donald N. 11 Sep '14

11 Sep '14

Hi Anastasia or anyone, Are there any other groups of labels which are, by default, produced in comparable less vs more restrictive ways? For instance, is there a way to produce lh.aparc.thresh.annot with comparably constrained labels? And does it make sense to do so? Regards, Don <snip> > > > On 14-09-08 12:39 PM, Anastasia Yendiki wrote: > > Hi David - On the difference between .thresh and "not .thresh" labels: > > The BA labels come from averaging histologically derived labels from > > a set of post mortem brains. The non-thresholded version is just the > > sum of the corresponding labels from the different brains in > > fsaverage space. So vertices are included even if only one of the > > brains had their BA in that vertex, which means that these labels > > are going to be rather large. In the thresholded version, a > > threshold has been applied to the average BA label, to make it have > > an area as close as possible to the average area of the individual BA labels. I hope this makes sense. > > > > a.y <snip>

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HCP Pipelines v3.4.0 Released
by Jennifer Elam 10 Sep '14

10 Sep '14

*News from the Human Connectome Project (HCP)* *September 10, 2014* *HCP Processing Pipelines Released * The WU-Minn HCP Consortium is pleased to announce the open source release of HCP data processing pipelines at https://github.com/Washington-University/Pipelines. To download, click *releases* (near the top of the page), then under v3.4.0, click the “Source code (zip)” or “Source code (tar.gz)” button. These v3 pipelines were used to process HCP image data from the HCP 500 Subjects Release (June 2014). The HCP Pipelines are set of tools (primarily, but not exclusively, shell scripts) for processing MRI images for the Human Connectome Project <http://www.humanconnectome.org>. Among other things, these tools implement the Minimal Preprocessing Pipeline (MPP) described in Glasser et al. 2013 <http://www.ncbi.nlm.nih.gov/pubmed/23668970>. We are releasing the HCP Pipelines now for use to the community, but we are still in the process of making the scripts more robust, well-documented, and usable in other environments (other versions of operating systems, other queueing systems, other versions of prerequisite tools, etc.). We cannot guarantee that you will not have to make modifications to the scripts for them to be used successfully in your environment. The HCP Pipelines require installation of FSL 5.0.6, FreeSurfer v5.3.0-HCP, and Connectome Workbench v1.0. See the README.md <https://github.com/Washington-University/Pipelines/blob/master/README.md> in the GitHub repository for detailed information on prerequisite software versions, installation and processing instructions, example data, and processing resource requirements. Answers to frequently asked questions can also be found on our Github Repository: HCP Pipeline FAQ <https://github.com/Washington-University/Pipelines/blob/master/FAQ.md>. We encourage user feedback and improvement suggestions on the HCP Pipeline tools and the documentation. Discussion of HCP Pipeline usage and improvements can be posted to the hcp-users discussion list. Sign up for hcp-users at http://humanconnectome.org/contact/#subscribe Best, The WU-Minn HCP Consortium Jennifer Elam, Ph.D. Outreach Coordinator, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elamj(a)pcg.wustl.edu www.humanconnectome.org

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Re: [Freesurfer] mri_cvs_register
by Lilla Zollei 10 Sep '14

10 Sep '14

Could you also send the log file along? Thanks, Lilla On Wed, 10 Sep 2014, BigBen2293(a)web.de wrote: > I'm using the version stable v5.3.0. > Ben > >

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mri_cvs_register
by BigBen2293＠web.de 10 Sep '14

10 Sep '14

2 1

Syntax Error: trac-all -bedp
by Robby De Pauw 10 Sep '14

10 Sep '14

Dear Anastasia, Barbara & FS-community, The preprocessing step of Tracula was succesfully completed. However when I try to do the next step: fitting the Ball & Stick model I get another error: mri@ge24c165:/media/mri/DATAPART11/ROBBY/FREESURFER$ trac-all -bedp -c dmrirc.info INFO: SUBJECTS_DIR is /media/mri/DATAPART11/ROBBY/FREESURFER/T1 INFO: Diffusion root is /media/mri/DATAPART11/ROBBY/FREESURFER/T1 Actual FREESURFER_HOME /usr/local/freesurfer INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /apps/gent/SL6/sandybridge/software/FreeSurfer/5.3.0-centos4_x86_64 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /media/mri/DATAPART11/ROBBY/FREESURFER/T1/INP_080_LISA_V_1/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected I have already searched through your mailing list and found a topic where the same problem is discussed:[Freesurfer] FreeSurfer 5.2 TRACULA and FSL 5. I've already checked for the things that were suggested here, but I didn't find a solution. Hoping for some help? Thanks, Regards, Robby

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Help with pial boundary
by Joann Poh 10 Sep '14

10 Sep '14

Dear All, I'm having issues with the pial surface - temporal lobe is being under-estimated (see wm-pial.png) where the red cross is. (Frontal lobe also has similar issues.) In wm.mgz, the white matter looks fine, as well as in aseg.mgz (see aseg-wm-pial.png) but just not the pial boundary. What can I do to rectify this? On a side note, I've tried adding control points (to the frontal lobe to solve a similar problem) but the pial boundary still does not cover the gray matter and I'm missing bits. Thank you. Kind regards, Joann

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Re: [Freesurfer] "thresh" labels
by Krieger, Donald N. 10 Sep '14

10 Sep '14

Are there any other groups of labels which are, by default, produced in comparable less vs more restrictive ways? Regards, Don <snip> > > > On 14-09-08 12:39 PM, Anastasia Yendiki wrote: > > Hi David - On the difference between .thresh and "not .thresh" labels: > > The BA labels come from averaging histologically derived labels from a > > set of post mortem brains. The non-thresholded version is just the sum > > of the corresponding labels from the different brains in fsaverage > > space. So vertices are included even if only one of the brains had > > their BA in that vertex, which means that these labels are going to be > > rather large. In the thresholded version, a threshold has been applied > > to the average BA label, to make it have an area as close as possible > > to the average area of the individual BA labels. I hope this makes sense. > > > > a.y <snip>

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"mri_convert"
by Nooshin Zadeh 09 Sep '14

09 Sep '14

Dear FreeSurfer experts, I get a new message when I use "mri_convert" command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I get the new message. In addition, it does not create mgz file, and goes to infinite loop. *mri_convert "/M1/t1_se_ax_5/IM-0004-0001.dcm" "/FS/M1/mri/orig/001.mgz"* mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /M1/t1_se_ax_5/IM-0004-0001.dcm... Getting Series No Scanning Directory INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5 INFO: Scanning for Series Number 5INFO: found 37 files in series INFO: loading series header info. I appreciate if you can advise me. Regards, Nooshin

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New deadline for the Alzheimer's Disease Sage/DREAM Challenge!
by Arno Klein 09 Sep '14

09 Sep '14

We have extended the Alzheimer's Disease Sage/DREAM Challenge #1 submission period to October 17th -- Time to enter! https://www.synapse.org/#!Synapse:syn2290704 Of particular interest to the members of this mailing list is subchallenge 3, which leverages brain imaging ( FreeSurfer was used in the processing of the data ) , in addition to genetics, cognitive assessments, and demographic information from cohorts ranging from cognitively normal to mild cognitively impaired to individuals with AD. Looking forward to your submissions to the leaderboard!: https://www.synapse.org/#!Synapse:syn2290704/wiki/65302 Cheers, @rno

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