Freesurfer September 2014

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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

2 2

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

3 3

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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Re: [Freesurfer] Error in creating stats using tracula
by Anastasia Yendiki 09 Sep '14

09 Sep '14

Hi Neeraj - The libnetcdf error you're getting probably means that you should install a different build of freesurfer (centos 4 instead of centos 6). Which one are you currently using? In the future please email the freesurfer list instead of me personally with questions about tracula. The purpose of the list is to get the messages archived so that people can search for questions that have been answered before in the archives. Thanks! a.y On Tue, 9 Sep 2014, Neeraj Upadhyay wrote: > Dear Anastasia Yendiki, > While analysing the DTI data with Tracula ,I stuck to a problem which is attached in the screen shot .Please guide me how to solve it because this is the > step to analyse the data group wise using voxelwise diffusion measures. > > hope for a positive reply soon. > With warm Regrads > -- > Neeraj upadhyay > PhD Fellow > Department of Neurology and Psychiatry > University of Rome La' Sapienza > Viale della Universita 30-00185,Rome,Italy > Guide: Professor Alfredo Berardelli > contact no:+393735282419 > >

1 0

From bedpostX and recon-all to tracula
by Katherine Damme 09 Sep '14

09 Sep '14

Hello Freesurfer Community! I have sucessfully completed diffusion preprocessing in FSL and the recon-all of the structural image and would like to use tracula for the tract reconstruction. I keep having trouble with my configuration file. Does anyone have a bedpostX tracula config file they could share as an example? Thank you! Kate

3 4

mri_glmfit problem
by Minjeong Wang 09 Sep '14

09 Sep '14

Dear all, i have some problem with mri_glmfit. The error message is "you must use '--surface subject hemi' with surface data" What do I do for solving this problem?? Help me.. :( M.J. --------------------------------- mri_glmfit \ --glmdir lh.cdr.glmdir \ --y lh.cdr.thickness.10.mgh \ --fsgd cdr.fsgd dods \ --C normal-CDR0.5.mtx \ --C normal-CDR1.mtx \ --C CDR0.5-CDR1.mtx \ --C group.effect.mtx \ --C normal+CDR0.5-vs-CDR1.mtx \ --surf fsaverage lh \ --cortex \? --glmdir lh.cdr.glmdir \ ? --y lh.cdr.thickness.10.mgh \ ? --fsgd cdr.fsgd dods \ ? --C normal-CDR0.5.mtx \ ? --C normal-CDR1.mtx \ gdfReadHeader: reading cdr.fsgd INFO: gd2mtx_method is dods $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Applications/freesurfer/subjects cmdline mri_glmfit --glmdir lh.cdr.glmdir --y lh.cdr.thickness.10.mgh --fsgd cdr.fsgd dods --C normal-CDR0.5.mtx --C normal-CDR1.mtx sysname Darwin hostname Youngui-Mac-Pro.local machine x86_64 user younghopark FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/lh.cdr.thickness.10.mgh logyflag 0 usedti 0 FSGD cdr.fsgd glmdir lh.cdr.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.cdr.glmdir Loading y from /Applications/freesurfer/subjects/lh.cdr.thickness.10.mgh ERROR: you must use '--surface subject hemi' with surface data [Youngui-Mac-Pro:/Applications/freesurfer/subjects] younghopark% --C CDR0.5-CDR1.mtx \ --C: Command not found. [Youngui-Mac-Pro:/Applications/freesurfer/subjects] younghopark% --C group.effect.mtx \ --C: Command not found. [Youngui-Mac-Pro:/Applications/freesurfer/subjects] younghopark% --C normal+CDR0.5-vs-CDR1.mtx \ ? --surf fsaverage lh \ ? --cortex \ ? --C: Command not found.

2 1

within individual multimodal correlation
by lorenzo pasquini 09 Sep '14

09 Sep '14

Dear Freesurfers, I am currently investigating the relationship between functional activation and cortical thickness at a within-subject vertex-based level. For this purpose I have mapped my activation on the vertex surface in the same subject. As you can see from the attached screenshot, I am able to visualize for the same vertex (e.g. coordinates vertex normal [0.97 -0.17 -0.14], curvature -0.190746) the value of the individual activation map (3.002379 on TkSurfer) and the individual cortical thickness value (2.61282 on FreeView). What I need, is for every vertex in my surface the activation value and the correspondent cortical thickness value to be able to compute a vertex-based individual correlation of both modalities. How ca I extract this information from my data? The activation map is saved in .w (paint format)... is it possible to extract such a matrix by saving my data in an other format? I have been trying read_annotation and other matlab commands as read_surf but could not access a matrix of vertex specific thickness/activation values. Is there a more elegant way to compute an individual correlation/general linear model in freesurfer (please note that the analysis in WITHIN a subject)? Or should I use softwares as SurfStat (http://www.math.mcgill.ca/keith/surfstat/)? Any help would be very appreciated, thanks, Lorenzo

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Freesurfer September 2014