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Running FreeSurfer Remotely
by obregon＠nmr.mgh.harvard.edu 23 May '11

23 May '11

Hi, Will FreeSurfer run remotely using NX Client for OSX or should I employ VNC only? Thanks, Gabriel

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loading qdec.table.dat error
by Tetiana Dadakova 23 May '11

23 May '11

Dear list, I am trying to load qdec.table.dat file using qdec, and get the following error: Loading data table /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat... QdecDataTable::Load: will attempt to open as Mac text file... Number of columns: 3 fsid column: 1 Number of factors: 2 Number of subjects: 126 ERROR: QdecDataTable::Load: problem parsing file /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat This line did not appear to end with a newline: PAT_ViOl 25 pat Error loading the data table. This is the last line in the file and therefore there is no new line after it. What can cause this error? Thank you, Tanja.

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flattenning question
by Gabriel Go.Es. 20 May '11

20 May '11

Dear FreeSurfers I'm wondering about the flattenning options of FS I've saw that the "mris-flatten" command does the trick but, it asks for a patch, my questions are: can I flat any cortical region? and, how do I create a patch to mris_flatten? Thanks in advanced, Gabriel

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FW: What is the difference between Cerebral-white-matter and Cortical-white-matter in Freesurfer?
by Righart, Ruthger Dr. 20 May '11

20 May '11

Hi Allison, Thank you very much for your help! I am using v5.0.0. Is the surface of the white-matter (from the surface-based stream) used here to calculate the volume in CorticalWhiteMatterVol and is this why I have sub-millimeter values here? This value is in fact different from the value that can be calculated in mri_segstats for cerebral-white-matter using the command "mri_segstats --seg aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --sum test1.stats". Is this because segstats makes the calculation here in voxels? Is it therefore better to take the value from CorticalWhiteMatterVol which would take the white-matter surface into account? Best, Ruthger ________________________________________ From: Allison Stevens [astevens(a)nmr.mgh.harvard.edu] Sent: Friday, May 20, 2011 2:56 PM To: Righart, Ruthger Dr. Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] What is the difference between Cerebral-white-matter and Cortical-white-matter in Freesurfer? Which version of FreeSurfer are you using? In the more recent versions, they are the same. Cortical White Matter is all the white matter contained within the white surface minus the subcortical gray matter and ventricles, etc. On May 20, 2011, at 7:37 AM, "Righart, Ruthger Dr." <Ruthger.Righart(a)med.uni-muenchen.de> wrote: > Dear All, > > I am working with the volume-based stream in Freesurfer and I have a question about what is the difference between the volumes given for Cortical-white-matter and Cerebral-white-matter? How are the volumes calculated for both in Freesurfer? Is it the difference of including or not including the subcortical gray matter and ventricles in the calculation? > > I have read previous mailings ( e.g. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15449.html ) but I am still confused what is the difference between these measures. > > Thank you very much in advance for your help! > > Ruthger Righart (PhD) > > Institute for Stroke and Dementia Research (ISD) > Klinikum der Universität München > Max-Lebsche-Platz 30 > 81377 Munich | Germany > > Ruthger.Righart(a)med.uni-muenchen.de > > > _______________________________________________ > 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.

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What is the difference between Cerebral-white-matter and Cortical-white-matter in Freesurfer?
by Righart, Ruthger Dr. 20 May '11

20 May '11

Dear All, I am working with the volume-based stream in Freesurfer and I have a question about what is the difference between the volumes given for Cortical-white-matter and Cerebral-white-matter? How are the volumes calculated for both in Freesurfer? Is it the difference of including or not including the subcortical gray matter and ventricles in the calculation? I have read previous mailings ( e.g. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15449.html ) but I am still confused what is the difference between these measures. Thank you very much in advance for your help! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany Ruthger.Righart(a)med.uni-muenchen.de

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ROI analysis in freesurfer
by abdurahman elkhetali 19 May '11

19 May '11

We have a functional image (beta weights generated in SPM and the original BOLD timeseries they came from ) and a structural image. We have flattened the anatomical image using freesurfer and have determined some ROIs based on that (retinotopy). Now we need to apply those ROIs to our BOLD images. What method would you suggest for this? How would you go about taking the BOLD images and transforming to the flattened space for our subject? TanksAboul Alkhtli

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little bug in mri_cvs_register
by GREGORY R KIRK 19 May '11

19 May '11

running mri_cvs_register --mov 004 --template 003 get error executing surf2vol at /apps/x86_64_sci5/freesurfer-latest/bin/elastic_registration_CVS.pl line 162. line 162 is system($cmdLine)==0 or die "error executing surf2vol"; i saw martin kavec posted the same error but did not see a response ' the command is $cmdLine is surf2vol -fixed_mri /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/mri/norm.mgz -moving_mri /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/mri/norm.mgz -fixed_surf /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/surf/lh.white -moving_surf /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/lh.resample.white -fixed_surf_2 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/surf/rh.white -moving_surf_2 /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/rh.resample.white -fixed_surf_3 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/surf/lh.pial -moving_surf_3 /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/lh.resample.pial -fixed_surf_4 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/surf/rh.pial -moving_surf_4 /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/rh.resample.pial -aparc /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/label/lh.aparc.annot -aparc_2 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/label/rh.aparc.annot -aparc_3 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/label/lh.aparc.annot -aparc_4 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/label/rh.aparc.annot -lin_res 20 -ksp_rtol 1.0e-9 -cache_transform /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/transform.txt -penalty_weight 1000 -fem_steps 17 -elt_vol_range 5.0,10.0 -log_summary -poisson .3 -topology_old -compress -pc_type none -ksp_type preonly -pc_type jacobi -ksp_type cg -ksp_view -ksp_converged_reason -out /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/el_reg_to003.mgz -out_surf /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/surf-mfc_to003 -out_mesh /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/el_reg_to003 &> /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/trace_el_reg_to003_004.txt if you cut and paste this in your freesurfer SUBJECTS_DIR it runs fine but executing strace -f -o /scratch/trace.foo mri_cvs_register --mov 004 --template 003 --step2 one of the output lines is 16837 open("iteration.node", O_WRONLY|O_CREAT|O_TRUNC, 0666) = -1 EROFS (Read-only file system) on another computer where i have freesurfer installed in my home directory the program runs fine. so it seems that when the perl script executes the command and freesurfer is installed in a system directory like /usr/bin/... that the perl script home dir at the point of the system call is in the system directory and it is trying to write there rather than somewhere in SUBJECTS_DIR or other user writable location and surf2vol fails when it tries to open a file in write mode in a system directory greg

2 1

error message from fast_selxavg.m
by Yang Liu 19 May '11

19 May '11

Hi, I was running selxavg-sess, and met this error: >> >> >> >> >> >> $Id: fast_selxavg.m,v 1.40.2.2 2009/04/09 20:01:57 greve Exp $ Parsing Arguments RescaleTarget = 1000 UseMRIread = 1, ext = nii Checking Parameters ??? Undefined function or variable "xyzscale". Error in ==> load_nifti_hdr at 138 hdr.pixdim(2:4) = hdr.pixdim(2:4) * xyzscale; Error in ==> load_nifti at 75 hdr = load_nifti_hdr(niftifile); Error in ==> MRIread at 159 hdr = load_nifti(fspec,headeronly); Error in ==> fast_selxavg>check_params at 1529 mri = MRIread(instem,1); Error in ==> fast_selxavg at 51 s = check_params(s); >> ??? Undefined function or variable 'r'. >> quiting matlab ------------------------------------------ ERROR: fast_selxavg() failed\n ERROR (/space/data/stan/cooked/2010/101204Castor): selxavg failed Done... It all goes back to the undefined "xyzscale". Does that mean the nifti fiel I am trying to load is wrong? This problem is quite annoying because it appearance is unpredicatable. Sometimes our analysis go through fine, sometimes it pops out, and I have no idea what is the difference from those successful runs. Thanks, Yang

1 0

recon-all tutorial data
by obregon＠nmr.mgh.harvard.edu 19 May '11

19 May '11

Hi, I'm new to the software and I'm having trouble finding the following file: ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz How can I download the "recon-all" tutorial data? Has it been replaced/relocated? Thanks a lot, Gabriel Obregon

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Fwd: sign mc-z
by René Besseling 19 May '11

19 May '11

Dear all, A beginners question: what does the sign mean in the multiple comparison simulations? I thought it defines the side of the t-test performed on the glm parameter estimates, but since you can run the simulations for a bunch of contrasts simultaneously and since in some cases you might be interested in H1: c^T B<0 and in others in H1: c^T B>0, I think the sign must mean something else... Hope you can help! Best regards, René

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