Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

error message in tkmedit
by Rashmi Singh 01 Feb '12

01 Feb '12

While opening tkmedit using terminal I gave following command % crick:~/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/FreeSurfer> tkmedit AA471.T0 brainmask.mgz -aux T1.mgz -segmentation aseg.mgz -surfs $FREESURFER_HOME/FreeSurferColorLUT.txt The output was Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. LoadSegmentationVolume main aseg.mgz /opt/freesurfer/FreeSurferColorLUT.txt Reading /opt/freesurfer/tktools/tkm_common.tcl Reading /opt/freesurfer/tktools/tkm_wrappers.tcl Reading /opt/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /opt/freesurfer/tktools/tkUtils.tcl % 3 new windows popped up 1. The view window with the brain image ( it was similar to the one shown in you tutorial document-showed the surfaces and the segmentation in color) 2. The tool box window 3. Error message window stating the following Error: Parsing arguments Unrecognized option: /opt/freesurfer/FreeSurferColorLUT.txt This option is not recognized by tkmedit. Please explain what does this error message mean. Rashmi. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

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error extracting label from annot
by kelsi＠nmr.mgh.harvard.edu 01 Feb '12

01 Feb '12

Hi, I am trying to extract the label for the calcarine sulcus from the annotation file. I would actually like to extract it from the aparc+aseg.mgz file, but when I use mri_extract_label, it creates an empty volume. Does this mean that it is not labeled in my volume? However, I found the label in the annot file, so I am using the command below, but no files output except for my segmentation volume, which causes fslview to crash when I try to load it. mri_annotation2label --subject fs --hemi rh --labelbase ./rh_annot --seg rh_annot.nii.gz --annotation aparc.a2009s --sd . Do you have any suggestions? Also, I would like to project the region 2mm into the white matter, how would I do this? Thank you! Kelsi

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error while dividing an annotation/label
by Ritobrato Datta 01 Feb '12

01 Feb '12

Hello, I am trying to divide lh.v1.predict.label into equal parts. So I did the following - A) Created a colorfile V1color.ctab which contains the following- # #No. Label Name: R G B A 1 V1 70 130 180 1 B) mris_label2annot --s 001raw --h lh --ctab V1color.ctab --a TrialV1 --l lh.v1.predict.label --maxstatwinner C) echo V1 4 > splittable.txt D) mris_divide_parcellation 001raw lh TrialV1.annot splittable.txt lh.TrialV1.split reading colortable from annotation file... colortable with 2 entries read (originally V1color.ctab) interpreting 4th command line arg as split file name dividing V1 (1) into 4 parts allocating new colortable with 4 additional units... Segmentation fault What am I doing wrong and how do I correct it ? Thanks Ri

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Error with mri_glmfit-sim -- sim perm
by Antonella Kis 01 Feb '12

01 Feb '12

Dear all, I was running the simulation: mri_glmfit-sim \ --glmdir GroupAnalysis_abs.glmdir \ --sim perm 1000 3 permcsd \ --sim-sign abs \ --cwpvalthresh .05 and unfortunately I got the following error: mri_volcluster --in GroupAnalysis_pos.glmdir/contrast/sig.mgh --mask GroupAnalysis_pos.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg fsaverage aparc+aseg.mgz --csdpdf GroupAnalysis_pos.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_pos.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_pos.glmdir/contrast/permcsd.sig.voxel.mgh ERROR: cannot find /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/fsaverage/mri/aparc+aseg.mgz Seems that the simulation was completed saying that mri_glmfit simulation done but I did not get any clusters or any file permcsd.sig.cluster.summary. Also I am not sure if I need to use the while running the mri_volcluster the fsaverage or I should use the cvs_avg35 since my FA data was registered over the CVS space. Can I just do something further to catch my corrected clusters? I attached my log file. Thank you very much. Antonella

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Retinotopy
by _andreia_＠sapo.pt 01 Feb '12

01 Feb '12

Hello! I'm moving to FS 5.1 and I will be analysing retinotipic data (and the anatomical data bas well). I would like to know if there are any changes or issues while running this analysis in this new version before I move. Thanks, Andreia

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Error with fsaverage/mri.2mm/reg.2mm.dat
by Antonella Kis 01 Feb '12

01 Feb '12

Dear All, Can someone help me to find out what is the equivalent of the fsaverage/mri.2mm/reg.2mm.dat when I use the cvs_avg35 template, I mean I register my FA data over the CVS space? I suppose I will need to repalce the fsaverage/mri.2mm/reg.2mm.dat in the following command: mri_volcluster --in GroupAnalysis_abs.glmdir/contrast/sig.mgh --mask GroupAnalysis_abs.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_abs.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 aseg.mgz --csdpdf GroupAnalysis_abs.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_abs.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.voxel.mgh Thank you very much! Antonella

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tabel with labels and name of brain regions for both atlases
by Maria Felber 01 Feb '12

01 Feb '12

Dear all, I am trying to use my freesurfer data for fibertracking. So far it is working and I can even specifically tell the programm, which labels/brain regions to use. However, I haven't found an overview tabel, where all labels stand together with the region's name. It would be painfull, to open for every subject tksurfer and then moving with the mouse over the region of interest to get the correct label. Is there such a table overview for both atlases and where can I find them? Thank you. Sincerely, Maria Felber -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522

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Question about .license
by Nooshin Zadeh 01 Feb '12

01 Feb '12

Hi Everyone I have a question about installation of freesurfer, license part. For placing the three lines in a file named ".license" in the directory pointed to by the $FREESURFER_HOME, I used "vi .license" in terminal and it did not work. Also, I can not use "sudo vi .license" because I do not have the password. Can you please guide me on how can I make the .license file? Thanks in advance, Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * *

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showedits bug
by Michael Harms 01 Feb '12

01 Feb '12

Hi Nick, I found a small bug in recon-all that prevents the -showedits flag from working in conjunction with expert-options: Line 785 in recon-all of v5.1 currently has an extraneous closing parenthesis: if (-e $XOptsFile)) then but should be: if (-e $XOptsFile) then Also, I'm puzzled how the resulting edits.mgz gets translated when you load it as a segmentation -- e.g., areas with an addition to wm.mgz appear to be assigned the value 2 in edits.mgz, and are labeled as "wm- ON" if you load edits.mgz as a segmentation, but I don't see any entry for "wm-ON" in FreeSurferColorLUT.txt itself. Where is the full "key" for the values in edits.mgz? thanks, -MH

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WG: Save segmentation results as nifi files
by Fellhauer, Iven 01 Feb '12

01 Feb '12

Hi Bruce And thank you for your hint, but where are the files for GM, WM and CFS stored in the Freesurfer output directory structur? Best regards, Iven -----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Montag, 30. Januar 2012 15:20 An: Fellhauer, Iven Cc: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Save segmentation results as nifi files Hi Ivan you can convert any volume to any supported output type using mri_convert. It will figure out the format from the extension, so: mri_convert aseg.mgz aseg.nii.gz or mri_convert aseg.mgz aseg.nii should do the trick cheers Bruce On Mon, 30 Jan 2012, Fellhauer, Iven wrote: > > Dear all, > > > > I run recon-all with the ?autorecon1 and ?autorecon2 options. Now I > want to store the segmentation results in a spm like way. One nifti > file for each matter. Can I do this with freesurfer? And how can I do > this with freesurfer? > > > > Best regards, > > > > Iven Fellhauer > > > > ---------------------------------------------------------------- > > Universitätsklinikum Heidelberg > > Zentrum für Psychosoziale Medizin > > Klinik für Allgemeine Psychiatrie > > Sektion für Gerontopsychiatrie > > Voßstr. 4 > > 69115 Heidelberg > > Tel.: +49 (0) 6221 - 56 7578 > > Email: iven.fellhauer(a)med.uni-heidelberg.de > > > > > 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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