Freesurfer

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30088 discussions

error messages in running mri_convert
by Yajun Fang 13 Jul '11

13 Jul '11

Hi, I used to be able to run command "mri_convert" in the matlab environment through "system" command. Now I received the error messages as below: mri_convert: error while loading shared libraries: requires glibc 2.5 or later dynamic linker Any suggestions ? Is it related to the new update of freesurfer ? If I switch to another server, the problem did not exist. But can I still run the command in the same server ? I am looking forward to your suggestions. Thank you ! best, Yajun

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tracula - fix bad bbregister's
by GREGORY R KIRK 13 Jul '11

13 Jul '11

Hi, I processed about 80 subjects with -prep stage and then checked the bbregister registrations with tkregister2 --mov /study5/aa-scratch/TEENEMO/freesurfer_local/toot/057/dmri/dwi.nii.gz --reg /study5/aa-scratch/TEENEMO/freesurfer_local/toot/057/dmri/xfms/anatorig2diff.bbr.dat --surf found 17 subjects with bad registrations, as always because the fsl registration initialization was bad. so now i manually fix the registeration and use the manual fix for the initialization and rerun bbregister and get a good registration. so now i need to rerun -prep phase but have it use the good registration instead of computing a new bbregister registration. will trac-all -prep -nointra -c configfile accomplish this or do i need to get in and tinker with the scripts to make it run everything including computing new fsl and inverse registration matricies but using my bbregister good registration. thanks greg

2 1

reg-feat2anat: correct anat2exf.register.dat only or also func2std?
by Agnieszka Burzynska 13 Jul '11

13 Jul '11

Dear experts, I am using reg-feat2anat to register my functional data from FSL to anatomical and starndard space in Freesurfer. For some subjects the registration is bad. I can easily fix anat2exf.register.dat. However, as specified in reg-feat2anat help, I know that the registration failed as the func2std is incorrect, too. Is it enough to correct anat2exf.register.dat to correctly transfer functional data from feat to the surface space or do I also need to correct func2std? It seems to me that in the next steps I am using, such as sampling the functional data to fsaverage and further calculations in the fsaverage space do not rely on func2std. Is this correct? Cheers, Aga

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Re: [Freesurfer] Corrections with brainmask volume
by Bruce Fischl 13 Jul '11

13 Jul '11

Hi Antonella those look good to me. Note that you can't tell defects from a single slice. You need to scroll back and forth and look in different orientations. That said, the surfaces look pretty accurate cheers Bruce On Wed, 13 Jul 2011, Antonella Kis wrote: > Good morning Bruce, > I am checking my data after recon-all data pre-process. I am not very sure about some defects (removing dura and pail surface corrections). I attached > two tiff files from > > tkmedit P1 brainmask.mgz -aux T1.mgz -surfs > > > Do I have a lot of defects to eliminate on this slides, are the gray/white boundaries good or any suggestion regarding manually corrections that should > be done on this images it will be very appreciated. > > Thank you very much for your help! > Antonella > > > > >

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-legacy flag in version 5.1
by Marie Schaer 13 Jul '11

13 Jul '11

Hi everyone, Just a quick question: I noticed that the -legacy option of recon-all was removed in version 5.1. Is there any way to keep the manual edits and all the processing from previous versions while reprocessing with 5.1? Thank you very much, Marie

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Request for DICOMS
by Satrajit Ghosh 12 Jul '11

12 Jul '11

hi, if you have pointers to publicly available DICOM data or willing to share such data publicly from different scanners and acquisition sequences for structural, diffusion and functional data from human participants, please contact me off list. currently, the more varied the scanners and sequences, the better. i'm not looking for full datasets here, but primarily the ability to mine the various tags and metadata that exist across common image acquisitions. cheers, satra

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(no subject)
by 林鄞 12 Jul '11

12 Jul '11

Dear everyone, I just have a problem when installing Freesurfer. I can’t process the command of “tkmedit”. How can I solve this problem? Thank you! setenv FREESURFER_HOME /usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh setenv FREESURFER_HOME opt/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh psylab-Lenovo:~> sudo tcsh [sudo] password for psylab: psylab-Lenovo:~# setenv FREESURFER_HOME /usr/local/freesurfer psylab-Lenovo:~# source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni psylab-Lenovo:~# sudo tkmedit bert orig.mgz sudo: tkmedit: command not found psylab-Lenovo:~# sudo tcsh psylab-Lenovo:~# tkmedit bert orig.mgz tkmedit: Command not found. psylab-Lenovo:~# apt -get tkmedit apt: Command not found. psylab-Lenovo:~#

3 2

Hippocampal subfield segmentation
by Tricia Merkley 12 Jul '11

12 Jul '11

Hi, I understand that the models for the hippocampal subfield segmentation were created using high resolution MRI scans. But it sounds like this procedure can be used for scans with 1mm ^3 resolution, right? The resulting values would just need to be divided by 8 in order to get the subfield volumes in 1mm^3 though, since the resulting volumes are reported as 0.5x0.5x0.5mm^3. Is that correct? Thanks, Tricia Merkley

4 7

Question about mri_label2label
by John Richey 12 Jul '11

12 Jul '11

Dear freesurfer experts, I have a question about the use of a registration matrix in the context of mri_label2label. I have a series of labels that were created through mri_volcluster (each significant cluster from a .sig map was saved as a uniqe label as a product of that command), and I wish to map each of these from average space (fsaverage) into native space. However, when I use mri_label2label for this purpose some of the clusters map into plausible subject-space, however others are obviously incorrect. Here is the command line that I have used: mri_label2label --srcsubject fsaverage --srclabel $SUBJECTS_DIR/group_analysis/${CONTRAST}/${LABEL} --trgsubject ${SUBJECT} --trglabel $SUBJECTS_DIR/${SUBJECT}/label/${CONTRAST}_${LABEL} --regmethod volume --reg $SUBJECTS_DIR/${SUBJECT}/bold/register.dat I have also tried this command without --reg, but no luck. It seems like I would need a registration matrix that maps each subject to fsaverage, no? Thanks very much in advance,

1 0

tkregister2
by Ignacio Letelier 12 Jul '11

12 Jul '11

Hi freesurefers I tried to visualize my functional data using the command: tkregister2 --s --reg --fslreg --surf orig --tag and i received this error : ERROR: trying to convert FSL registration matrix to FreeSurfer, but FSLOUTPUTTYPE variable is not set. Can anyone help me with this , Thanks in advance , best regards. -- Ignacio

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