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[TRACULA] trac-preproc error while reruning with an 'init=1' option
by Juke Cha 27 Sep '12

27 Sep '12

Hi Anastasia, After an intial tracula pipeline procedure, I found some tracts were not successfully reconstructed. Their aparc+aseg looked fine to me. So I reran the trac-preproc -prior and trac-path with an option, 'init=1' in a dmrirc file. Now, the analysis's running well on some, but not the other. I've got an error in trac-preproc -prior: INFO: Rejected 536 streamlines for straying off mask INFO: Rejected 36 streamlines for reversing direction INFO: Rejected 0 streamlines as length outliers INFO: Have 4722 total streamlines (min/mean/max length: 8/57/104) Loading list of excluded streamlines from /home/brain/F/JOSH/fs/1006/dlabel/mni/lh.unc_AS_avg33_mni_flt_cpts_all.bad.txt INFO: Found 3 streamlines to be excluded Loading segmentation from /usr/local/freesurfer//trctrain/trc001/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer//trctrain/trc001/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer//trctrain/trc002/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer//trctrain/trc002/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer//trctrain/trc003/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer//trctrain/trc003/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer//trctrain/trc004/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer//trctrain/trc004/dlabel/mni/cortex+2mm.nii.gz trac-preproc exited with ERRORS at Tue Sep 11 11:03:52 EDT 2012 What would cause this and how can I fix this? Thanks for your help in advance. -Jiook

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Re: [Freesurfer] DTI Spatial Normalization
by Ali Ezzati 27 Sep '12

27 Sep '12

Hello, I am new to DTI analysis and I am trying to follow up the manual. I have 2 questions: 1) I cannot find any data related to CVS space in the $FREESURFER_HOME/subjects Can you please help me find or get the "cvs_avg35/mri/norm.mgz"? Currently, I am using FreeSurfure 5.1 on Linux, is CVS space available for the latest version? 2) How should I change these commands to use MNI space instead of CVS? mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \ --mov $SUBJECTS_DIR/$subj/dtrecon/fa-masked.mgz \ --o $SUBJECTS_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg Thank you for your help. Ali Ezzati

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mri_glmfit-sim with pre-cached fails
by Ed Gronenschild 27 Sep '12

27 Sep '12

Hi, I want to apply a cluster correction with mri_glmfit-sim with the --cache option: mri_glmfit-sim --glmdir my_glmdir --cache 1.3 abs It fails with the error message that it can't find the file: FSDir/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/th1.3/mc- z.csd (FSDir is the directory where FreeSurfer is located, version 5.0.0, Mac OSX10.5) Looking at the content of the ....fsaverage/lh/cortex directory than indeed, only the directories fwhm01, fwhm02, ..., fwhm30 are present. In the log file from mri_glmfit I can read that the residualFWHM is 34.005014. Since this FWHM is automatically derived by mri_glmfit, does it mean that I can never use the --cache option in this case? Cheers, Ed

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help about the testing Freesurfer
by yawu Liu 27 Sep '12

27 Sep '12

Hi Experts, I have baseline and followup MRI data, when I run"recon-all -s AndiS \ -i /home/d4201z/Desktop/fs/1/18991230_000000anonymouss002a1001.nii -i /home/d4201z/Desktop/fs/2/18991230_000000anonymouss004a1001.nii" Only the first dataset(baseline) were processed with out any problem, but it stops at "d4201z-CELSIUS-M470-2:~> -i /home/d4201z/Desktop/fs/2/18991230_000000anonymouss004a1001.nii" , When I click return key, the software says -i could not found. Could you give me hints on how to fix the problem?

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Should control points be removed?
by Jonathan Holt 26 Sep '12

26 Sep '12

Quick small question, I'm editing a few brains at the moment that have needed multiple script runs. I've added control points as necessary before each run and afterward the resulting brain will typically need either more control points added, white matter aux volume edits, or both. I'm wondering whether or not I should remove "older" control points after they've done their job in editing the pial and main surfaces. I only ask as I fear they may interfere with newer edits I've made and muck up the script running process, or is this not the case? best, jon Research Asst. Dept. of Radiology University of Michigan

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Re: [Freesurfer] questions about recon-all pipelines
by Darren Gitelman 26 Sep '12

26 Sep '12

Pietro You should first import your *.dcm files with the command recon-all -i first_dicom_image_name.dcm -s subjID Then when you process your data you would type recon-all -s subjID -autorecon1 -autorecon2 or whatever steps you are using. Darren On Wed, Sep 26, 2012 at 9:33 AM, pietro de rossi <derossi05(a)gmail.com>wrote: > Dear FreeSurfers, > > I am a beginner, trying to process some 3T MPRAGE scans on my own for a > project. > > I have a couple of simple questions > > > 1. When I run the recon-all –autorecon1 –autorecon2 command it asks me > for 001.mgz in mri/orig so I copy and paste the volume into the folder and > the command works. My question is: do I need to change 001.mgz to 002, 003 > an so on for every scan I process? > 2. I have to process 3T scans in a .dcm format. Can I just process the > scan as it is? Do I have to save the .dcm files as another format, maybe a > .mnc file? > > thank you very much in advance, > > Pietro > > -- > Pietro De Rossi, MD > ------------------------------------- > Sapienza Università di Roma, Facoltà di Medicina e Psicologia, > Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), > Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma > > NESMOS Department (Neurosciences, Mental Health and Sensory Functions), > School of Medicine and Psychology, Sapienza University, Sant’Andrea > Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy > > Neurobehavioral Clinical Research Section, Social and Behavioral Research > Branch, National Human Genome Research Institute (NHGRI), National > Institutes of Health (NIH), Bethesda, Maryland 20892, USA > -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

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question about fsaverage vs. my subjects average
by Darren Gitelman 26 Sep '12

26 Sep '12

Hi I have 3 questions: 1) Does it affect the stats (or does it just affect the display) if I use the fsaverage brain vs. the average of my subjects brains when running mris_preproc or when simulating the cluster statistics using mri_glmfit-sim? 2) I downloaded the simulations for multiple comparisons correction mult-comp_cor.tar.gz. (which I later realized were also in freesurfer/average/mult-comp-cor). How do I apply the simulations to my data (assuming I used fsaverage)? It doesn't really say on the group analysis page how to apply the *.cdf file (or I missed it). 3) I see on the list that mention is made of a possible symmetric template, and there is an fsaverage-sym directory in the file I downloaded. Is this template available? Thanks, Darren -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

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questions about recon-all pipelines
by pietro de rossi 26 Sep '12

26 Sep '12

Dear FreeSurfers, I am a beginner, trying to process some 3T MPRAGE scans on my own for a project. I have a couple of simple questions 1. When I run the recon-all –autorecon1 –autorecon2 command it asks me for 001.mgz in mri/orig so I copy and paste the volume into the folder and the command works. My question is: do I need to change 001.mgz to 002, 003 an so on for every scan I process? 2. I have to process 3T scans in a .dcm format. Can I just process the scan as it is? Do I have to save the .dcm files as another format, maybe a .mnc file? thank you very much in advance, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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how to make avgsubject for hippocampal subfields
by BumSeok Jeong 26 Sep '12

26 Sep '12

Dear Freesurfer expert, I'm interested in hippocampal subfields and performed it at each subject. If I'd rather get average hippocampal subfields (volume or surface), what I have to do? The make_average_subject command did not produce it. Does Freesurfer have average hippocampal subfield volume? Best wishes, Jeong --

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Longitudinal processing 3 time point error
by Kawadler, Jamie 26 Sep '12

26 Sep '12

Hello, I have a dataset of patients with 3 time points each. While 2-time point processing works just fine in the longitudinal stream, when I run a base with 3 time points, the process fails and exits with errors. Please see the output below: Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 -- diff. to prev. transform: 0.160049 Iteration(f): 2mri_robust_template(778) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 129th slice Cannot allocate memory Darwin Jamies-iMac.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 recon-all -s EB1312_61-66-77_base exited with ERRORS at Wed Sep 26 12:19:11 BST 2012 This is similar to a message on the mailing list from Liz Bowman (30 Jul 2012), in which the response was to get more memory. My command was done on a Mac with 16GB of RAM and ample disk space. I'd appreciate any help! Thanks, Jamie Kawadler

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