Freesurfer September 2012

freesurfer@nmr.mgh.harvard.edu

89 participants
154 discussions

TRACULA - failed corpus callosum forceps major
by Gibbard, Clare 27 Sep '12

27 Sep '12

Hello, I have tried out running TRACULA on 20 subjects. It all seemed to work well except that in 8 of the subjects the corpus callosum forceps major was either missing or was a very small cluster. The same happened for the temporal SLF of 2 subjects. I read previous posts related to this and tried re-running the affected subjects with set reinit =1. However, the results were very similar to before. I have checked the registrations and they are not perfect, but not wildly inaccurate. Are you able to suggest any options for me to try? I have attached the dmrirc file I used for the first run (called dmrirc-original) as well as the one for re-running the subjects whose CC was not segmented (called dmrirc). Thank you. Best wishes, Clare

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Longitudinal processing
by Allison Gruber 27 Sep '12

27 Sep '12

Hello, I am using the longitudinal processing stream to analyze a data set. I have two questions: 1: We are expecting there to be significant changes in the volume of certain structures and gray matter between time point 1 and 2. We wanted to make sure the longitudinal stream is still appropriate. 2: If some subjects do not have both time points, should we process them as individual time points or should we use a template brain in order to use the longitudinal stream? Thank you very much, Allison

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[TRACULA] short thin tracks
by Akvile Lukose 27 Sep '12

27 Sep '12

Hello Freesurfers, I ran into a problem running TRACULA that I couldn't solve myself, and I would really appreciate if you could have a look. I am running a FS 5.1 on mac os x 10.7.4 (intel 64bit) machine with 16GB RAM. I extracted the bvals and bvecs with the dcm2nii converter and adjusted the format to what FS expects (scans acquired on a non-Siemens scanner). I attach the dmrirc file as well. First, I had a memory problem (cannot alloc memory) during the prep stage. The new compiled update from here (http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula )helped and prep stage finished without any errors. I was not able to run bedpostx from dmrirc configuration file. I could work around it by running bedpostx directly on dmri directory (as described here http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html) Then I had a problem with symlinks, I created them manually and after that it worked fine, I had all the output files as listed here (http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html) -path worked also without any errors, but I keep getting very short thin tracks (all tracks) (snapshot attached). There is nothing wrong with the aparc+aseg.mgz. I tried rerunning every stage after I added option "set reinit=1" (as described here http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21990.html) but unfortunately it didn't help. Do you have any ideas how to fix it? Thank you very much in advance! Kind regards, Akvile Lukose

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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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Freesurfer September 2012