Freesurfer May 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
219 discussions

Installing and enabling cuda
by Ramesh Babu 25 May '17

25 May '17

Dear Expert, I have come across that I have freesurfer support cuda version 5, but I have already installed latest version. Can I use latest version for freeesurfer or should I install version 5? Since I am not expert in this field I need guidance to remove latest version of cuda and installing and enabling version 5. Your help will be appreciated. PC details: I am using Intel® Core™ i7-4790 CPU @ 3.60GHz × 8 processor with 15.6 GiB ram, GeForce GT 610/PCIe/SSE2 graphic card. Thanks RB

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Optseq2
by Tabassi Mofrad, F. 25 May '17

25 May '17

Hi, I have a question about software input. --ntp 340 --tr 1.8 --psdwin 0 20 1.8 --ev L1 1.6 60 --ev L2 1.6 60 --ev Blank 1.6 15 --evc 1 -1 0 --nkeep 3 --o IAPS --tnullmin 2 --tnullmax 5.6 --nsearch 10000 Here is the input that I have provided but it is problematic. Please could you let me know how I should improve it? Best, Simin

2 1

Cortical thickness repeated measures
by Worker, Amanda 25 May '17

25 May '17

Hi all, I have a repeated measures design with two groups (drug and placebo) and two time points (baseline and follow-up). The groups are not very well matched so I'd like to control for age and gender. The data was also acquired across three sites which I'll need to control for. I do not have any drop outs. Essentially, I want to know if there is a significant effect of drug on cortical thickness. I've tried this out in qdec, but because I have site (with three levels) qdec isn't appropriate, so I'm trying to set up my own fsgd and contrast matrix. Because I have already created the percent change and symmetrized percent change files (as part of qdec prep) I thought I might be able to simply run a t-test on those. Which would answer the question...'is there a significant difference in percent change for the drug and placebo groups'. Does this seem like a sensible approach? If the above does seem sensible, I am not quite sure how to set up my contrast matrix. As I have three categorical variables to include (Treatment, Gender, Site) and only one continuous variable (age). This would leave me with 12 classes (DrugFemaleSite1, DrugMaleSite1, DrugFemaleSite2, DrugMaleSite2 etc etc) and one variable. Would it look something like this? Or is this absurd? 0.333 0.333 0.333 0.333 0.333 0.333 -0.333 -0.333 -0.333 -0.333 -0.333 -0.333 0 0 0 0 0 0 0 0 0 0 0 0 Thanks in advance, Amanda

2 1

Cortical thickness extraction from analysis
by gaubert 25 May '17

25 May '17

Hello, I am performing a group analysis to compare the cortical thickness between controls and patients (in fsaverage space with a smooth of 15) and I obtain two clusters. I want to extract the average cortical thickness in these clusters for each participant of the analysis. And I have a couple of questions on this extraction: 1/ when I take a look at the generated files during the processing, there is a file named "cache.th20.pos.y.ocn.dat" which contained (from FS wiki) "the average value of each subject in each cluster". Is that right that these values are generated from individuals "rh.thickness.fwhm15.fsaverage.mgh" files (meaning, they are in the fsaverage space with smooth at 15)? 2/ I try to perform this extraction in native space (without smooth). And I wanted to be sure that my process is correct. Here are the different steps: 1_ Get the labels from annotation files: mri_annotation2label --subject fsaverage --hemi $hemi --labelbase './'$annot_filename'_label' --annotation ${contrast_dir}/${annot_filename}.annot 2_ register the clusters to native space: mri_label2label --srclabel './'$annot_filename'_label-001.label' --srcsubject fsaverage --trgsubject $subj --trglabel $trg_label --regmethod surface --hemi $hemi 3_ get thickness in the cluster: mris_anatomical_stats -l $trg_label -t ${SUBJECTS_DIR}'/'${subj}'/surf/'${hemi}'.thickness' -f $th_result_filename -b $subj $hemi Thanks for your help. Malo

2 1

(no subject)
by Huang, Caleb (NIH/NINDS) [F] 25 May '17

25 May '17

Hi all, I'm trying to figure out a way to do create seed-based structural covariance networks through Freesurfer like the one shown in the link below. From the images, it looks like it's done through QDEC. Any tips how to get started? https://ww5.aievolution.com/hbm1601/index.cfm?do=abs.viewAbs&abs=3331 Thanks, -Caleb

2 1

smoothing kernal
by Trisanna Sprung-Much 25 May '17

25 May '17

Hi there I labelled sulci in 40 T1 volumes and have created surface overlays using mri_vol2surf and then registered these to fsaverage using mri_surf2surf. I want to generate a statistical probability map using mri_concat and then mris_fwhm for each sulcus. What is an acceptable FWHM to use? It is the width of a sulcus on a pial surface of an individual brain, i.e. about 2mm? Or on fsaverage, i.e. about 7mm? Thanks Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

3 6

cuda-gpu problem
by Ramesh Babu 25 May '17

25 May '17

Dear Experts, I am using Intel® Core™ i7-4790 CPU @ 3.60GHz × 8 processor with 15.6 GiB ram, GeForce GT 610/PCIe/SSE2 graphic card. I have successfully installed cuda runtime version 5.0. After that I performed cuda detect and output result is pasted below. $ cudadetect Detecting CUDA... There is 1 device supporting CUDA: Device 0: "GeForce GT 610" CUDA Driver Version: 8.0 CUDA Runtime Version: 5.0 CUDA Capability Major revision number: 2 CUDA Capability Minor revision number: 1 Total amount of global memory: 2080440320 bytes Number of multiprocessors: 1 Number of cores: 32 Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 49152 bytes Total number of registers available per block: 32768 Warp size: 32 Maximum number of threads per block: 1024 Maximum sizes of each dimension of a block: 1024 x 1024 x 64 Maximum sizes of each dimension of a grid: 65535 x 65535 x 65535 Maximum memory pitch: 2147483647 bytes Texture alignment: 512 bytes Clock rate: 1.62 GHz Concurrent copy and execution: Yes Run time limit on kernels: Yes Integrated: No Support host page-locked memory mapping: Yes Compute mode: Default (multiple host threads can use this device simultaneously) Then statrted recon-all with use-gpu flag. $ recon-all -all -i grp229_t1.nii -s grp229 -sd grp229 -use-gpu But it was giving some error report continuously and I interrupted the process. Please see the attached log report and help me to use gpu effectively. Thanks Ramesh

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Download link not responding
by Sabir Saluja 24 May '17

24 May '17

Hi there, I am trying to download the latest version of Freesurfer but the download link is not responding. Is this a known problem or am I the only one who is facing this? Sabir

2 1

Question - how to smooth and transform into a template
by Gwang-Won Kim 24 May '17

24 May '17

2 1

Question regarding errors with TRACULA pre-processing
by Simon, Katrina R 24 May '17

24 May '17

Hi, I keep trying to run TRACULA and getting the following errors: ERROR: run list is longer than subject list and : Command not found. : Command not found. : Command not found. Badly placed (. **My configuration file is below: *** # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR $SUBJECTS_DIR/surfaces/ # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR set dtroot = $SUBJECTS_DIR/surfaces/ # Subject IDs set subjlist = ( BPD0067A ) # Input diffusion DICOMs # If original DICOMs don't exist, these can be in other image format # but then the gradient table and b-value table must be specified (see below) set dcmroot = $SUBJECTS_DIR/dicoms/ set dcmlist = ( $SUBJECTS_DIR/dicoms/BPD0067A/001_000011_000001.dcm ) # Diffusion gradient tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # The tables must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # set bveclist = ( $SUBJECTS_DIR/niftis/BPD0067A/dti.bvec ) # Diffusion b-value tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # set bvallist = ( $SUBJECTS_DIR/niftis/BPD0067A/dti.bval ) set doeddy = 1 set dorotbvecs = 1 set usemaskanat = 1 set thrbet = 0.3 set doregflt = 0 set doregbbr = 1 set doregmni = 1 set doregcvs = 0 set pathlist = ( lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) Then, I am running this command in a script : trac-all -prep -c /data/picsl/mackey_group/BPD/scripts/config_test.txt And to run the command I perform on my group’s cluster is the following: qsub -V trac.sh trac.sh is the name of the script. I just ran this exact same script on another subject a few days ago and it worked fine- which is why I am confused as to why I am getting strange errors now. I checked to make sure reconstruction finished without errors and it did. Thank you! Katrina

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Freesurfer May 2017