Freesurfer

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30133 discussions

Error from trac-all prep: data and bvals/bvecs do not contain the same number of entries
by Hao wen 04 Jan '17

04 Jan '17

Hello: I followed the tutorial for tracula, because of the tutorial data that you give dont have the T1 image, so I use on of my own diffision data and the reconall-ed T1 image, and I always get the same errors: data and bvals/bvecs do not contain the same number of entries , So I guessed that it is the problem from the data(dwi.nii, T1.nii, .bvec, bval), but I tried to figure out the data dimension differences between my data and the tutorial data(tutorial_data/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm), Here is the output: 1) FS tutorial data(dicom format): This is the bval info and i guess the bvec dimension is the same bValue = 700 nB0 = 10 nDir = 60 this is the dwi.dicom information: dimensions: 128 x 128 x 60 x 70 So the nFrames is equal to the bvel and bval columns(70), which makes sense. 2) My data information(which is .nii.gz format): The bvec and bval info: number of columns for bval and bvec is 136 The dwi.nii.gz dimensions: dimensions: 96 x 96 x 59 x 137 So for my data, the number of columns(or transpose the files, the same spirit) is nFrames-1, I guess that is the problem, but my data can be run for Mrtrix and Dipy, even in the dipy tutorial, the data that they offer, the number of columns is the number of frames(volumes) minus 1, So for TRACULA, is it a mandatory that the number of columns in bvec and bval is equal to the number of volumes in dwi image??? I know sometime people dont write the first 0 in bvec and bval, so if I just add it, and run it for TRACULA, it will work??? I will try it tomorrow!!! Really need your help, I stuck for this in a while:) the log file is attached. Thanks in advance

2 2

View sig map on anatomical volume from volume-based group anaysis
by Hao wen 04 Jan '17

04 Jan '17

Hello: I have a question, after recon-all, I did some group analysis with the aseg.stats( not surface-based), so my question is : Does freesurfer has some volume-based group analysis(not for fMRI) for plotting the significance map, I searched google, and wanna some results like this: [cid:e4f431a9-4e18-4dec-8275-ce4080b061f2] I know here is for fMRI-sMRI based analysis: So i want to map some values for the subcortical structures in the anatomical image, but for the command here, how can I get the sig.nii(right now, we just have the result p-value for every subcortical structures), I know in FS, we can use mri_glmfit to have the significance map Any advice will be appreciated Hao

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Tracula Set: No Match
by Katherine Damme 03 Jan '17

03 Jan '17

Hello! I have been getting a "set: No match." error. I haven't been able to sort out what is causing it. Attached you will find the configuration file, command, and log files associated with this error. "mv -f /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs set: No match."

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Assign p value for every voxel and plot it in freeview
by Hao wen 03 Jan '17

03 Jan '17

Hello: I have a very simple question, after recon-all, I did some statistical analysis with some other softwares, so for example I got the p value for every voxel(volume_based),or p value for every vertex(surface-based), so I know how to map theses p values for surface-based pipeline, but for volume-based, how can we do that??? I know that in FMRI pipeline, we can use the significance map(sig.nii) as the overlay, but this is created by the group analysis(mri_glmfit), but can we created this sig.nii mannually and upload it to the oig.mgz and apar+aseg.mgz??? Really need your help. Thanks in advance

2 1

preproc-sess brain masks in masks subdirectory
by Ladan Shahshahani 03 Jan '17

03 Jan '17

Dear experts, Hi, I ran the preproc-sess command. I was following the tutorial page. looking at the files in the the masks directory, I see one mask: brain.nii.gz. However, the tutorial mentions more masks. Should I be worried?? What may be the cause? Bests, Ladan

2 1

Problem with trac-all correction step for DTI image processing
by Farahbakhsh, Mahtab 03 Jan '17

03 Jan '17

Dear FreeSurfer, I am trying to pre-process my DTI data using TRACULA. But I receive an error when I run the pre-processing stage of DTI image processing. On the Correction step (1st step) I receive this error: ------------------------------------------------------------- MRIresample(): error inverting matrix; determinant is nan, matrix is: -0.000 -0.000 nan nan; -0.000 -0.000 nan nan; 0.000 0.000 nan nan; 0.000 0.000 0.000 1.000; Darwin Mahtabs-MBP 16.3.0 Darwin Kernel Version 16.3.0: Thu Nov 17 20:23:58 PST 2016; root:xnu-3789.31.2~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Jan 2 03:23:23 IRST 2017 ------------------------------------------------------------ My DTI images are in enhanced DICOM format. In addition, I receive a warning earlier in the processing stage. The warning is: WARNING: it appears that the image position for all slices is the same. This is a problem with the DICOM file. Using direction cosines from col and row to compute slice direction, but the output may be misoriented. Please also find my log file attached to the mail. Any kind guidance from you is much appreciated. Kind Regards, Mahtab. -- Mahtab Farahbakhsh PhD Candidate Dept. Visual Neuroscience, UCL Institute of Ophthalmology 11-43 Bath Street London EC1V 9EL

2 1

flirt: command not found
by michal heker 03 Jan '17

03 Jan '17

Hello freesurfer developers, I am trying to use TRACULA reconstruction with *Virtual Box* on my data (I have my own nii files). I have followed all the stages in the freesurfer tutorial. I get the following problem: INFO: SUBJECTS_DIR is /media/sf_share/diffusion_recons INFO: Diffusion root is media/sf_share/diffusion_ourbrains Actual FREESURFER_HOME /usr/local/freesurfer flirt: Command not found. dcmlist: Subscript out of range. What am i doing wrong? find attached is a copy of my dmrirc file Thanks for your help, Michal

2 1

Use CA and other subfields as seed for FS-FAST
by stdp82＠virgilio.it 03 Jan '17

03 Jan '17

Hi list, I would like to obtain the functional connectivity maps of CA1, CA2/3... by using FS-FAST (VERSION 5.3). Which are the codes in FreeSurferColorLUT.txt, that I should use, please? The ranges from 500 - 508 and from 550 - 558 are useful by using 5.3? Thanks Kind regards, Stefano Delli Pizzi

2 1

Re: [Freesurfer] creating labels from aseg.mgz
by Ladan Shahshahani 02 Jan '17

02 Jan '17

Hi, Thanks for the reply.

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Volume-based group analysis
by Hao wen 02 Jan '17

02 Jan '17

Hello: I want to do some volume-based group analysis with Freesurfer mri_glmfit, and I know in Qdec, this has not been implemented, the problem here is very simple: I want to do the regression between the sub-cortical structure voxels number and age, so try to find the correlation significance between age and subcortical structure in aseg.stats, from the tutorial of command-line of FS from here: it is important to realize that most of the concepts learned here apply to any group analysis in FreeSurfer<https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer>, surface or volume, thickness or fMRI. So I guess I can do it, but I can not find any tutorial about this for volume-based group analysis(fMRI pipeline, I got stats from recon-all), if I use third-party software to do the statistical analysis, the difficulties are how to mapping the p-value to the brain just like VBM in SPM. Actually, this is not really different for you, but I can not just find the relevant information, can you help me??? Thanks in advance Hao

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