Freesurfer

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30087 discussions

samseg permissions error
by Russo, Andrew William 06 Mar '20

06 Mar '20

Hello Freesurfer Developers, I am trying to use the "samseg" function in /usr/local/freesurfer/dev but do not have permission to access the directory /usr/local/freesurfer/dev/subjects/fsaverage. Is this a restricted directory? ValueError: file /usr/local/freesurfer/dev/subjects/fsaverage/mri/orig.mgz does not exist ERROR: fs_time run_samseg I did not find any related issues with samseg on the archive and I have had it work in the past. Before running samseg I sourced the freesurfer environment: export FREESURFER_HOME=/usr/local/freesurfer/dev source $FREESURFER_HOME/SetUpFreeSurfer.sh (Using Freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) Thank you in advance, Andrew ____________ Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531

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Re: [Freesurfer] Apply transformation
by Adam Rytina 06 Mar '20

06 Mar '20

External Email - Use Caution Hello all, is it possible to transform a binary mask (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) and change a final FOV by specifying a diffusion reference image? Or the transform can be applied only on structural image? I am still struggling with the transformation of my binary mask as explained below. Thanks a lot Regards Adam ________________________________ Od: Adam Rytina <adam.rytina(a)outlook.cz> Odesláno: středa 19. února 2020 8:11 Komu: Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> Předmět: Fw: [Freesurfer] Apply transformation Hello, please, could you help me with this case? What am I doing wrong? Thanks a lot ________________________________ Od: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> za uživatele Adam Rytina <adam.rytina(a)outlook.cz> Odesláno: sobota 15. února 2020 19:52 Komu: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Předmět: Re: [Freesurfer] Apply transformation External Email - Use Caution Thanks, unfortunately, I am making some mistake but I don´t know where. First of all I run autorecon1 on my anatomical T1 data (the orig.mgz image is saved in /usr/local/freesurfer/subjects/anatomical). Then in the /usr/local/freesurfer/data I run mri_robust register command of the T1 and diffusion DWI data. The registration.lta file is saved here. Now I add an anatomical mask "3D_T1_brain_mask.nii" to the same folder /usr/local/freesurfer/data that I want to transform to the anatomical T1 space. In the same /usr/local/freesurfer/data I run : "mri_vol2vol --lta registration.lta --mov 3D_T1_brain_mask.nii --o f-in-anat3.nii --s anatomical --fstarg" To sum up, I am aiming to apply a transformation matrix on the T1 anatomical brain mask and transform it to the T1 space defined by 3D T1 image. The problem is this command transforms orig.mgz file (a skull stripped T1 image) instead of 3D_T1_brain_mask.nii. Please, do you know where I make mistake? Thanks a lot ________________________________ Od: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> za uživatele Douglas Greve <dgreve(a)mgh.harvard.edu> Odesláno: sobota 15. února 2020 17:15 Komu: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Předmět: Re: [Freesurfer] Apply transformation Yes, mri_vol2vol On 2/15/20 11:07 AM, Adam Rytina wrote: External Email - Use Caution Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV by specifying a diffusion reference image (its voxels size). It means to apply the same command as the command ApplyXFM in FSL FLIRT. Does this option exist also in Freesurfer? Thanks a lot Regards Adam _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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questions about vertex information
by Jedy 06 Mar '20

06 Mar '20

External Email - Use Caution Dear FreeSurfer friends, Does anybody know how to extract vertex information of lh.white and lh.pial?  I would like to extract normal vector and other information of each vetex. I would be very appreciated if someone can give me some suggestions. Thank you very much! Best -jedy

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PetSurfer reference region
by Dincer, Aylin 06 Mar '20

06 Mar '20

External Email - Use Caution Hello PetSurfer experts, We are using the cerebellum cortex as our reference region, but noticed that the SUVR values for lh/rh cerebellum cortex do not have a value of 1 (which is what we were expecting). The actual SUVR values are 1.31 for the lh and 1.35 for the rh cerebellum cortex. I attached the stats file (gtm.stats.dat) and below is the command we ran. mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf ${FWHM} --seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF+2 .01 --mgx .01 --rescale 8 47 -o regmean_gtmpvc_output Let me know if you need any more details. Thanks so much, Aylin -------------------- _____________________________ Aylin Dincer Senior Research Technician NeuroImaging Laboratories Imaging Core, Benzinger Lab 314-362-3629 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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sphere.reg file
by Marina Fernández 06 Mar '20

06 Mar '20

External Email - Use Caution Dear freesurfer experts, I run the following commands to perform analysis with projected surfaces on my average subject: make_average_subject --out my_avg_subject --fsgd fsgd.txt surfreg --s s_001 --t my_avg_subject --o my_avg_subject.sphere.reg mris_preproc --fsgd nfsgd.txt --target my_avg_subject --meas thickness --srcfmt curv --hemi [l/r]h --out [l/r]h.fsgd.mgh Theoretically, the mri_preproc function will automatically use the my_avg_subject.sphere.reg file because I specify my_avg_subject as the target subject. The problem is that in the output that comes out in the terminal while this function is running, it is specified that the file [l/r]h.sphere.reg is selected instead of [l/r]h.my_avg_subject.sphere.reg. Additionally, I did a test specifying the flag "--surfreg my_avg_subject.sphere.reg" in mris_preproc and the values of the output surface are different from the output that I have when I don't specify the flag --surfreg in mris_preproc (so, If I don't specify it, I think that definitely the function doesn't automatically use the file generated in surfreg, I think the default sphere.reg is used). What should I do? Is it better to specify the “--surfreg my_avg_subject.sphere.reg” flag in the mris_preproc function? Thanks in advance. Best regards, Marina.

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Extract specific LGI and Volume values
by Tien Pham 06 Mar '20

06 Mar '20

External Email - Use Caution Dear FreeSurfer Experts, I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI changes in my data set with two time points using longitudinal pipeline. Now I would like to extract the regional LGI and gray matter volume in my longitudinal results using QDEC to draw the ROIs which is showed significant differences, label it and map to all subjects. Then I get the LGI value of the ROI I saved before using the command below: cd $SUBJECTS_DIR mris_anatomical_stats -l lh.untitled.label \ -t lh.pial_lgi \ -b \ -f subject_id/stats/lh.untitled.stats subject_id lh And this is the result: [toyama-no-iMac:/applications/freesurfer/subjects] toyama% mris_anatomical_stats -l lh.frontoinsula.label \ ? -t lh.pial_lgi \ ? -b \ ? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh limiting computations to label lh.frontoinsula.label. using thickness file lh.pial_lgi. reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz... reading input surface /applications/freesurfer/subjects/VC019_1/surf/lh.white... reading input pial surface /applications/freesurfer/subjects/VC019_1/surf/lh.pial... reading input white surface /applications/freesurfer/subjects/VC019_1/surf/lh.white... table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 6595 4368 15935 3.311 0.895 0.158 0.077 135 19.7 lh.frontoinsula.label As I saw there was no columns showing the LGI value, I did similar with gray matter volume, the result displayed the different in some values of the columns. Could you please help me to explain about this? Thank you very much. Best regards, Tien Pham

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2 surface mri_glmfit as independent variables
by Adam Martersteck 06 Mar '20

06 Mar '20

External Email - Use Caution Hi FreeSurfer team, I have a question about running mri_glmfit with 2 different surface modalities as the independent variable and a single value per participant as the dependent variable. I'm trying to examine the unique and shared contribution of the 2 surfaces to predict a cognitive measure. E.g. Cognition ~ ?h.thickness + ?h.PET I tried mri_glmfit with the "--table" option, giving it a column of scores per participant (in the aseg2stats table format), and then using "--pvr lh.thickness-stack.fsaverage.mgh" and a second "--pvr lh.PET-stack.fsaverage.mgh", using contrasts matrices as [0 0 1], [0 1 0], and [0 1 1]. *When I run mri_glmfit it returns:* ERROR: mri_reshape: number of elements cannot change nv1 = 163842, nv1 = 1 It continues to run, but all surface maps are full of zeroes. Any suggestions? Is there a better way to do this? Thanks, Adam

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Registration of DIR (Double Inversion Recovery) series
by Xiaojiang Yang 06 Mar '20

06 Mar '20

External Email - Use Caution Hi all, I want to register DIR (Double Inversion Recovery) series to T1 series using Freesurfer. I used the command line similar to that used for FLAIR registration: bbregister --s subject001 --mov dicom/subject001/20141003_MR/3_Sag_Space_DIR/2.25.97015757385982906453797720915266163627.dcm --lta subjects/subject001/mri/transforms/DirTest.auto.lta --init-coreg --T2 where the option --T2 is still used. Since in DIR series, gray matter is brighter than white matter, I use --T2 as the contrast argument. I wan's able to check how precise the results are. I will take some time to do check that. But anyone can tell me: Did I do it correctly? what is the better way or correct way to do the above-mentioned registration? Thank you! Xiaojiang

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petsurfer
by Laboratorio de Neurociencia Funcional 06 Mar '20

06 Mar '20

External Email - Use Caution Dear Freesurfer experts, I have compared the PVC uptake values of gtm.stats with the values of gtm.nii.gz with the function load_nii in matlab. I noted that values in matlab are reversed, i. e., the first value in gtm.stats matches with the last value in gtm.nii.gz and so on. Could you confirm me that nopvc.nii.gz values are also reversed when loaded with load_nii in matlab? I have no way to check this. Thank you in advance. Best, Marina

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Issue with BBR and Applying CVS Warps to Diffusion Data
by Austin Patrick 06 Mar '20

06 Mar '20

External Email - Use Caution Dear All, I have used CVS to align around 180 scans to a single, representative subject. I have then used BBR to align the mean b0 image to register the diffusion data to the native space T1 and then apply CVS warps; however, the resulting aligned images for calculated maps from the DWIs are very poor with a great deal of heterogeneity, especially at the boundary but also within white matter. The coefficient of variation of the mean b0 BB registered to the T1 is around 30% globally (excluding the edges of the brain) and 40% or greater for FA. I have reviewed the initial rigid registration of the b0s to the T1s for gross misalignment and found that FLIRT performed pretty well and didn’t fail for any of my subjects and didn’t require manual adjustment; however, the result of after applying the CVS warps is quite poor. The data T1s are 1mm (MPnRAGE) and the b0s are at 2mm. The DWIs were corrected for eddy currents, Gibbs’ ringing, rician noise, and B0 distortions and look pretty great. The DWIs are 70x180x180 at 2mm isotropic and the T1s are 256x256x256 at 1mm isotropic. Are there any suggestions for this issue? I have tried re-aligning the DTI parameter maps to the b0s before applying the CVS warps (although they should be in the same space) and I have tried using both the –t2 and –dti, as well as with/out the –fsl-init flag. Is bbregister shifting the origin for the images at all? Any help would be appreciated. Cheers, -Austin -- Austin M. Bazydlo, MS PhD Candidate Dept. of Medical Physics University of Wisconsin-Madison

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