Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Re: [Freesurfer] -autorecon2-cp
by Jaiashre Sridhar 14 Mar '16

14 Mar '16

Bruce, Thanks! Apart from the control points on the lesions, I have control points that were placed on consequent slices on the coronal view but they look stacked upon one another from a different view. But these control points are placed on voxels that are definitely white matter. Does placing controls points really close to each other change the intensity of the nearby region or whole brain in general? Thanks, Jaiashre.

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-autorecon2-cp
by Jaiashre Sridhar 14 Mar '16

14 Mar '16

Hi, I have a general question about control points. I have added control points to fix the white matter boundary errors throughout the brain. I think that some of these control points that were placed in brain lesions (lower intensity voxels or black spots that are supposedly white matter) have changed the overall intensity and boundaries of the structures. I would like to remove some of these control points but they have gone through several iterations of recon already. Would removing the control points at this point and running -autorecon2-cp set the intensities back to original (orig.mgz)? Or should I go back and fix them from scratch? Thanks, Jaiashre.

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Editing Lesions in FreeSurfer 5.1
by Allison Rainford 14 Mar '16

14 Mar '16

Hi Freesurfer Team, In FSTutorial, it states that control points should not be placed on lesions to try to normalize the intensity there and only white matter edits should be made. What should be done in the case that white matter edits alone do not resolve reconstruction issues at the site of a particularly bad lesion? Thank you! Allison

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group analysis all measures same results
by Kaiming Yin 14 Mar '16

14 Mar '16

Dear guys, I was doing group analysis (command-line) on two groups (patients and control, no age or other information). The data has been "qcached", and after following the three steps as "mris_preproc, mri_glmfit and mri_glmfit-sim" shown in the tutorial on the Freesurfer website, I obtained the difference on thickness in both left and right hemispheres, which seems great. However, when I repeated the above steps on other measures, e.g. area, area.pial, volume (also replaced the parts of "thickness" in the command lines), the results seemed to be exactly the same again as those in the thickness comparison, even the p-value numbers in the file "cache.th40.neg.sig.cluster.summary" were the same. I was using Freesurfer v6.0-beta, and I performed the individual data analysis on a linux cluster and I copied/downloaded the whole "qcached" subject directory to my linux laptop to perform the group comparison, both using the same version of Freesurfer, does it matter? Or do you know why it happened like this? Thanks, Kaiming

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mris_anatomical_stats -th3
by Kaiming Yin 14 Mar '16

14 Mar '16

Dear guys, I checked one of my subjects file /stats/lh.aparc.stats, in which it said the commandline as: mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject1 lh white what does the flag "-th3" mean? I'm using Freesurfer v6.0 beta. Thanks, Kaiming

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unknown option in new brainstem segmentation
by Claudia Testa 14 Mar '16

14 Mar '16

Dear Freesurfers, I've installed Freesurfer 6.0 beta in a virtual machine, and run the -brainstem-structures option to recon-all. The process stopped with an error: "ERROR: Option --DKTatlas40 unknown" In the following, all the information: _____________________________________________ FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer_Linux_centos6_x86_64-dev-20160229 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.el6.x86_64 x86_64 ______________________________________________ 1) subject name is 11960 2) the command line is: recon-all -all -i /usr/local/freesurfer/input/11960_3D_lf.nii.gz -s 11960 -brainstem-structures 3) mri_aparc2aseg --s 11960 --volmask --aseg aseg.presurf.hypos --DKTatlas40 ERROR: Option --DKTatlas40 unknown Linux freesurfer-fabio 2.6.32-573.el6.x86_64 #1 SMP Thu Jul 23 15:44:03 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 11960 exited with ERRORS at Wed Mar 9 23:53:10 CET 2016 4) in attach the recon-all.log file Thank you for your help Claudia

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Anterior to Posterior Length
by Heather Acuff 14 Mar '16

14 Mar '16

Good morning, I would like to use anterior to posterior length as a covariate in my DTI analysis. Is there an easy way to obtain this information for each subject? Thank you, Heather Acuff

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Re: [Freesurfer] hippocampal subfields - multispectral segmentation with FLAIR
by Luigi Antelmi 14 Mar '16

14 Mar '16

Ciao Eugenio, thanks a lot for the support. We made some tests and clearly the high res T2 gives the best subfields contrast. We will proceed with the ADNI like parameters. Have a nice day, Luigi.

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General diffusion workflow questions: QC and extracting FA from subcortical structures
by Elijah Mak 13 Mar '16

13 Mar '16

Dear Freesurfer Community, 1) I am just starting out on some diffusion analyses and I'd like to use the dt_recon for this. Is there any information about a general workflow for quality control for the outputs from dt_recon? From the tutorials, I only see information about checking the registration. In particular, I would like to know how dt_recon cope with the occasional flipping/swapping of some components of the diffusion gradient directions? 2) Another aim of mine is to quantify DTI indices in subcortical regions segmented from the ASEG pipeline. How does Freesurfer handle partial volumning via seg-erode in "mri_vol2vol"? I have pasted my workflow below and I'd like to check if this is correct, thanks! 1) After processing the scans on recon-all and dt_recon , i resample the structural data to diffusion space mri_vol2vol --mov subjectname/dtrecon/lowb.nii.gz --targ subjectname/mri/aparc+aseg.mgz --inv --interp nearest --o subjectname/mri/aparc+aseg2diff.mgz --reg subjectname/dtrecon/register.dat --no-save-reg Should I use ASEG instead of APARC+ASEG or WMPARC (which also has labels for the subcortical regions?) 2) Then, I mask the FA/MD maps with mri_mask subjectname/dtrecon/fa.nii.gz subjectname/mri/aparc+aseg2diff.mgz subjectname/dtrecon/fa-masked_aparcaseg.mgz; done 3) Finally, I collect the FA in the regions with mri_segstats --seg subjectname/mri/aparc+aseg2diff.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subjectname/dtrecon/fa-masked_aparcaseg.mgz --seg-erode 1 --sum subjectname/stats/fa_aparc+aseg2diff_segerode_1;done Thanks a lot for your time and help! Best Wishes, Elijah -- Elijah Mak PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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Alpha channel in color lookup tables (CLUT)
by Michael Bannert 12 Mar '16

12 Mar '16

Dear Freesurfer community, I have a problem using the alpha channel in the color lookup tables. No matter what values I choose, none of them seem to affect the transparency in any way. Here is what I would like to do: I have a number of labels that I want to visualize on an inflated brain surface of fsaverage (with a binarized curvature map). So I use mris_label2annot to create an annotations file which I later load in freeview. mris_label2annot \ --s fsaverage \ --h rh \ --annot-path path/to/rh.output.annot \ --ctab /Applications/freesurfer/SegmentNoLUT.txt \ --l path/to/first.label \ --l path/to/second.label When I load this file into freeview, I can see the two labels without a problem. However, everything outside the labels is just black. I assume that's because all vertices that don't fall into any of the labels, are assigned the first RGBA value, which is [0 0 0 0] by default. Now, I would of course like to see the rest of the brain surface. I figured I could do that by changing the alpha channel of the Seg0 entry in the color lookup table. But no luck: everything outside the labels appears black. I also don't understand the function of the --no-unknown argument. I was under the impression that this would make sure that vertices that are not part of any label would not be assigned any color and therefore... well, appear transparent? (which whould be good) ... appear black? (which would be bad) Any ideas? Thanks & best, Michael

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