Freesurfer

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17 participants
30099 discussions

Freeview - Vector and Spline information for Sufaces
by Güllmar, Daniel 27 Nov '14

27 Nov '14

Dear all, I'm currently trying to view face and/or vertex normals in freeview (of an existing surface). I've seen the option to load "vector display" data, but I do not know the format of such a file. Can someone help me with that issue? Regards, Daniel Universitätsklinikum Jena - Bachstrasse 18 - D-07743 Jena Die gesetzlichen Pflichtangaben finden Sie unter http://www.uniklinikum-jena.de/Pflichtangaben.html

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TRACULA mask error
by Worker, Amanda 27 Nov '14

27 Nov '14

Dear All, I have run all of the pre-processing steps on my DTI data and as I am checking my nodif_brain_mask I have realised that some of the masks have become distorted and twisted in some way. I have attached screenshots of both the raw data (which looks fine) and the white mask (which is distorted). In addition, as I have read that it is important to check the dtifit_V1 and dtifit_FA I have also included these in the word document, incase this helps. This distortion has occured for approximately a quarter of the subjects that I have processed and the rest look good. Please can you let me know if you have any ideas about what has gone wrong and how to fix this? Thanks in advance for your help, Amanda

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Eccentric lesions
by Octavian Lie 27 Nov '14

27 Nov '14

Dear All, I am interested at getting as good pial/cortical reconstructions as possible on a series of epilepsy pt scans, some showing eccentric (cortical) lesions (focal encephalomalacias, infarcts, or after focal resections). One particularly difficult lesion type to get an accurate cortical surface is where there are prongs of grey matter bulging out (like a bag of worms), (mostly) without visible wm, see attached picture. These prongs are maintained in the brainmask.mgz and brain.finalsurfs.mgz, but not included in the pia with the default recon. Lesion voxel intensities vary from 30-90. I tried cp, wm edits (using brainmask or T1 as referece), both, did not matter, it did not work. Since I am not intested in wm/subcortical segmentation but just in a good pia, I was wondering if I 'create' thin wm tracts through the center of these gm prongs to help pial segmentation. If this is a valid option, should I create those in brainmask, brain.finalsurfs or wm.mgz, and should I use 110 or 255 for the brush? Any other suggestions are appreciated. Nevertheless, I know there is a lot of tweaking of each lesion, and I try for more of a global approach to these kinds of lesions. Thank you, Octavian.

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Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch
by Jens Offenbach 27 Nov '14

27 Nov '14

We are currently working on a solution that brings FreeSurfer in the cloud. Unfortunately, we are facing a lot of problems. Hopefully, someone can help me: I want to run FreeSurfer on Ubuntu 14.04 or 14.10. What package is required to download (CentOS 4 x86_64 (64b))? Does it work anyway on the Ubuntu family? On the FTP server I have found a patch for 5.3.0, but I am not sure how to apply it or if I must apply it? The Readme says to replace “mri_segstats”. What about the other files “recon-all, fsfast, tksurferfv, …”? I want to reduce the archive to its bare minimum, otherwise the automated deployment process takes too long. It should contain only those files which are necessary to execute the pipeline without any viewer or examples. Which files and folders can be deleted safely? The most important issue is to monitor the FreeSurfer pipeline execution. I know that the scripts folder contains some status files which offer important data helping me to monitor the pipeline execution progress of “recon-all”. Unfortunately, that is not enough… If one step takes e.g. approximately 20 hours, I have to say something about the progress within this current step. Is there any possibility to monitor the progress of a single step. We need something that allows us to say e.g. that Step “CA Reg” has 34 % of its work done so far which means that the overall pipeline progress is e.g. 63 %. Is it possible to say that a specific step takes a specific portion of the overall pipeline execution time. What influences this portion (format or quality of input, platform, …)? Thank you very much for your help! Regards Jens

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A question of preproc-sess -fsd
by zhang mingxia 27 Nov '14

27 Nov '14

Dear Freesurfer experts, Could you please give me more detail of "-fsd"? It is asked to "specify a functional subdirectory with -fsd" when i preprocess the functional data. If, for example, the current directory is /home/Proj, the f.nii is in /home/Proj/sess01/bold/002/ and /home/Proj/sess01/bold/003/, what the -fsd should be? Thanks. Mingxia

1 0

Speeding Freesurfer
by Francesco Cardinale 27 Nov '14

27 Nov '14

Dear Freesurfer experts, I've been using Freesurfer on Mac computers for some years with great satisfaction. I just bought a "monster computer", a Mac Pro with 12-core Xeon E5, 64 Gb RAM, GPU AMD FirePro D700. This is, out of doubt, a marvellous machine to compute many subjects simultaneously, but quite often we need to run one single subject as fast as possible. What can I do? OpenMP optimization is available only for CentOS, isn't it? What about CentOS in a VM, will it be able to exploit multithreading, or is it necessary to configure a multiboot machine with BootCamp? Any suggestions to do that? Moreover, what about CUDA and GPU acceleration? Is it available for FirePro graphic cards? Any other suggestions? Anything really new in the field with the next version of Freesurfer? Thanks a lot Francesco Cardinale, MD Neurosurgeon "Claudio Munari" Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda "Ca' Granda" Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia phone 0039 02 64442917 fax 0039 02 64442868 e-mail francesco.cardinale(a)ospedaleniguarda.it

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mri_glmfit error
by Bronwyn Overs 26 Nov '14

26 Nov '14

Dear Freesurfer Mailing list, I have been attempting to run the following command in freesurfer v5.3.0: mri_glmfit --y site-gender-group-prothaplotype.thick.lh.10.mgh --fsgd site-gender-group-prothaplotype.fsgd dods --C me_site-BrisVsMelb.mtx --C me_site-BrisVsPer.mtx --C me_site-MelbVsPer.mtx --C --surf fsaverage lh --cortex --glmdir site-gender-group-prothaplotype.thick.lh.glmdir Unfortunely, I keep getting the following error: "ERROR: Option lh unknown" Do you know why this would be? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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ERROR:dimension mismatch between X and contrast con.mtx
by Xinfa Shi 26 Nov '14

26 Nov '14

Hi everyone, I get this error when running group analysis of cortical thickness by command-line: xin-fa@xinfa--PC:/media/E/FREESURFER/VisualData$ mri_glmfit --y lh.group_differ.thickness.10.mgh --fsgd group_differ.fsgd dods --C con.mtx --surf fsaverage lh --cortex --glmdir lh.group_differ.glmdir gdfReadHeader: reading group_differ.fsgd INFO: gd2mtx_method is dods Reading source surface /media/E/FREESURFER/VisualData/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /media/E/FREESURFER/VisualData cmdline mri_glmfit --y lh.group_differ.thickness.10.mgh --fsgd group_differ.fsgd dods --C con.mtx --surf fsaverage lh --cortex --glmdir lh.group_differ.glmdir sysname Linux hostname xinfa--PC machine x86_64 user xin-fa FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/E/FREESURFER/VisualData/lh.group_differ.thickness.10.mgh logyflag 0 usedti 0 FSGD group_differ.fsgd labelmask /media/E/FREESURFER/VisualData/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.group_differ.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.group_differ.glmdir Loading y from /media/E/FREESURFER/VisualData/lh.group_differ.thickness.10.mgh INFO: gd2mtx_method is dods Saving design matrix to lh.group_differ.glmdir/Xg.dat Normalized matrix condition is 1 Matrix condition is 1.04762 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 149953 voxels in mask Saving mask to lh.group_differ.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74612.446501 ERROR: dimension mismatch between X and contrast con.mtx X has 2 cols, C has 1 cols The data is altogether 43 subjects,including 22 subjects in expert group.I just want to explore the difference between both groups. Attached is the FSGD file ,which is two groups ,zero covariates . The contrast matrix is 1 -1 . Subsequently I try it only with a few subjects ,and it succeeds. Can you help me ? Best wishes. Xin-Fa .

2 1

prefrontal cortex label
by Anna Jonsson 26 Nov '14

26 Nov '14

hi, I have tried to make prefrotnal cortex label by doing first mri_annotation2label --subject "$subject" --hemi rh --outdir "$subject"/label mri_mergelabels -i lh.caudalanteriorcingulate.label -i lh.caudalmiddlefrontal.label -i lh.lateralorbitofrontal.label -i lh.medialorbitofrontal.label -i lh.parsopercularis.label -i lh.parsorbitalis.label -i lh.parstriangularis.label -i lh.rostralanteriorcingulate.label -i lh.rostralmiddlefrontal.label -i lh.superiorfrontal.label -i lh.lateralorbitofrontal.label -o lh.prefrontalcortex.label -d /directory/subject/label which does create a label called x.prefrontalcortex.label in each persons directory. then however when i try to do mris_anatomical_stats -l $SUBJECTS_DIR/"$subject"/label/lh.prefrontalcortex.label "$subject" lh pial | grep "thickness" >> left_prefrontal i get error and say it cant find label. any pointers on what im doing wrong? thank you

3 3

Different significant regions with different cluster wise thresholds
by Bronwyn Overs 26 Nov '14

26 Nov '14

Dear Freesurfer Mailing list, While running a glm anlaysis with monte carlo correction (using cluster wise thresholds of .05 & .01), I encountered the following issue: When examining the clusters formed for each of the different cluster wise thresholds, the .05 threshold resulted in a superior temporal cluster, while the .01 threshold resulted in a two lateral occipital clusters that did not overlap with the cluster from the .05 threshold. Do you know why there would be no overlap between significant regions at different cluster wise thresholds? I was aware that a cluster which is significant at .05 may split or be smaller at .01, but I do not know why entirely different regions would be significant. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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