Freesurfer June 2016

freesurfer@nmr.mgh.harvard.edu

152 participants
213 discussions

Fwd: TRACULA stat extraction issue
by Shashwath Meda 12 Jul '16

12 Jul '16

Dear Group - I seem to have run into an issue when attempting to assimilate the averaged pathway information from TRACULA into a group table. I have attached my input list of paths and my output table for one of the tracts. The below is the command that i have used but as you can see the values in my final table are all from one subject (just replicated) despite my input list having paths from different subjects, Has anyone encountered a similar situation? tractstats2table --load-pathstats-from-file fmajor_PP_avg33_mni_bbr.txt --overall --tablefile fmajor_PP_avg33_mni_bbr.table -- Best, Shashwath

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LGI
by Walid Yassin 07 Jul '16

07 Jul '16

Hello again, Sorry for posting twice, but does someone know what might be the problem? Thank you in advance. I’m trying to run recon-all -lgi - s Subjectname on my data but i am getting this error! ******************************************************* Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); >> ERROR: make_roi_paths did not complete successfully! ******************************************************* *I checked the archives and saw a reply by Marie to someone who had the same problem.* *She recommended changing the info inside “SearchProjectionByPial.m" in the ~/Application/freesurfer/matlab directory to:* ******************************************************* function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim, step) % step is typically set between 5 and 10. Default is 7, increasing it will % limit redundancies in the resulting path file. verticeslist=[]; si=max(size(perim)); for t=1:step:si [nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:)); verticeslist= [verticeslist nearestIndexMT]; end verticeslist=unique(vertices list); ******************************************************* Which i did, but i am still getting this error!* Any recommendations on what to do next? I am running MATLAB_R2016. Thank you in advance, WY

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BrainSeg Volume Clarification
by Cook, Bernie 07 Jul '16

07 Jul '16

All, Upon looking at online forums and the FreeSurfer wiki, I have come to the understanding that "BrainSeg" volume in the aseg.stats file includes all cortical and subcortical gray matter, cerebellar gray matter; cortical, subcortical and cerebellar white matter and white matter hypointensities; and all ventricle volumes, but excludes the brain stem. When using the aseg.stats file for included subject "bert" to check my understanding of which volumes are used, I cannot seem to produce identical "BrainSegVol-to-TIV" ratios. I am adding the following volumes, all in mm^3, to obtain the brain volume: TotalGrayVol: 658087.056198 CorticalWhiteMatterVol: 485627.161537 Left-Lateral-Ventricle: 6562.6 Left-Inf-Lat-Vent: 228.3 Left-Cerebellum-White-Matter: 15708.2 3rd-Ventricle: 997.5 4th Ventricle: 1714.2 Right-Lateral-Ventricle: 6039.9 Right-Inf-Lat-Vent: 160.3 Right-Cerebellum-White-Matter: 15694.5 5th-Ventricle: 14.1 WM-hypointensities: 1002.6 Sum of individual measures: 1191836.418 Output of BrainSegVol: 1193318 And when normalizing the subject's brain volume by the eTIV measure (1594882.911364), I obtain the following: Individual measures: 0.7473 BrainSegVol-to-eTIV: 0.7482 Is there a reason that these two measurements are slightly off? I'm wondering whether there's certain volumes used for BrainSegVol that I missed, or ones that I included that would not be present in the output. Moreover, I'm wondering whether this could potentially be a result of using surface volumes (BrainSegVol) versus using both surface and voxel-space calculations (my addition method). Any help is appreciated. Thank you in advance. Best, [1455168447449_PastedImage] Bernard L. Cook Biomedical Engineering | Class of 2017 BMES at Ohio State | Professional Development Chair '16-'17 IBRC | Undergraduate Research Assistant 440-623-4710 cook.1327(a)osu.edu<mailto:cook.1327@osu.edu>

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continuity in volumes converted from labels
by MIKHAEL Shadia 07 Jul '16

07 Jul '16

Hello, I am interested in the cortical parcellations at the pial (grey matter) and white matter layers I have extracted grey matter (pial) and white matter (white) labels for a gyrus (right superior frontal gyrus, label 2028) mri_annotation2label --subject s1/12copy --hemi rh --labelbase ./12copy/label/rh.cortex --surface pial mri_annotation2label --subject s1/12copy --hemi rh --labelbase ./12copy/label/rh.cortex --surface white then converted the above 2 files (renamed to ...-wm and ...-gm) for the superior frontal gyrus to nifti's for viewing in other applications mri_label2vol --label ./label/rh.cortex-028.label --o rh-cortex-028-rsfg-wm.nii --identity --temp ./mri/T1.mgz mri_label2vol --label ./label/rh.cortex-028.label --o rh-cortex-028-rsfg-gm.nii --identity --temp ./mri/T1.mgz My goal is to run some statistics on 2 nifti's, which requires continuity in the nonzero voxels, in at least 1 of the 3 directions (x/y/z). This isn't the case for this gyri, particularly at the pial layer (shown in blue in the attachment). Is there a way in which this could be achieved? Have I missed any steps? Many thanks in advance. Shads The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Qdec-correction for multiple comparison
by John Anderson 06 Jul '16

06 Jul '16

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Seed based volume output to surface
by Taha Abdullah 06 Jul '16

06 Jul '16

Good Afternoon Freesurfers, I am running a seed-based connectivity for one individual subject. The seed is in the L_parahippocampus. I have followed the steps outlined in FSFast walkthrough. Below is a list of my commands. Mind you that I was trying to keep my analysis as simple as possible before delving deeper into it. I have a question on the sig.nii.gz output. Please see at the end. preproc-sess -s taha_brain -fwhm 0 -surface self lhrh -mni305-2mm -fsd resting_scans -per-run fcseed-config -segid 1016 -fcname L_parahipp -fsd resting_scans -mean -cfg mean.L_parahipp.config -overwrite -fillthresh 1 fcseed-sess -s taha_brain -cfg mean.L_parahipp.config mkanalysis-sess -analysis L_parahipp_seed.surf.lh -surface self lh -fwhm 0 -notask -taskreg L_parahipp 1 -fsd resting_scans -TR 0.555 -mcextreg -polyfit 2 -per-run selxavg3-sess -s taha_brain -a L_parahipp_seed.surf.lh Output files /home/tabdullah/Project/Sess01/fsd/L_parahipp_seed.surf.lh/L_parahipp/sig.nii.gz amongst others *Is there a way to convert the volume to a surface and then extract per vertex the sig value?* I used tmri_vol2surf see below: mri_vol2surf --mov ./sig.nii.gz --reg /home/tabdullah/resting_state_1/taha_brain/resting_scans/001/register.dof6.dat --trgsubject taha_brain --interp nearest --projfrac 0.5 --hemi lh --o /home/tabdullah/sig.mgh --noreshape --cortex I tried using mris_convert -c mris_convert -c ./sig.mgh /usr/local/freesurfer/subjects/taha_brain/surf/lh.white sig.asc The last column is all zeros. I am not entirely sure what I am doing wrong here, it is probably somewhere in the last two commands. Possibly using mri_segstats or mri_read.m? Any help would be greatly appreciated. Apologize in advance for the long email. -- Taha Abdullah Department of Physiology Northwestern University Feinberg School of Medicine Masters of Science Physiology and Biophysics, Georgetown University 2015 Work: (312)-503-0413

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FSFAST- Cerebellum
by Sabin Khadka 06 Jul '16

06 Jul '16

Hi all, I am trying to extract mean time series BOLD data using FSFAST from Cortical ROIs + sub cortical ROIs and cerebellum. preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 -per-run -stc odd mri_segstats --annot fsaverage lh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt mri_segstats --annot fsaverage rh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt and for cortical time series mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf subCorticalTimeSeries.txt But I am not sure on how exactly to extract time series from cerebellar regions. So if I want to extract time series from regions as described in Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in FreeSurferCololLUT.txt? If not could you please direct me to processes that I can use. Cheers, Sabin Khadka

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Applying the lta transformation to PET image | mri_coreg | mri_segstats
by Pradeep 06 Jul '16

06 Jul '16

Hello All, I am trying to extract the SUV values a PET image mri_segstats --seg wmparc.mgz --sum petsuv.segstats.dat --i rPET --ctab-default since rPET is supposed to be coregistered to MRI, I did the following mri_coreg --s MRI --mov PET --lta mri_coreg.lta which did not generate the coregistered image but just transformation. Is there a way to generate this image or to just input the mri_coreg.lta as a flag to mri_segstats? Thanks, Pradeep

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Unsupported slice timing pattern 5 in version 5.3.0
by Leonardo Tozzi 06 Jul '16

06 Jul '16

To Whom it may concern, I have tried to run the recon-all pipeline on some T1 data and have encountered the following error: nifti1Read(): unsupported slice timing pattern 5 I have browsed the previous threads about it and it appears that it should have been fixed in version 5.3 but that is the version I run and the error is still there. The data has been converted to NIFTI from DICOM using MRIcron and I don't have access to the original DICOMs. I have seen that someone posted a modified version of nifti1Read() in the past and I was wondering if it was still available. I am running Freesurfer 5.3.0 on MacOSX El Capitan 10.11.3. Would you have any suggestions on how to proceed? Thank you very much. Yours faithfully, Leonardo Tozzi, MD PhD Student Trinity College Institute of Neuroscience College Green, Dublin 2 Ireland

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Not able to find file in gtmseg
by Lee Subin Kristine 06 Jul '16

06 Jul '16

Dear FreeSurfer experts, Hello, I am trying to use Freesurfer's (developmental version) PVE correction tool and I haveone question. The data to be PVE-corrected are some preprocessed PET data downloaded from the Alzheimer's DIsease Neuroimaging Initiative (ADNI) database. Basiclly, the dynamic PET images have been co-registered to one another, averaged, and spatially normalized to a common space. Now I am trying to apply PVE-correction. It seems from your answers here (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html)<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html>that you run the following commands: (1) gtmseg (2) bbregister (3) mri_gtmpvc (4) mri_glmfit When I enter gtmseg --s subject such as below ('Desktop/forFSsubin_2' is location of the subject MRI and '019_S_4835_N3m_cub_ACPC.nii' is the filename) ~/Desktop/forFSsubin_2$ gtmseg --s 019_S_4835_N3m_cub_ACPC.nii I get: ERROR: cannot find 019_S_4835_N3m_cub_ACPC.nii I have changed directory to the folder where the subject MRI file is, and I have typed the subject's filename correctly, but it keeps saying the subject file cannot be found. Any ideas on what is wrong here? Any help would be appreciated. Thank you in advance. Regards, Subin

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Freesurfer June 2016