Freesurfer February 2016

freesurfer@nmr.mgh.harvard.edu

123 participants
179 discussions

Permission denied error with mri_surfcluster command
by Jennifer Legault 04 Mar '16

04 Mar '16

Dear experts, I am trying to use the cluster thresholding command for my freesurfer LME outputs as referred to here <https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels>. Any feedback or comments would be greatly appreciated. I am aware that there have been permission denied errors when using mri_surfcluster and that applying this patch <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mni152reg> should solve the problem (which I tried), however I am still either receiving errors stating the permission is denied. This is the command I am trying to run: mri_surfcluster --subject fsaverage --hemi rh --in rh_time_spval.mgh --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster --sum rh_time_cluster_sum Here is the error log: mri_surfcluster --subject fsaverage --hemi rh --in rh_time_spval.mgh --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster --sum rh_time_cluster_sum thsign = pos, id = 1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = rh srcid = rh_time_spval.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = pos thmin = -1 thmax = -1 fdr = 0.05 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = rh_time_cluster paint sumfile = rh_time_cluster_sum subjectsdir = /gpfs/home/jtl190/work/structurals FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /gpfs/home/jtl190/work/structurals/fsaverage/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.white Done reading source surface Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 1 at vertex 27 overall min = 1.52021e-05 at vertex 125620 surface nvertices 163842 surface area 65020.929688 surface area 65020.765625 Setting voxel-wise threshold with FDR = 0.050000 Assuming input map is -log10(p) MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=1.04576 FDR Voxel-wise threshold is 1.04576 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Searching for Clusters ... thmin=1.045757 (0.744727), thmax=-1.000000 (-1), thsignid=1, minarea=0.000000 Found 9803 clusters Max cluster size 5993.586426 INFO: fixing MNI talairach coordinates Saving thresholded output to rh_time_cluster Can't create file /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.rh_time_cluster.w Permission denied Thank you for taking the time to read this email. Sincerely, Jennifer Legault -- Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania State University

3 16

The name of regions of annotation file issue viewing by tksurfer
by Faeze Vedaei 03 Mar '16

03 Mar '16

Hi Freesurfer experts, I have created an annotation file by several label files using mris_label2annot command in Freesurfer. The problem is that when I open this annot file in tksurfer and click on colored regions which corresponded to specific labels I had chosen them, I do not have their name on the vertex information part at the bottom of tksurfer GUI. It shows very different names for these regions. May you explains me what is the problem I could not see the exact region's name as I have them for label files? Thanks, Faezeh Vedaei

2 25

AAL atlas question
by pfotiad＠nmr.mgh.harvard.edu 03 Mar '16

03 Mar '16

Hi FS community, I have recon-ed a set of subjects and I was interested in also obtaining structural info (cortical thickness, gray matter volume, surface area etc.) based on a different atlas than the ones FS is using, and in particular the AAL atlas. I was wondering whether my approach would be the correct one or whether there is another (better and more accurate) approach: 1) Convert the AAL atlas into a surface (with mri_vol2surf) from the MNI space into the native subjects' space, 2) Use mris_anatomical_stats to calculate the structural stats Sorry for the potentially trivial question, and thank you for your time! Best, Panos

3 3

Extract LGI at MaxVertex and extract effect-sizes in table format
by Bittner, Nora 03 Mar '16

03 Mar '16

Dear FreeSurfer Experts, Sorry for reposting this massage again, but I still have two questions, which you can hopefully answer to: 1) I calculated several analyses with LGI as my dependent variable, resulting in several significant clusters. Now, I would like to extract the individual LGI value at the maximum vertex of each significant cluster to plot it against my experimental variables (instead of working with the mean LGI values of the clusters). What I tried so far is to use mri_segstats to extract the LGI at the maximum vertex: mri_segstats --i $SUBJECTS_DIR/qdec/glm/y.mgh --crs vertexno 84367 0 0 --avgwf vertexno84367.dat where y.mgh is my input file from the glm and vertexno 84367 is the maximum vertex of the cluster as reported in the cluster.summary-file. I found the command in the FS helpline documentation (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42655.html) but regrettably<http://dict.leo.org/ende/index_en.html#/search=regrettably&searchLoc=0&resu…> I get the following error message: "ERROR: Option --crs unkown" In the fswiki I also couldn´t find the "mri_segstats - - crs option" in the user description. Is there any other option or argument I can use in mri_segstats (or in any other command) to extract the LGI value per person at the given vertex? 2) I would like to calculate effect sizes of my results. Therefore I used fscalc: fscalc $SUBJECTS_DIR/qdec/glm/contrast/gamma.mgh div $SUBJECTS_DIR/qdec/glm/rstd.mgh -o $SUBJECTS_DIR/qdec/ glm/contrast/effectsize.mgh This worked fine and resulted in a surface overlay displaying the effect sizes. Now, I would like to extract these effect sizes in 'table' format. I tried to use mri-segstats: mri_segstats* --i effectsize.mgh --annot fsaverage lh aparc --avgwf effectsize.dat I am not sure, if this gives me the correct results. Is this the right command? I would really appreciate<http://dict.leo.org/ende/index_en.html#/search=appreciate&searchLoc=0&resul…> your help. Thank you in advance, Nora ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

2 1

Reading values from overlays with PETcoreg
by Benjamin Spurny 03 Mar '16

03 Mar '16

Dear Freesurfer experts! I am currently working on PET analysis using FS I coregistered my PET with the processed MR using bbregister, transfered it to a surface using mri_vol2surf and now createt an overlay in freeview with the lh.inflated and used the labels from the lh.aparc.a2009s.annot file. In freeview i get the corresponding BP value for each vertex now but is there a way to get a list of vertices with the corresponding BP value and the corresponding ROI this vertex belongs to? Or is there a better to do this analyis? Many thanks in advance! Benjamin

3 14

[FreeSurfer] Repeated Measures ANOVA in FSFAST
by Afzal, Afsana 03 Mar '16

03 Mar '16

Hi, I'm analyzing a decision making task with a 3x3 condition matrix: pairings of low, medium, high levels of risk with low, medium, high levels of reward. I've set up the following FSGD file to do a repeated measures/within-subject ANOVA: GroupDescriptorFile 1 Class hc001 Class hc002 Class hc003 Class hc004 Class hc005 Variables lRsk_lRwd lRsk_mRwd lRsk_hRwd mRsk_lRwd mRsk_mRwd mRsk_hRwd hRsk_lRwd hRsk_mRwd hRsk_hRwd Input hc001 hc001 1 1 1 1 1 1 1 1 1 Input hc002 hc002 1 1 1 1 1 1 1 1 1 Input hc003 hc003 1 1 1 1 1 1 1 1 1 Input hc004 hc004 1 1 1 1 1 1 1 1 1 Input hc005 hc005 1 1 1 1 1 1 1 1 1 I've also created the following contrast matrices: Con1: Does difference between highRisk and LowRisk differ from 0? 0 0 0 0 0 -1 -1 -1 0 0 0 1 1 1 Con2: Does difference between highRisk and MedRisk differ from 0? 0 0 0 0 0 0 0 0 -1 -1 -1 1 1 1 Is this an appropriate way of setting up the ANOVA? Thanks for your help, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

2 5

mri_label2vol projfrac missing voxels
by dgw 01 Mar '16

01 Mar '16

Hi, I am having trouble with the projfrac option in mri_label2vol (on the current dev freesurfer environment). When I use the following command: mri_label2vol --annot label/lh.lang.annot --subject nmr00937 --o lang_seg.mgz --hemi lh --identity --temp mri/T1.mgz --proj frac 0 1 .01 I get many missed voxels from the gray matter (see the attached image, with the yellow representing the label overlaid on the ribbon.mgz). I have tried more extreme delta values and this doesn't help. (note scrolling to nearby slices indicates the neighboring voxels are included, so it isn't from the angle projecting oddly (that is why I took a slice from the middle of this large label)). Is there a better way to convert the annotation to a volume just in the gray matter, but including all of the relevant voxels? Is there a fundamental algorithmic difference between mris_volmask and mri_label2vol? If yes, why? Thanks, D

1 2

Very urgent matlab command line to transform vol to label.
by stdp82＠virgilio.it 01 Mar '16

01 Mar '16

Hi list,I have read on your mail list that I could use the command line reported below to covert vol to label.I'm confused on the matlab command line.Specifically, if I using an MRS voxel (in native space or MNI, as preferred) located bilaterally of 3.0x3.0x3.0 mm, which are lindex, lxyz, ovals? v = load_mgh('file_created_by_vol_2_surf.mgz'); ind = find(v > threshold); write_label(ind-1, [], v(ind), 'label_file_want_to_create'); Thanks,Stefano

2 1

Fwd: View several Annot files in Tksurfer
by Faeze Vedaei 01 Mar '16

01 Mar '16

Hi Freesurfer Experts, In order to view specific annot files by tksurfer in Freesurfer, I used mris_label2annot command to create annot files based on Destrieux atlas. Now, I can import annot file in tksurfer, but just one file at the time. My aim is to view several annot files by their specific colors in tksurfer simultaneously. May you help me how can I do this? In advance, I'd appreciate your consideration. Regards, Faezeh Vedaei

3 2

-qcache of v5.0 data with newer versions
by Daniel Ferreira 01 Mar '16

01 Mar '16

Dear experts, Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been recon-all -all with FS 5.0.0? Thanks Dani

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Freesurfer February 2016