Freesurfer

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30135 discussions

GLM error in QDEC
by McLaughlin, Katie 01 Aug '14

01 Aug '14

Hi Doug et al, I'm trying to run an analysis in QDEC and continue to get an error that says that the QDEC GLM design creates 0 factors. I'm attaching my data table here as well as the output of QDEC. I've tried deleting all variables in my data file other than one and testing just that comparison, but no luck. Any thoughts are much appreciated. Thanks, Kate SUBJECTS_DIR is '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3' Input table: /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat Subj#, SubjID, Data... 1 1009 c 2 1014 c 3 1032 c 4 1034 c 5 1041 m 6 1043 m 7 1047 c 8 1058 m 9 1077 c 10 1094 m 11 1096 c 12 1097 c 13 1099 c 14 1100 m 15 1114 m 16 1119 m 17 1123 m 18 1125 c 19 1126 c 20 1128 c 21 1134 c 22 1137 m 23 1139 m 24 1142 m 25 1143 m 26 1153 m 27 1154 m 28 1157 c 29 1158 m 30 1163 m 31 1165 m 32 1166 m 33 1167 m 34 1171 c 35 1173 c 36 1175 c 37 1176 c 38 1177 m 39 1178 m 40 1179 c 41 1180 c 42 1181 c 1 maltreatment discrete 2 1 c 2 m Continuous Factors: Mean: StdDev: ------------------- ----- ------- Number of subjects: 42 Number of factors: 1 (1 discrete, 0 continuous) Number of classes: 2 Number of regressors: 2 ============================================================ ERROR: QdecGlmDesign::Create: zero factors!

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grey matter density
by Qiongmin 01 Aug '14

01 Aug '14

Dear All, I wonder if there are any functions that can calculate the grey matter density of the vertices or in the ROI manner? I figured out that Freesurfer can give the thickness, area, volume, curv, but I can not find grey matter density anywhere. Thanks for any advice! Qiongmin

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Editing the pial surface
by Lindsay Gubernick 01 Aug '14

01 Aug '14

Hi, I am doing manual corrections of topological errors and am wondering if there is a way to bypass recomputing the surfaces as suggested by the topographical errors tutorial and instead doing some sort of manual editing of the pial surface. Does such an editing option exist? Thank you, Lindsay Gubernick

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Surface reconstruction and quality checks in atrophied temporal lobes
by Makaretz, Sara Johanna 01 Aug '14

01 Aug '14

I have a set of subjects with moderate to severe temporal lobe atrophy. Surfaces are generally good everywhere except for portions of temporal lobes. It seems like control points are usually helpful in cases with problematic temporal lobes (ie. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-July/039596.html) but I'm hesitant to add too many control points in areas with limited/no wm (aka severely atrophied areas) for risk of misidentifying gm as wm. My goal is to run a cortical thickness analysis and look specifically at the temporal lobes, so I want to process/troubleshoot the subjects in as similar a manner as possible and produce generally accurate thickness maps. Attached are three screenshots: 1. tl_subj_A.jpeg : a subject with cp added across several slices and -autorecon2-cp -autorecon3 reprocessing; pial missing some gm in both lobes 2. tl_subj_B.jpeg : a subject after standard recon-all; generally good wm/gm recognition; good wm recognition but poor gm recognition in temporal lobes 3. tl_subj_C.jpeg : a subject after standard recon-all; generally similar to tl_subj_B.jpeg, but surfaces really went rogue in part of the atrophied lobe Questions: - Is there a combination of flags that would help identify gm in the temporal lobes of most subjects while maintaining wm accuracy? - Any suggestions for adding cp (or other edits) in a semi-standard/efficient way that would still allow for a valid cortical thickness analysis? - What happened to the surfaces in subjects like the one in tl_subj_C.jpeg? - In terms of checking output quality for a cortical thickness analysis, would it be most useful to use QA Tools (https://surfer.nmr.mgh.harvard.edu/fswiki/QATools) or another method such as creating histograms from one of the stats files and looking for outliers? - (In general) How much quality checking / editing is appropriate for a cortical thickness study? Thank you for any suggestions and/or resources!! Sara

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Help with mris_convert
by Tara Miskovich 01 Aug '14

01 Aug '14

Hi all, I am trying to convert a group cluster to GIFTI (.gii) format. I just need some help running mris_convert. The example for a label to GIFTI is mris_convert --label lh.V1.label V1 lh.white lh.V1.label.gii I'm trying to figure out what is required here. I understand I put in the label after label and the output at the end, but in this example I am not sure what the V1 and lh.white are for. Thanks, Tara

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YANQ follow-up
by Krieger, Donald N. 01 Aug '14

01 Aug '14

Thanks again for the pointer, Bruce. You wrote: ... mri_convert -rl rawavg.mgz <input vol> <output vol> which does produce an output volume from which I now need to extract RAS voxel coordinates. A pointer to a keyboard command would be most welcome. Of interest is the difference between the color mappings for the input and output volumes in freeview. When using the lookup table in freeview they are quite different whereas in grayscale they are almost identical. I wonder if this is contributing to my difficulty in finding a tool to extract the voxel coordinates. Thanks again. Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text

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recon-all.log error: "_FindFacePath: could not find path!"
by Alejandra Machado 01 Aug '14

01 Aug '14

Hi, i'm a novel freesurfer user and i'm afraid i need some help here, please! ----------------------------------------------------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer-5.1 Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-65-generic x86_64 command executed: fully-automated processing, no flags! (-autorecon-all) ERROR: _FindFacePath: could not find path! /data-02/alejandra/projects/genic/nc155_modif/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux siv 3.2.0-65-generic #99-Ubuntu SMP Fri Jul 4 21:03:29 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s nc155_modif exited with ERRORS at Tue Jul 15 19:02:51 CEST 2014 --------------------------------------------------------------------------------------------------------------------------- I'm having trouble with the processing of one subject, which exited with Errors. I understand the process fails before completing the recon-all2 part, after topology fixing but then, while correcting surfaces, i don't exactly know what's happening. It seems it can't find the proper output (lh.orig_corrected), is that right? In that case, how should i proceed or which processing step should i try manually to try to solve this issue? thank you!! Alejandra

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tkmedit error
by wang kangcheng 01 Aug '14

01 Aug '14

Dear experts when I use the tkedit, it report the error (in the following). How could I solve it? tkmedit started: Thu Jul 31 10:41:56 2014 /Applications/freesurfer/tktools/tkmedit.bin patient_con_sub126 brainmask.tight.mgz -aux T1.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /Users/haha/Desktop/brainmask/control Set subject home dir to /Users/haha/Desktop/brainmask/control/patient_con_sub126 Using interface file /Applications/freesurfer/tktools/tkmedit.tcl Segfault Setting global interpreter xDebug stack (length: 2) 01: main() 01: Setting global interpreter 00: 00: Wang Kangcheng

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ERROR: dimension mismatch between input volume and seg
by Jon Wieser 31 Jul '14

31 Jul '14

hi freesurfer experts I am compiling the FA segment stats for several subject I used mri_vol2vol --mov fa.nii --reg register.dat --fstarg ../mri/orig.mgz --interp nearest --o fa.anat.mgh then I used: mri_segstats --seg mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i dti/fa.anat.mgh --sum dti/fa.stats for some of my subjects, Iam getting the following error: mri_segstats --seg mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i dti/fa.anat.mgh --sum dti/fa.stat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --i dti/fa.anat.mgh --sum dti/fa.stat sysname Darwin hostname psy-blackbird.ad.uwm.edu machine x86_64 user wieser UseRobust 0 Loading mri/wmparc.mgz Loading dti/fa.anat.mgh ERROR: dimension mismatch between input volume and seg input 256 256 192 seg 256 256 256 can you tell me how to fix this? thanks Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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Global mean FA
by Alshikho, Mohamad J. 31 Jul '14

31 Jul '14

Hi Fs Experts, In order to calculate the global white matter fractional anisotropy FA I used (wm.mgz ) the output of recon-all as a mask in the following command line mri_segstats --seg $SUBJECTS_DIR/015601/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --mask wm.mgz --i fa.anat.mgh --sum fa.stats Kindly, Is this correct? Thanks Mohamad

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