Freesurfer

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19 participants
30088 discussions

Error in qdec longitudinal 5.1
by Natalia h 25 Jul '11

25 Jul '11

Dear list, I got an error after following the newer version of the longitudinal stream 5.1. long_mris_slopes worked without problems for my data which was longtudinally processed in 4.5. I also split the qdec.table to the cross for being able to be loaded in qdec GUI. Somehow I got the error that the Templatesubxx/surf/xh.thickness.fwhm.xx.fsaverage.mgh. I went back to check inside the Templatesubxx/surf has only the xh.long.thickness-xxx.fwhmx.fsaverage.mgh Is there something I am missing? Thanks a lot for the help

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long_mris_slopes error
by Derin Cobia 25 Jul '11

25 Jul '11

I received the follow error while running a set of subjects under 'long_mris_slopes,' and wasn't able to decipher the problem. It appears that mris_calc is not able to do the division for these files (dividing by 0 perhaps?). Any help appreciated, here's the command and tail end of output/error, thanks. -Derin > long_mris_slopes --qdec ./qdec/CH_prog.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time scan_interval --qcache fsaverage > > > =============================================================================== > SUBJECT CH1840 fwhm 0 computing SPC > > mris_calc -o /disk/NIACAL_01/Trio/NMorph/PROCESSED_DATA/FREESURFER-v5.1.0/CH1840/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-CH1840_lh_thickness_FFrRIR/beta1.mgh div ./tmp-CH1840_lh_thickness_FFrRIR/beta0.mgh > > ERROR 1 : mris_calc compute sym. pct. change (spc) problem?

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longitudinal version
by Natalia h 25 Jul '11

25 Jul '11

Dear list, I have a question about the longitudinal stream´s version. I used Freesurfer 4.5 and followed the longitudinal tutorials (the tutorials "before" June 2011) for my data. I saw on the updated version, there are scripts which can do the post-process longitudinal data, like long_mris_slopes, long_stats_slopes, long_qdec_table. Can I use these scripts to do the stats even though I used version 4.5 for the longitudinal process? Thanks for the help

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Longitudinal Analysis Error
by Silvia Juanes 25 Jul '11

25 Jul '11

Dear all, We are preprocessed our data to perform a longitudinal study using longitudinal pipeline of Freesurfer 4.5. However, when we try to do the group-analysis using qdec (Freesurfer 5.1), we obtain the following error: ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels ninputs = 64 Checking inputs nframestot = 64 Allocing output Done allocing nframes = 64 Writing to /home/barbara/subjects/qdec/Untitled/y.mgh gdfReadHeader: reading /home/barbara/subjects/qdec/Untitled/qdec.fsgd INFO: gd2mtx_method is dods Reading source surface /home/barbara/subjects/fsaverage/surf/lh.white ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y /home/barbara/subjects/qdec/Untitled/y.mgh --fsgd /home/barbara/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /home/barbara/subjects/qdec/Untitled --surf fsaverage lh Has anyone experienced a similar problem and is there any way to correct it? Best,

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Cortical segmentation error
by Carolina Valencia 25 Jul '11

25 Jul '11

Dear FS experts, I'm trying to analyse a case of cortical dysplasia, but after recon-all I see some errors in tkmedit that I don't know what to edit. I found some errors in cortical and subcortical segmentation, I don't find in the failure mode presentation a way to solve this. I saw the pial surface (yellow line) with acceptable accuracy but the GM (the red one) in some regions are misplaced (WM classified as GM and some GM not classified (empty color)) I tried to attached an image to illustrate the problem but I don't succeed, because the mailing list reject my email. How I can send you an image of ~700kb? Thanks a lot, Carolina

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Atlas coordinates provided by QDEC
by Maria Serra 25 Jul '11

25 Jul '11

Hi FreeSurfer experts, I have a doubt regarding the atlas coordinates that uses QDEC. In the power point titulated "fscoordinates" found in the FreeSurferWiki seems that the coordinates used are aligned with Talairach Atlas, but when you enter de coordinates provided by QDEC in a particular area (Right isthmus for example: -32 -29 26) in a Talairach client software ( http://www.talairach.org/client.html) , the area that it gives you is totally different: Label at (-32, -29, 26) Left Cerebrum, Frontal Lobe, Sub-Gyral, White Matter, * Do you know why this discrepancy is caused for? Thank you in advance, -- Maria Serra PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Telf. +34 93 586 8232 www.pic.es

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Problems with the .Qdecrc file
by dolphinede＠aol.com 25 Jul '11

25 Jul '11

Hi, i am trying to add new measures (pial_lgi) to qdec. I created the .Qdecrc file in my SUBJECTS_DIR/qdec, with the described text (MEASURE1 = pial_lgi), but it does not work, i cannot select in the qdec menu pial_lgi as a dependent variable. A qdec.fsgd file is also in the same place. I also renamed the .Qderc file in qdec.Qdecrc but it is the same. I am using freesurfer version 4.5.0. I am a little bit confused what i can do? Thanks you a lot, Best regards Daniel

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Fwd: questions about high resolution atlas on the Freesurfer
by Jixin Liu 24 Jul '11

24 Jul '11

Dear FS experts, Freesurfer could provide for every participant a standardized partition of the cortex into 66 regional areas. My aim is to use freesurfer to subdivide these regional areas into a set of small and compact regions, resulting in high resolution atlas covering the entire cortex (taken from Hagmann et al. (2008) in PLoS Biol). We tried to used the mris_divide_parcellation fsaverage rh aparc.annot 100 rh_annot_100 (However, this creates a parcellation of long strips per region, that is not a good partition for what we want.) Then, we used the "mris_make_face_parcellation lh.orig $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot". The results look nice, but I have the following questions: (1)Can i used the "mris_make_face_parcellation" based on the "aparc.annot"? (2)How can i conver the .annot file into .hdr/.img mask files? I read the introduction about "mri_label2vol", but i was still confused. If i want to convert aparc.annot files in fsaverage, what the input files are for "--temp" and "--seg"? (3)I read the "lh.ic3.annot" in Matlab (read_annotation.m). For "colortable.struct_names", the name is "ic3.tri_vertex_0"(to "ic3.tri_vertex_641"), how to know which brain regions it belong to? how to know each vertex's MNI coordinate? (4)"mris_make_face_parcellation lh.orig $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot" . I only see 7 options in: $FREESURFER_HOME/lib/bem/ic[1-7].tri (as per the program usage). Can I specify custom ic*.tri files (and also, how would those be generated)? -- Good Luck ============================================ Life Sciences Research Center Xidian University Xi'an China http://life.xidian.edu.cn liujixin(a)life.xidian.edu.cn liujixin2010(a)gmail.com ============================================

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Problems with mri_label2vol
by Jixin Liu 24 Jul '11

24 Jul '11

i want to convert the ".annot" files to nifti. When i used "mri_label2vol", I used this command mri_label2vol --subject fsaverage --annot $FREESURFER_HOME/subjects/fsaverage/surf/lh.ic3.annot --o test.img --hemi lh --regheader $FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz --temp $FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz But the error is: Number of labels: 0 Annot File: /usr/local/freesurfer/subjects/fsaverage/surf/lh.ic3.annot Template Volume: /usr/local/freesurfer/subjects/fsaverage/mri/brain.mgz Outut Volume: test.img Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: fsaverage Hemi: lh UseNewASeg2Vol: 1 DoLabelStatVol 0 $Id: mri_label2vol.c,v 1.32 2009/10/22 23:35:53 greve Exp $ Template RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; -0.000 -0.000 -1.000 128.000; -0.000 1.000 -0.000 128.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0 Computing registration based on header RegMat: -------- 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; Label RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; 0.000 0.000 -1.000 128.000; 0.000 1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.white nvertices = 163842 Reading thickness /usr/local/freesurfer/subjects/fsaverage/surf/lh.thickness Loading annotations from /usr/local/freesurfer/subjects/fsaverage/surf/lh.ic3.annot reading colortable from annotation file... colortable with 642 entries read (originally /usr/local/freesurfer/lib/bem/ic3.tri) annotidmax = 640 Allocating Hit Volume (-2147483648) voxels MRIalloc(256, 256, 256): could not allocate 131072 bytes for 22494th slice Cannot allocate memory Does anyone know, why is that happening and how can I correct it? -- Good Luck ============================================ Life Sciences Research Center Xidian University Xi'an China http://life.xidian.edu.cn liujixin(a)life.xidian.edu.cn liujixin2010(a)gmail.com ============================================

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Question about if there is constant number of vertexes across different brains
by Knut J Bjuland 24 Jul '11

24 Jul '11

Hi I have read (Dale, Fischl et al. 1999) and (Fischl, Sereno et al. 1999) . I have a question about if I understood the tessellation procedure right. There are two vertexes in each voxel, but is the total number of vertex constant across brains. I believe that number of total vertex does not change over brain since it will be difficult to do statically measure if the total numbers of vertex change. Nevertheless, the shape and size of the vertex do change. Is this a correct assumption? Knut J Referanse liste Dale, A. M., B. Fischl, et al. (1999). "Cortical surface-based analysis. I. Segmentation and surface reconstruction." Neuroimage 9(2): 179-194. Fischl, B., M. I. Sereno, et al. (1999). "Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system." Neuroimage 9(2): 195-207.

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