Freesurfer

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30096 discussions

error in longitudinal processing "dimension mismatch"
by Qi Wu 21 May '13

21 May '13

Dear Freesurfer experts, I have a dataset of 2 time points. I ran into problems when I tried to use the two-stage approach to pull out statistics such as the rate of change in Freesurfer 5.1. I could not even get the first stage working. The error messages I got were “ERROR: MRISar1: Surf/Src dimension mismatch” “ERROR -11 : mri_glmfit did not work?” I did further trouble-shooting for this particular message "nv1 = 140942, nv1 = 143525", and I found out that "143525" was in the "base" folder (kp5_base), and "140942" was for the two longitudinally registered images (kp5.long.kp5_base, and kp5b.long.kp5_base). The command line I used was : “long_mris_slopes --qdec ./qdec/AS_long_qdec.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time weeks –nosmooth”. The first three lines in the qdec file: “fsid fsid-base weeks age sex FSS avgPain kp5 kp5_base 0 48 0 4.1 7 kp5b kp5_base 20 48 0 8.6 6” This error was similar to what was in a previous post ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024576.html… joost janssen Jun 29, 2012). I tried to fix any similar problems, but still wasn’t able to get it working. What else could I have been doing wrong? The on screen error output is provided as follows Many thanks Keith Postdoctoral fellow Toronto Western Hospital Toronto, Ontario Canada *********************************** Parsing the qdec table: ./qdec/AS_long_qdec.dat Working in SUBJECTS_DIR: /data/keith/freesurferdata/subjects_longitudinal_5.1_old Subject-Template: kp5_base INFO: 2 TPs in kp5_base , mean age: 10.0 =============================================================================== SUBJECT kp5_base Intersecting Within-Subject Cortex Label cp /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/label/lh.cortex.label /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label mris_label_calc intersect /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base/label/lh.cortex.label /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label LabelWrite: saving to /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label =============================================================================== SUBJECT kp5_base Stackinbg Within-Subject Maps mri_concat /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/surf/lh.thickness /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base/surf/lh.thickness --o /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh =============================================================================== SUBJECT kp5_base Running Within-Subject GLM Writing ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat ... mri_glmfit --y /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh --X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat --allow-zero-dof --no-contrasts-ok --surf kp5_base lh --label /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label --glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm Reading source surface /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.white Number of vertices 143525 Number of faces 287046 Total area 91438.851562 AvgVtxArea 0.637094 AvgVtxDist 0.873064 StdVtxDist 0.245806 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /data/keith/freesurferdata/subjects_longitudinal_5.1_old cmdline mri_glmfit --y /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh --X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat --allow-zero-dof --no-contrasts-ok --surf kp5_base lh --label /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label --glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm sysname Linux hostname davissvr1.uhnres.utoronto.ca machine x86_64 user qwu FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh logyflag 0 X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat usedti 0 labelmask /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label maskinv 0 glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory ./tmp-kp5_base_lh_thickness_6PR2rH/glm Loading y from /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh Saving design matrix to ./tmp-kp5_base_lh_thickness_6PR2rH/glm/Xg.dat Normalized matrix condition is 1 Matrix condition is 10 Found 131455 points in label. ERROR: mri_reshape: number of elements cannot change nv1 = 143525, nv1 = 140942 Pruning voxels by thr: 0.000000 Found 134956 voxels in mask Saving mask to ./tmp-kp5_base_lh_thickness_6PR2rH/glm/mask.mgh Reshaping mriglm->mask... ERROR: mri_reshape: number of elements cannot change nv1 = 140942, nv1 = 143525 search space = 91439.090793 DOF = 0 Starting fit and test Fit completed in 0.0042 minutes Computing spatial AR1 on surface ERROR: MRISar1: Surf/Src dimension mismatch. ERROR -11 : mri_glmfit did not work?

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Can I mask out NaN vertices for smoothing?
by Glen Lee 21 May '13

21 May '13

[image: Inline image 1] Hi freesurfer experts, > > I'm dealing with an issue with smoothing on surface data that > unfortunately contain 'NaN' in the ventral temporal region (which is a > region that we are interested in). > > This may be due to the slab data acquisition, where the bottom of the > slice meant to be at the bottom of the tomporal lobe for every subject. > Apparently, we didn't quite succeed in this as we saw missing data points > that are filled with 'NaN' during 2D reconstruction in some subjects' 2D > data. > > In the cartoon above, the yellow color depicts vertices with 'NaN' in the > ventral temporal region , and you can easily see how this is affected by > smoothing (4mm FWHM), such that a large swath of ventral regions have NaNs > after smoothing. > > I've tried smoothing both with and without --cortex flag, but the results > were the same regardless. > > So, the best bet would be masking out those NaN vertices before smoothing > and I wonder if there is any way of doing it in freesurfer. > Otherwise, I may need to consider smoothing outside of the freesurfer > using Matlab (but I have no experience about this approach). > > If anyone has previously dealt with this issue (hope I'm not the only one) > and know how to get around with it either inside or outside of the > freesurfer, please help me. > -Glen > > > > > >

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brain parenchymal fraction calculation
by Ritobrato Datta 21 May '13

21 May '13

Hi All, I am using freesurfer 5.1 and I want to compute the brain parenchymal fraction (GM+WM/GM+WM+ventricularCSF). In aseg.stats, I get the whole GM vol and I can also get the total ventricular CSF by adding the vols of different ventricles. But I am confused abt the terminology - CorticalWhiteMatterVol is this volume the total white matter in the brain or does this exclude something ? Please advise. Best Ri

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Autorecon2 missing ribbon.mgz error?
by Jamie Hanson 21 May '13

21 May '13

Hi Freesurfer List- My group just recently installed 5.3.0 and I kept running into the same error during -autorecon2 where mri_segstats could find ribbon.mgz. I was slightly stumped on the issue, as the ReconAllTable says mri_segstats isn't run until autorecon3? I attached my bugr output and also my log file for one subject (I have about 10+ subjects that error in the same way). It looks like -inflate2 finished fine (which was previously one of the last steps in autorecon2). Any thoughts? Any help is greatly appreciated! Thanks much! Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Email: jamielarshanson(a)gmail.com Homepage: http://brainimaging.waisman.wisc.edu/~hanson/ --------------------------------------------------------------------- FREESURFER_HOME: /apps/x86_64_sci6/freesurfer-latest Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: Scientific Linux release 6.2 (Carbon) Kernel info: Linux 2.6.32-279.22.1.el6.x86_64 x86_64 ---------------------------------------------------------------------

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missing DOSS option in QDEC
by Andreas Berger 21 May '13

21 May '13

Hi surfers, as of FreeSurfer version 5.3, i am missing the option to choose between DOSS and DODS design in QDEC. The radiobuttons in the design tab are no longer there. The default behaviour, judging from the results, seems to be DODS. Has this option been removed? regards, Andreas

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question abt optic chaism volume
by Ritobrato Datta 21 May '13

21 May '13

Hi All, I am using freesurfer 5.1 for my analysis. In FS 5.1, does the Supratentorial volume include the Optic chaism volume ? Please let me know. Thanks Ri

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Re: [Freesurfer] mkbrainmask-sess
by Joseph Dien 20 May '13

20 May '13

I imagine this issue has been solved by now but just for the record I ran into a similar issue. In my case the problem turned out to be that FSL installs by default in /usr/local/fsl/bin but FSFAST was looking for it in /bin This was on OS X 10.8.2 with FSL Installer - Version 2.0.10 and Freesurfer 5.2.0. Is there some way to set up Freesurfer so it'll look in the correct directory? For now I'm copying the critical files to /bin but am hoping there is a better solution. Thanks! Joe > It could be. It uses fsl only to create a mask of the brain, so it probably does not need a full fsl install, but it might need more than you have. > doug > > On 3/25/12 7:05 AM, Kiley Seymour wrote: > Hi again, > Could this error be due to the fact that I don't have a full version > of fsl installed and configured on my ubuntu virtual machine? i.e. > does fsfast require fsl to be installed? > > Thanks > > K > > ------------------------------------------------------------------------ > *From:* Kiley Seymour <kiley_seym...(a)yahoo.com.au> > *To:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Friday, 23 March 2012 3:04 PM > *Subject:* mkbrainmask-sess > > Dear Freesurfers, > > I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and motion corrected my files in SPM). > I was unable to run this command as freesurfer could not find/media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat > So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below). > Any help with this would be much appreciated. > > Thanks > > Kiley > > FreeSurfer:~/data1/RETINOTOPY> mkbrainmask-sess -s IFEE2211 -d~/data1/RETINOTOPY > ------------------------------------------------ > /media/sf_DATA1/RETINOTOPY/IFEE2211 > Fri Mar 23 09:42:26 EDT 2012 > mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 > FSLMATHS fslmaths.fsl > Scratch Dir is /tmp/mkbrainmask_7930 > /media/sf_DATA1/RETINOTOPY/IFEE2211/bold > mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii > mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii > $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ > reading from template.nii.gz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.998558, -0.0534653, -0.00482299) > j_ras = (-0.0536701, 0.992375, 0.110955) > k_ras = (0.00114604, -0.111054, 0.993814) > writing to /tmp/mkbrainmask_7930/in.nii... > # ---------- Using FSL's BET to Extract Brain------------------ # > /media/sf_DATA1/RETINOTOPY/IFEE2211/bold > bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1 > /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found > /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found > /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found > [: 158: =: unexpected operator > /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found > mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o/tmp/mkbrainmask_7930/brain_mask.nii > niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii > > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ > cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold > cmdline mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii > sysname Linux > hostname FreeSurfer > machine i686 > user virtualuser > > input /tmp/mkbrainmask_7930/brain_mask.nii > frame 0 > nErode3d 0 > nErode2d 0 > output /tmp/mkbrainmask_7930/brain_mask.nii > Binarizing based on threshold > min 0.01 > max +infinity > binval 1 > binvalnot 0 > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com//

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shape difference in subcortical structures using FSL vertex Analysis
by M.Shakeri 20 May '13

20 May '13

Hi All, I need to do a shape analysis between the freesurfer segmentation results with manual segmentation. Does anyone know how can I use FSL Vertex Analysis (first_utils) ? Fsl Vertex Analysis input file is .bvars . Is there a documentation or guide to create this file type? Mah

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failures more frequent in one hemisphere
by Joshua Lee 20 May '13

20 May '13

Hi All, I recently ran a number of 2-yr-old brains through Freesurfer, and overall Freesurfer did well considering the age group. However, a subset (~10%) had catastrophic failures in the left termporal lobe in which parahippocampal cortex bled over into the hippocampal region. I've since added control points and am rerunning. However, what I found curious was that almost every failure was in the left hemisphere, not the right. Any ideas why that might happen? Using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Joshua

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Re: [Freesurfer] Tracula longitudinal "nan" values for highest probability path
by Anastasia Yendiki 20 May '13

20 May '13

Hi Vincent - If you upload the tracula dirs for this particular time point, I'll take a look. a.y On Mon, 20 May 2013, Vincent Brunsch wrote: > Hi Anastasia, > Thanks for your help! I had this issue with 4 tracts in total. I just want to > add that before rerunning dmri_pathstats not only pathstats.overall but also > pathstats.byvoxel was affected (in the latter there were no matrix entries at > all). > I found some information in the trac-all.log but not explicitly the command > line <- this was found in pathstats.overall.txt, though. > > After rerunning dmri_pathstats everything looks great now for 3 out of the 4 > tracts, YEAH! I am not sure what to do with the last one, though: Here, the > same error occurs but in cpts.map.txt no two lines are identical: > > For lh.cst: > 58 48 10 > 62 51 21 > 65 55 26 > 70 58 35 > 72 57 39 > 64 55 56 > > Would you suggest deleting randomly one time point for this tract of this > subject? Thanks! > Vincent > > > Am 5/20/2013 10:31 AM, schrieb Anastasia Yendiki: >> >> Hi Vincent - Thanks for bringing this to my attention. I can see what might >> cause this glitch (only in the longitudinal case) and I'll fix it in the >> next version. >> >> In the meantime, if you delete one of the two identical lines from >> cpts.map.txt, and then rerun the dmri_pathstats command line that you'll >> find in the trac-all.log of your subject, it should regenerate the stats >> files correctly. Sorry for the inconvenience. >> >> a.y >> >> On Fri, 17 May 2013, vbrunsch(a)nmr.mgh.harvard.edu wrote: >> >>> Dear Anastasia, >>> >>> When running the longitudinal tracula version on our 39 subjects I found >>> for some of them "nan"-values for the center_avg variables of some tracts. >>> When I have a look at the tract distribution and the highest probability >>> path, everything seems to be ok. However, when checking the control points >>> of this path, two of them are the same. Do you know how this could have >>> happened / what to do? >>> >>> E.g. control points of forceps major from a subject (cpts.map.txt), see >>> 4th and 5th control point: >>> >>> 63 20 39 >>> 67 31 39 >>> 59 43 38 >>> 52 42 38 >>> 52 42 38 >>> 43 32 38 >>> 50 19 33 >>> >>> And the respective pathstats.overall.txt: >>> Count 1500 >>> Volume 370 >>> Len_Min 62 >>> Len_Max 99 >>> Len_Avg 78.9307 >>> Len_Center 0 >>> AD_Avg 0.00155598 >>> AD_Avg_Weight 0.00158424 >>> AD_Avg_Center -nan >>> RD_Avg 0.000438439 >>> RD_Avg_Weight 0.000401328 >>> RD_Avg_Center -nan >>> MD_Avg 0.000810952 >>> MD_Avg_Weight 0.000795633 >>> MD_Avg_Center -nan >>> FA_Avg 0.662419 >>> FA_Avg_Weight 0.696257 >>> FA_Avg_Center -nan >>> >>> Thanks for your help!! :) >>> Best, >>> Vincent >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> > > >

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