Freesurfer July 2011

freesurfer@nmr.mgh.harvard.edu

129 participants
195 discussions

Re: [Freesurfer] Dimension error - mri_segstats
by Jaichander S 25 Jul '11

25 Jul '11

Hi, For others who are looking for the solution to the problem I mentioned earlier - Running mri_vol2surf in step3 of the instructions given here ( http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) replacing '--reshape' with '--rf 6' did the trick for me. I tried this after going throught the help for mri_vol2surf command. Cheers, Jaichander From: Jaichander S <jaichander.s(a)gmail.com> > Subject: [Freesurfer] Dimension error - mri_segstats > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CABc7hshQM0Gszc0_uC8GEY85wVdVKq6rgXM7YyEdFwu8YkFgKA(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi freesurfers, > > I performed ROI cortical thickness measurements earlier on an older version > of FS as described on > http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and I > was able to get the required values. > > Now I have the latest version of FS. I draw an ROI mask using FSL software > and then use it to follow the instructions on the tutorial. The ROI and the > initial T1 image are in the same coordinate space (with different > dimensions) as is required by the procedure. After following all the steps > I > get > > ERROR: dimension mismatch between input volume and seg > input 27307 1 6 > seg 23406 1 7 > > when running mri_segstats. > > This has been reported by some other people already on the mailing list but > the suggestions do not work for me. Any light that you can shed to sidestep > this dimensions problem will be greatly appreciated. > > Is there any other workflow to define a volume ROI and then get the > cortical > thickness in the area. > > Thanks! > Jaichander >

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Dimension error - mri_segstats
by Jaichander S 25 Jul '11

25 Jul '11

Hi freesurfers, I performed ROI cortical thickness measurements earlier on an older version of FS as described on http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and I was able to get the required values. Now I have the latest version of FS. I draw an ROI mask using FSL software and then use it to follow the instructions on the tutorial. The ROI and the initial T1 image are in the same coordinate space (with different dimensions) as is required by the procedure. After following all the steps I get ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7 when running mri_segstats. This has been reported by some other people already on the mailing list but the suggestions do not work for me. Any light that you can shed to sidestep this dimensions problem will be greatly appreciated. Is there any other workflow to define a volume ROI and then get the cortical thickness in the area. Thanks! Jaichander

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QC Montages error
by Chindhuri Selvadurai 25 Jul '11

25 Jul '11

Hello, I have tried troubleshooting this problem in various ways, but I am still not able to figure out the problem. I probably gave more output than necessary. Does anyone have any idea? Thank you! > I am getting an error when using a script that combines these 3 actions: > > preproc.sh > std_map_qc_montages.bash > put_tpef.bash > > > Freesurfer version 4 > SUBJECTS_DIR: /cluster/manoach/AS/RespMon12C/subjects > Script: > /cluster/manoach/AS/RespMon12C/scripts/preproc_std_qc_montages_put_tpef.sh > > It looks like the preproc-sess finishes okay, but the problem starts > afterwards, but I'm not sure how to fix this easily.. it looks like it's > looking for files that aren't there, but I haven't gotten this error > before. > > Thanks! > > Output, with error at end: > > ----------------- mkbrainmask Done ----------------------------- > > Thu Jul 7 17:15:21 EDT 2011 > mkbrainmask-sess done > ---------------------------------------- > Started at Thu Jul 7 16:54:00 EDT 2011 > Ended at Thu Jul 7 17:15:21 EDT 2011 > preproc-sess done > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./009/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./009/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./009/lightboxes/tmean_lightbox.png': No such file or > directory > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./011/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./011/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./011/lightboxes/tmean_lightbox.png': No such file or > directory > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./013/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./013/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./013/lightboxes/tmean_lightbox.png': No such file or > directory > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./015/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./015/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./015/lightboxes/tmean_lightbox.png': No such file or > directory > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./017/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./017/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./017/lightboxes/tmean_lightbox.png': No such file or > directory > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./019/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./019/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./019/lightboxes/tmean_lightbox.png': No such file or > directory > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./021/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./021/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./021/lightboxes/tmean_lightbox.png': No such file or > directory > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./023/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./023/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./023/lightboxes/tmean_lightbox.png': No such file or > directory > > Cannot open tsnr_lightbox1.png for reading > /autofs/cluster/manoach/AS/RespMon12C/scripts/RM12C_lightbox_runs.bash: > line 35: 28671 Segmentation fault pngappend tsnr_lightbox1.png + > $((gap)) tsnr_lightbox2.png + $((gap)) tsnr_lightbox3.png - $((gap)) > tsnr_lightbox4.png + $((gap)) tsnr_lightbox5.png + $((gap)) > tsnr_lightbox6.png tsnr_all.png > > Cannot open tstd_lightbox1.png for reading > /autofs/cluster/manoach/AS/RespMon12C/scripts/RM12C_lightbox_runs.bash: > line 36: 28672 Segmentation fault pngappend tstd_lightbox1.png + > $((gap)) tstd_lightbox2.png + $((gap)) tstd_lightbox3.png - $((gap)) > tstd_lightbox4.png + $((gap)) tstd_lightbox5.png + $((gap)) > tstd_lightbox6.png tstd_all.png > > Cannot open tmean_lightbox1.png for reading > /autofs/cluster/manoach/AS/RespMon12C/scripts/RM12C_lightbox_runs.bash: > line 37: 28673 Segmentation fault pngappend tmean_lightbox1.png + > $((gap)) tmean_lightbox2.png + $((gap)) tmean_lightbox3.png - $((gap)) > tmean_lightbox4.png + $((gap)) tmean_lightbox5.png + $((gap)) > tmean_lightbox6.png tmean_all.png > mv: cannot stat > `/autofs/cluster/manoach/AS/RespMon12C/subjects/RMAUT021/bold/all_lightboxes/*all*': > No such file or directory > rm: cannot remove > `/autofs/cluster/manoach/AS/RespMon12C/subjects/RMAUT021/bold/0*/lightboxes/': > No such file or directory > Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307

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Pial Edits on Base Template
by Jeff Sadino 25 Jul '11

25 Jul '11

Hello, I have a subject with three timepoints I am putting through the longitudinal stream in fs 5.0.0. After the base template was created, I edited some of the pial surfaces on the base. Now when I run the command: "recon-all -base subject -autorecon2-pial -autorecon3", it says: "ERROR: /mnt/fs5/050079 exists, delete or re-run with -force" This is confusing to me because if I delete the folder, then wont my edits also be deleted? I ran it using the force flag, and it seems to be going ok. I just want to ask if this is the best way to do this. Thank you, Jeff Sadino

3 2

Problems with segmentation
by leonardo kay 25 Jul '11

25 Jul '11

Hi freesurfers After checking recon-all -autorecon-all processing, I realized that a part of the duramadre has been not fully removed (please see attached file). Can anyone help me how to solve this please. Best regards. -- Leo Kay.

2 1

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

2 1

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?

2 1

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

2 3

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,

2 2

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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Freesurfer July 2011