Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Converting from volume label RAS to Talairach
by Jed Singer 26 Jul '11

26 Jul '11

I'm at my wits' end with what seems like it should be an easy question. I have a lot of volume labels that have been saved for a lot of brains. I want the Talairach coordinates corresponding to those points. It seems like mri_label2label should be able to do this, by putting in 'talairach' as the target subject, but this returns an error that the subject 'talairach' isn't found: mri_label2label --srcsubject m00045 --srclabel label/all.label --trgsubject talairach --trglabel all_talairach.label --regmethod volume It seems like I should be able to do it manually by loading the talairach.xfm generated by recon-all and multiplying that matrix by the RAS points in the labels; this yields results that are pretty close to those given in tkmedit, but not that close. Usually within a few, sometimes off by more. Probably my inability to do this reflects some misunderstanding or lack of information, but I've been poring over documentation, forum, and wiki for hours now and feel like I've hit a wall. Any suggestions? Thanks so much, Jed

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Re: [Freesurfer] Cortical segmentation error
by Carolina Valencia 26 Jul '11

26 Jul '11

Hi Bruce, thanks for your explanation. I was thinking the the segmentation region is used to calculate cortical thickness, by the way, is it used for calculate something? such as the GM volumes? I want to know this to be sure if in some point I have to fix this. About the heterotopias, is a good output to have someones classified as WM, other as GM and sometimes are outlined by the yellow line and sometimes are not? Best regards, Carolina 2011/7/19 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Carolina, > > it looks mostly to me like the surfaces are in the right place (the yellow > and red lines). Don't look at the colored overlay - that is the aseg voxel > segmentation and not what we typically use for cortical morphometry. Only > look at the yellow and red lines. > > > cheers > Bruce > On Tue, 19 Jul 2011, Carolina Valencia wrote: > > tiff I guess, I took the pictures from FS >> >> 2011/7/19 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> what format are the files in the archive in? They don't have an >> extension >> >> On Tue, 19 Jul 2011, Carolina Valencia wrote: >> >> >> I hope this attachement works.I also noticed that some heterotopias >> are classified as WM, other as GM and sometimes are outlined by the yellow >> line and >> sometimes are not. >> >> Best regards, >> >> Carolina >> >> 2011/7/19 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Carolina, >> >> can you gzip it or use compression? Usually people can send a >> few images to the list. >> >> cheers >> Bruce >> On Tue, 19 Jul 2011, Carolina Valencia wrote: >> >> 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 >> >> >> >> >> 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<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. >> >> >> >> >> > >

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Re: [Freesurfer] Longitudinal Analysis Error
by Martin Reuter 26 Jul '11

26 Jul '11

Hi Silvia, it is never a good idea to mix versions and we did not test any such combinations. Also because 5.1 is much better than 4.5 I would definitely recommend to rerun. However, I still believe that it should be possible to use the 5.1 post-processing scripts to e.g. create rate maps for each subject and qdec to analyze them even with 4.5 processed data. Best, Martin On Tue, 2011-07-26 at 10:45 +0200, Silvia Juanes wrote: > Hi Martin, > > We used the preprocessing pipeline from 4.5 version and then we used > the 5.1 version to perform the longitudinal analysis. Do you think > that we should repeat the preprocessing using 5.1 version? or do you > know any other solution to do the analysis with the 4.5 preprocessing > data? > > Best, > > Silvia > > 2011/7/25 Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> > Hi Silvia, > > qdec does not support any longitudinal analysis (only cross > sectional). > So I assume you either compare groups cross sectionally (e.g. > at > baseline) or you constructed your own longitudinal measure > (e.g. percent > change, within each subject) and then do a cross sectional > analysis of > that statistic? > Both these things should work. I think your qdec table is > setup > incorrectly? > > Best, Martin > > > On Tue, 2011-07-19 at 12:45 +0200, Silvia Juanes wrote: > > 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, > > > > > > > > > _______________________________________________ > > 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. > >

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Re: [Freesurfer] Error in qdec longitudinal 5.1
by Martin Reuter 26 Jul '11

26 Jul '11

Hi Natalia, /TemplateSub1/surf/lh.thckness.fwhm10.fsaverage.mgh there is an 'i' missing in thckness (but that might be just a typo). also this is a regular thickness file. You cannot analyze the thickness in the base. That is meaningless, you need to select one of the other files in qdec, e.g. the spc. (there is a selection field). Best, Martin On Tue, 2011-07-26 at 14:01 +0200, Natalia h wrote: > Hi Martin, > > > I rechecked the .Qdecrc file, I put it as suggested on the tutorials. > inside my qdec folder, I put a .Qdecrc file and contains the 4 lines. > But still qdec cannot recognize the new types of files, am not sure > why. > > > Thanks again > Natalia > > > On Tue, Jul 26, 2011 at 11:25 AM, Natalia h > <natalia.himalaya(a)gmail.com> wrote: > Hi Martin, > > Thanks for the reply. my .qdecrc file is correct. > What I tried to say is that, > the error appear when I click analyze button. (qdec 1.4) > Error in Analyize: Couln´t open > file /TemplateSub1/surf/lh.thckness.fwhm10.fsaverage.mgh > > > > p.s TemplateSub1 is the -base name > > > > While I looked back into this folder, Indeed there is no such > file > What i have are > lh.long.thickness-spc-fwhm10.fsaverage.mgh > lh.long.thickness-rate-fwhm10.fsaverage.mgh > lh.long.thickness-pc1-fwhm10.fsaverage.mgh > ....etc > > > > > > > The qdec 1.4 seems to be not able to see these files... > > > Regards > Natalia > > > On Mon, Jul 25, 2011 at 5:08 PM, Martin Reuter > <mreuter(a)nmr.mgh.harvard.edu> wrote: > > Hi Natalia, > > > > check your qdec/.QDECRC file, it needs to contain: > > > > MEASURE1 = long.thickness-avg > > MEASURE2 = long.thickness-rate > > MEASURE3 = long.thickness-pc1 > > MEASURE4 = long.thickness-spc > > > > probably you put a .spc instead of -spc > > > > Best, Martin > > > > On Fri, 2011-07-22 at 18:51 +0200, Natalia h wrote: > >> 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 > >> _______________________________________________ > >> 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. > > > > > > > >

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lesion question
by Rebecca McCourt 25 Jul '11

25 Jul '11

Hello everyone, I have several patients with large cortical lesions (haemorrhage). I want to have subcortical structure volumes reflect the lesion, i.e. show up as hypointensities in aseg.mgz (which they're not right now). However I also want to calculate cortical thickness, and the WM & GM surfaces around the lesion are way off. The lesion is much too big to fill manually in wm.mgz. Any suggestions? - Rebecca

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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

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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.

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