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30132 discussions

Re: [Freesurfer] Artefactual skull stripping for some subjects
by Tudor Popescu 09 Jul '13

09 Jul '13

Dear FSers, Still haven't got to the bottom of this, any suggestions would be much appreciated, thanks in advance! Tudor On 5 July 2013 17:26, Tudor Popescu <tudor3(a)gmail.com> wrote: > Hi everyone > > The skull-stripping step of recon-all must have gone bad for my sample, > because I noticed that there are artefacts (chips) in the brain-extracted > structurals of several of my subjects. Since I ran recon-all on all my > sample without having noticed this initially, this of course also lead to > the surfaces being created wrongly, i.e. following the wrong volumetric > information. > > I attach screenshots showing some of the more obvious artefactual skull > extractions, corresponding to subjects 04, 06 and 17, and also the > brain.mgz and T1.mgz for subject 17. > > FSL's BET extracted the skull with no problems from the same original > structurals, so I'm guessing it's maybe the case that I need to override > some parameters in recon-all in order for the initial recon-all to produce > good brain extractions? > > And by the way, I noticed that, in any one subject's folder, the images > /mri/T1.mgz, /mri/orig.mgz and /mri/orig/001.mgz all seem to contain the > subject's original structural scan. Why does this exist in 3 separate > copies, which also seem to be of different file sizes? The only difference > I can see between them is in terms of brightness correction... > > Many thanks! > > Tudor >

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likelihood of identical subcortical volumes
by Satrajit Ghosh 08 Jul '13

08 Jul '13

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Re: [Freesurfer] importing from nifti
by Martin Reuter 08 Jul '13

08 Jul '13

Yes that is done that way. I thought you wanted to rerun the cross sectional data from scratch. But you can use your existing setup and run base and long on top of it. But avoid mixing freesurfer versions if posdible. Best martin Sent via the Samsung Galaxy S™ III, an AT&T 4G LTE smartphone -------- Original message -------- From: Jonathan Holt <whatsdac(a)umich.edu> Date: To: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: importing from nifti would it be possible to use volumes generated from recon-all -s <subjID> into the second and third steps of the longitudinal processing workflow? On Tue, Jul 2, 2013 at 2:24 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: In the meantime you can check how the mri/orig/001.mgz and the mri/orig.mgz and mri/orig_nu.mgz look. Best, Martin On 07/02/2013 02:16 PM, Jonathan Holt wrote: Thanks Martin, I have attached recon-all.log. I tried to run the process several times, I clearly forgot to pass -all that time but I know for certain the first time I tried I passed -all and it provided the same issue. I can pass the dicom images but I'll have to wait for my PI to return in lab. On Tue, Jul 2, 2013 at 2:05 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Jonathan, I changed the subject of the thread, to better reflect this problem, it (so far) has nothing to do with longitudinal processing. Next time, can you send the log file, it is in /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/scripts/recon-all.log not the output on the screen. But first lets check these: - your command in the email below seems to be missing "-all"? Probably you passed it? - and from your screen output it looks like there is a problem importing the nifit: WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information in the input to assign orientation to the volume... So you need to check the orientation of your /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/mri/orig/001.mgz... Not sure why your nifti files are incomplete. Can you point -i to the original dicom? Best, Martin On 07/02/2013 01:13 PM, Jonathan Holt wrote: and the command nohup recon-all -s 100922dt_01 -i 100922dt_nifti_revised.nii On Tue, Jul 2, 2013 at 12:40 PM, Jonathan Holt <whatsdac(a)umich.edu> wrote: Here ya go (to list) On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt <whatsdac(a)umich.edu> wrote: Here ya go. On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: No, it's not nifti, that should work. Can you send me your log file and the command you issued. Thanks, Martin On 07/01/2013 03:13 PM, Jonathan Holt wrote: Martin, definitely passing my images and naming time points appropriately. I have been passing nifti as opposed to dicom and it's entirely possible that may be the issue? jon On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote: Hi Jon, are you passing your images? <tpNid> is a placeholder for the id of your subject+time point, for example it could be jon_01 the "path_to_tpN_dcm" needs to specify the path to the dicom files, point it to the first file in the MPRAGE series (or multi echo mprage or what you are using). This is the full path on your file system to that file. Best, Martin On 07/01/2013 02:29 PM, Jonathan Holt wrote: I have tried to inspect the tal xfms that were created in the brief time this string was running recon-all -all -s <tpNid> -i path_to_tpN_dcm while viewing orig.mgz in tkmedit. they were talairach.xfm and talairach.auto.xfm, both were empty and the tkmedit window was empty. upon further inspection the log file is complaining about my nifty. WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: can you cc the list so that others can answer? On Mon, 1 Jul 2013, Jonathan Holt wrote: I have not and I am not certain how to do so On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote: Hi Jon have you visually inspected the results of the tal xform? Bruce On Mon, 1 Jul 2013, Jonathan Holt wrote: Log file indicates manual talairach alignment may be necessary. ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0079, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary Can anyone provide direction. Alternatively, the error indicates talairach alignment can be skipped with -notal-check flag. Is this step completely necessary? jon 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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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Cutting into a surface of grey matter
by ye tian 08 Jul '13

08 Jul '13

Dear Freesurfers, When an image cuts through a surface of grey matter (e.g. attached Freesurfer.png), will freesurfer overestimate cortical thickness? If so, how do you go about editing the image? Thank you very much! Sincerely, Ye

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Help with QDEC error
by Manish Dalwani 08 Jul '13

08 Jul '13

Hello Freesurfers, I am trying to run regression analyses within patients and one variable of interest which adjusting for the nuisance variables age, IQ, thickness. When i select the group and the CD (variable of interest) and run analyses (DODS), I get the following error: Qdec 1.4 (Qdec1.4) Type: Error Time: Fri Jun 14 14:49:37 2013 Description: Error in Analyze: command failed: mri_glmfit --y /Applications/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-CD-Cor.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Cor-thickness-CD.mat Please advice! Regards, Manish Dalwani Instructor Dept. of Psychiatry University of Colorado

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Registration of FLAIR to MPRAGE
by Xinyang Liu 08 Jul '13

08 Jul '13

Dear all, I want to obtain mean intensity value for each segment (GM, WM, subcortical) from FLAIR images. Now I have processed the MPRAGE image (same subject) using "recon-all". The next step I figured is to register the FLAIR image to the MPRAGE and transfer the segmentation of MPRAGE to FLAIR, and then calculate mean intensities based on FLAIR image. Can anyone give me some clues on how to proceed with the registration and transfer of the segmentation labels? Any command that I can check into? Thanks a lot, Xinyang

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Is there any way of finding out RESEL number in the GLM output?
by Glen Lee 08 Jul '13

08 Jul '13

Hello Freesurfer users, I'd hope to know the RESEL number in my group GLM analysis data. I can calculate the number of vertices and also see the fwhm.dat in the ouput GLM folder, but I wonder if there is anyway of finding out RESEL size if freesurfer also provides that info like SPM does. -Glen

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mri_glimfit paired analysis
by Gayane Aghakhanyan 08 Jul '13

08 Jul '13

Dear FreeSurfers I'm using Freesurfer 5.1 on Ubuntu 12.04 LTS. Currently running paired analysis as described here https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis After mri_glmfit \ --glmdir lh.paired-diff \ --y lh.paired-diff.thickness.sm05.mgh \ --fsgd paired-diff.fsgd \ --C mean.mtx \ --C age.mtx I've got an error "ERROR: you must use '--surface subject hemi' with surface data". Any idea how to fix it? Below is the full output: utente@RM-user:~/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis$ mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx --C age.mtx gdfReadHeader: reading paired-diff.fsgd INFO: ignoring tag ,9 INFO: ignoring tag ,9 INFO: ignoring tag ,3 INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 57 11.0454 Class Means of each Continuous Variable 1 Main 57.0000 INFO: gd2mtx_method is dods $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis cmdline mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx --C age.mtx sysname Linux hostname RM-user machine x86_64 user utente FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis/lh.paired-diff.thickness.sm05.mgh logyflag 0 usedti 0 FSGD paired-diff.fsgd glmdir lh.paired-diff IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.paired-diff Loading y from /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis/lh.paired-diff.thickness.sm05.mgh ERROR: you must use '--surface subject hemi' with surface data Thanks for yuo help Gayane

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Error for mri_glmfit contrast
by Catherine Bois 08 Jul '13

08 Jul '13

Dear Freesurfer experts, I am currently trying to do a cortical thickness group analysis with one factor, three levels . I have run mri_preproc and mri_surf2surf, and am now trying to run mri_glmfit --y lh.group.thickness.10B.mgh --fsgd easy2.file --C contrast1.mtx --surf fsaverage lh --cortex --glmdir lh.group However, I keep getting this error; INFO: gd2mtx_method is doss Saving design matrix to lh.group/Xg.dat Normalized matrix condition is 1 Matrix condition is 7 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 149953 voxels in mask Saving mask to lh.group/mask.mgh Reshaping mriglm->mask... search space = 74612.446501 MatrixReadTxT: could not scan value [2][1] The format of both the fsgd file and the contrast file is ASCII text My fsgd file is formatted as follows: GroupDescriptorFile 1 Title Group analysis Class HR Class Con Class ILL Input EHRS_XXXX_2 HR Input EHRS_XXXX_2 HR Input EHRS_XXXX_2 HR Input EHRS_XXXX_2 Con Input EHRS_XXXX_2 Con Input EHRS_XXXX_2 ILL and my contrast file is; 1 -1 0 I do not understand why I keep getting this error. When I include the flag -no-contrasts-is-ok, the mri_glmfit does work. There are no commas in either file. This leads me to believe something is wrong with my contrast file? However I am not certain what this could be. Help would be greatly appreciated. Thank you very much, Cathy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Re: [Freesurfer] Longitudinal Processing Error
by Jonathan Holt 08 Jul '13

08 Jul '13

Here ya go (to list) On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt <whatsdac(a)umich.edu> wrote: > Here ya go. > > > On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu > > wrote: > >> No, it's not nifti, that should work. >> >> Can you send me your log file and the command you issued. >> >> Thanks, Martin >> >> >> On 07/01/2013 03:13 PM, Jonathan Holt wrote: >> >> Martin, >> >> definitely passing my images and naming time points appropriately. I >> have been passing nifti as opposed to dicom and it's entirely possible that >> may be the issue? >> >> jon >> On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote: >> >> Hi Jon, >> >> are you passing your images? >> <tpNid> is a placeholder for the id of your subject+time point, for >> example it could be jon_01 the "path_to_tpN_dcm" needs to specify the path >> to the dicom files, point it to the first file in the MPRAGE series (or >> multi echo mprage or what you are using). This is the full path on your >> file system to that file. >> >> Best, Martin >> >> On 07/01/2013 02:29 PM, Jonathan Holt wrote: >> >> I have tried to inspect the tal xfms that were created in the brief time >> this string was running >> >> recon-all -all -s <tpNid> -i path_to_tpN_dcm >> >> >> while viewing orig.mgz in tkmedit. they were talairach.xfm and >> talairach.auto.xfm, both were empty and the tkmedit window was empty. >> >> upon further inspection the log file is complaining about my nifty. >> >> WARNING: neither NIfTI-1 qform or sform are valid >> WARNING: your volume will probably be incorrectly oriented >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from >> /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... >> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 >> WARNING: it does not appear that there was sufficient information >> >> >> >> >> >> On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: >> >>> can you cc the list so that others can answer? >>> >>> On Mon, 1 Jul 2013, Jonathan Holt wrote: >>> >>> I have not and I am not certain how to do so >>>> >>>> >>>> >>>> On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote: >>>> >>>> Hi Jon >>>>> >>>>> have you visually inspected the results of the tal xform? >>>>> Bruce >>>>> On Mon, 1 Jul 2013, Jonathan Holt wrote: >>>>> >>>>> Log file indicates manual talairach alignment may be necessary. >>>>>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >>>>>> ***FAILED*** (p=0.0079, >>>>>> pval=0.0000 < threshold=0.0050) >>>>>> Manual Talairach alignment may be necessary >>>>>> Can anyone provide direction. Alternatively, the error indicates >>>>>> talairach alignment can be skipped >>>>>> with -notal-check flag. Is this step completely necessary? >>>>>> jon >>>>>> >>>>>> >>>>> >>>>> 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. >>>>> >>>> >>>> >>>> >>>> >>>> >> >> >> _______________________________________________ >> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- >> Martin Reuter, Ph.D. >> Assistant in Neuroscience - Massachusetts General Hospital >> Instructor in Neurology - Harvard Medical School >> MGH / HMS / MIT >> >> A.A.Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, MA 02129 >> >> Phone: +1-617-724-5652 >> Email: >> mreuter(a)nmr.mgh.harvard.edu >> reuter(a)mit.edu >> Web : http://reuter.mit.edu >> >> >> >> -- >> Martin Reuter, Ph.D. >> Assistant in Neuroscience - Massachusetts General Hospital >> Instructor in Neurology - Harvard Medical School >> MGH / HMS / MIT >> >> A.A.Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, MA 02129 >> >> Phone: +1-617-724-5652 >> Email: >> mreuter(a)nmr.mgh.harvard.edu >> reuter(a)mit.edu >> Web : http://reuter.mit.edu >> >> >

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