Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

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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Re: [Freesurfer] color scale for longitudinal analysis using freeview
by Salil Soman 08 Jul '13

08 Jul '13

Dear experts, Could someone point me to the color key for the output of the longitudinal analysis as viewed in freebies (as generated by the freesurfer longitudinal analysis tutorial)? Thank you, Sal Salil Soman, MD, MS

1 0

Exporting freesurfer images
by ye tian 08 Jul '13

08 Jul '13

Dear Freesurfers, Is there a way to export a large number of tkmedit images? I would like to show other people how certain areas evolve as I change coordinates, and I find myself capturing a lot of screenshots. Thank you very much! Sincerely, Ye

2 2

Painting voxels vs. adding control points
by ye tian 08 Jul '13

08 Jul '13

Dear freesurfers, I would like a second eye on my decision to edit wm.mgz. I think that the boundary between the gray and the white is unrealistic (e.g. Coronal.png). Furthermore, there is a discrepancy between -surfs and -surfs -aseg (e.g. attached coronal_aseg.png). If I indeed need to edit these slices, which way is more preferable, adding voxels or control points? Thank you very much! Sincerely, Ye

3 6

Exporting data from "Find Clusters and Goto Max"
by Sean Hatton 08 Jul '13

08 Jul '13

Hi all, Within QDEC, when I click on the "Find Clusters and Goto Max" button I can see the individual thickness values per datapoint. 1. I am co-vaying for age: would these values be raw thickness values or estimated margin means? 2. Considering I have 100s of subjects and several ROIs, how do I export these values for all subjects? I can click on each data point and copy the terminal readout or create an ROI, map label to subjects and export it out but both approaches are time consuming and prone to human error. Is there a way of using existing QDEC setup files to export all this data out more cleanly? Cheers, SEAN HATTON Brain & Mind Research Institute THE UNIVERSITY OF SYDNEY

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Freesurfer July 2013