Freesurfer

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Re: [Freesurfer] Odd Extremely High/Low Banding of Functional Values in Volume
by Dowling, Kevin Francis 13 Dec '16

13 Dec '16

Hi Doug, My apologies for omitting the previous emails when replying earlier. To create the sig.mgh file we used a volume specific mri_glmfit analysis, with volume specific inputs / no --hemi/hemis flag. I don't know if this information is helpful but when we've run a nearly identical analysis (using almost all of the same participants and a slightly different covariate of interest) the volume came out completely fine. In case there was an error in one of our scans omitted from the successful mri_glmfit I re-ran the mri_glmfit/concatenation, excluding participants not also included in our successful mri_glmfit. However, the abnormal activation persisted (see attached screen grabs). I've also tried de-meaning our covariate of interest values (RBC Folate) and re-running the mri_glmfit, with no improvement. This is our mri_glmfit command: mri_glmfit --y /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/137_GDD_RBC_Folate_Cond2vfix_KD/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/ces.nii.gz --fsgd /cluster/roffman/users/fsgd/GDD/137_GDD_Cond2vFix_Covary_RBC_Folate_linear_KDcorrect.fsgd --C /cluster/roffman/users/fsgd/TwoGroups1CovariateRegressOut1Covariate_KD --glmdir /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/137_GDD_RBC_Folate_Cond2vfix_KD/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/2vFix_ClassUsed_Covary_RBCFOLATE_Nuis_Age_Gender --fwhm 6 --no-prune Thank you very much, I am most appreciative of your help and would be grateful for any other troubleshooting suggestions you might have! Kind regards, Kevin Message: 2 Date: Mon, 5 Dec 2016 14:41:15 -0500 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Odd Extremely High/Low Banding of Functional Values in Volume To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <52df3c71-0cdc-61ba-2491-5bebffa114c1(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed How did you create sig.mgh? If you used a surface-based mri_glmfit analysis, then you'll need to convert sig.mgh to the volume (mri_surf2vol) On 12/05/2016 02:25 PM, Dowling, Kevin Francis wrote: > > Hello Freesurfer Experts, > > I?m attempting to look at activity in a working memory paradigm using > blood folate levels as my covariate of interest while controlling for > gender and age in 137 subjects. There were no errors (that I could > find) in the concatenation or mri_glmfit commands, and subject > registration looked ok for the functional data. When visualizing the > right and left hemisphere surface sig.mgh files using tksurfer > everything looks reasonable. However, when using tkmedit (tkmedit > fsaverage1 orig.mgz ?overlay sig.mgh ?fminmax 1.3 3.3 ?fmid 2.3) I am > getting odd continuous bands of incredibly high and incredibly low > activation spanning throughout most the volume (I?ve attached some > screen grabs ? the functional values in these bands are either > 10000000000 or -10000000000 and look continuous from slice to slice). > > I?ve taken a look at the list and was not able to find a similar > problem discussed. I would be most grateful for any guidance or > trouble shooting suggestions you might have! > > I?ve also attached a text file copy of the glm and tkmedit results in > case they would be of use. > > I'm using Freesurfer version 5.3 (nmr-stable53-env) on a Linux > (Release 6.7 (Santiago), Kernel Linux 2.6.32-573.12.1.el6.x86_64 > and GNOME 2.28.2) > > Thank you! > > Kevin > > Kevin Dowling > > Clinical Research Coordinator > > Brain Genomics Laboratory > > Division of Psychiatric Neuroimaging > > Massachusetts General Hospital > > 149 13th Street > > Charlestown, MA, 02129 > > (p) (617) 643 - 2479 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.2479

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question white matter
by tom parker 13 Dec '16

13 Dec '16

Dear Freesurfers, Could anyone tell me what the white.H and white.K measures in Qdec are? Thank you so much!

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hard time with mris_pmake
by salma bougacha 13 Dec '16

13 Dec '16

Hi Freesurfer experts, I am new to freesurfer. I installed the last freesurfer version (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) and I am trying to compute the shortest cortical path between two sets of vertices. 1- Using the command mris_pmake updated If I understand correctly according to https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027543.h… mris_pmake has been updated, but the command mris_pmake --subj bert --hemi lh --surface smoothwm --mpmProg autodijk --mpmArgs vertexPolar:0 --mpmOverlay euclidean throws the following error #####################" mris_pmake: option '--surface' is ambiguous; possibilities: '--surface0' '--surface1' #####################" Following the complain, I tried mris_pmake --subject bert --hemi lh --surface0 smoothwm --surface1 smoothwm --mpmProg autodijk --mpmArgs vertexPolar:11 --mpmOverlay euclidean This seems to work and produces options.txt and user_msg.log files in the current directory. However I am unable to find the output lh.autodijk.crv and that's where the path lengths are stored, right ? 2- making dsh work: I get the following error when trying to run dsh Traceback (most recent call last): File "/usr/local/freesurfer/bin/dsh", line 16, in <module> from dgmsocket import * ImportError: No module named dgmsocket So I commented this import as well the line "G_socket = C_dgmsocket(Gstr_host, string.atoi(Gstr_port))". Now dsh seems working in the begining but then I have the following ################################################# sh: 1: SSocket_client: not found 46.860310 Engine successfully started and environment parsed. Ready for user input. Type 'HELP' for help. 1 > Start->End vertices [ 11->6398 ] Total path cost [ 46.860310 ] process died. /usr/local/freesurfer/bin/dsh Sorry, but some error occurred. While attempting dijkstra_spawn(), the process died unexpectedly Exiting to system with code 10. ########################################### Any help is appreciated ! Thanks. Salma

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mris_apply_reg
by Matthew Defenderfer 13 Dec '16

13 Dec '16

Hi All, I am trying to mirror labels across hemispheres and found various threads using mris_apply_reg. Unfortunately the version of that command I have does not recognize labels and all of the links in the mailing list seem to be broken. Would it be possible to get a link to the updated command? Thank you. -Matthew Defenderfer

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(no subject)
by Abigail Noyce 13 Dec '16

13 Dec '16

Hi Doug et al, I would like to get a different cluster summary stat out of mri_glmfit-sim. Rather than size, I'd like to use the "sum of t-scores" (after Maris & Oostenwald 2007, for example). That is, set a cluster inclusion threshold, and then for each cluster of adjacent vertices that clear the threshold, sum their t-scores. For the permutation significance testing, then, the largest such clusterwise sum would be the statistic used to generate the null distribution... I'm happy to write my own scripts, but can't figure out where to try to pull this number out. Thanks! Abby Noyce

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Re: [Freesurfer] Odd Extremely High/Low Banding of Functional Values in Volume
by Dowling, Kevin Francis 13 Dec '16

13 Dec '16

Hi Doug, Thank you for your note and my apologies for a delayed response. To create the sig.mgh file we used a volume specific mri_glmfit analysis, omitting the --surf flag and using our volume specific input (ces.nii.gz in SIRP_LoadRegression_Stable5.3_012616_sm5_mni305). I don't know if this information is helpful but when we've run a nearly identical analysis using almost all of the same participants and a different blood folate marker (serum folate) the volumes came out completely fine. I've tried de-meaning the RBC folate values and re-running the mri_glmfit, but the odd activation persists. This is our mri_glmfit command: mri_glmfit --y /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/137_GDD_RBC_Folate_Cond2vfix_KD/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/ces.nii.gz --fsgd /cluster/roffman/users/fsgd/GDD/137_GDD_Cond2vFix_Covary_RBC_Folate_linear_KDcorrect.fsgd --C /cluster/roffman/users/fsgd/TwoGroups1CovariateRegressOut1Covariate_KD --glmdir /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/137_GDD_RBC_Folate_Cond2vfix_KD/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/2vFix_ClassUsed_Covary_RBCFOLATE_Nuis_Age_Gender --fwhm 6 --no-prune Thank you very much, I am most appreciative of your help! Kind regards, Kevin Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.2479

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Freesurfer longitudinal analysis accuracy
by Gabor Perlaki 13 Dec '16

13 Dec '16

Dear all, We've run longitudinal Freesurfer on 30 healthy subjects. We have two subgroups (n=15) and we found a significant longitudinal change in the left and right cerebellar cortex in one of our subgroups. However, this change is very small: mean=0.67% range: -1.61-2.3% for the right cerebellar cortex; mean=0.86% range: -1.64-3.7% for the left cerebellar cortex. Although statistics indicate significant cerebellar cortex increase, we are sceptical that Freesurfer's accuracy allows reliable detection of such small differences. Is there any article on how accurate the longitudinal Freesurfer for cerebellum segmentation or any suggestion on how to decide whether our results are reliable? Best, Gabor

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MS Lesions effects on cortical thickness in FS 6.0
by Ismail Koubiyr 12 Dec '16

12 Dec '16

Dear Freesurfer experts, We are facing a problem in our study and would need your advice on it. We want to get an accurate measurement for the cortical thickness from our MS patients data. For that we are using 3D T1 and FLAIR (recon-all will be used with the FLAIR option so that we can a more accurate pial surface). However, we were wondering if running recon-all on the raw data would lead to some errors specially because of the juxtacortical lesions or not. Or, is it better to first apply a lesion filling using our lesion mask ? I should specify that we will use the longitudinal pipeline if it is of any use. Thank you all. Ismail PhD candidate Neurocentre Magendie, INSERM Bordeaux, France

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white matter segmentation incorrect after intensity change
by Rizvi, Batool 12 Dec '16

12 Dec '16

Hi FreeSurfer experts, After running -autorecon2 and -autorecon3, we're seeing issues for some of the subjects, which now start showing changes in intensity/brightness in some voxels, and this increased intensity is now missed by the white matter and grey matter segmentation, and is labeled as non-brain matter. Attached is an example of a subject's brain that was segmented incorrectly, which we think is due to the intensity around that frontal region. We hadn't added control points in that region, so we are unsure what the cause of the intensity change is. In our first pass before running -autorecon2 -autorecon3, we did not notice this error or the intensity values to be so bright for that region. Thanks for your help! BR

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longHippoSubfields
by Christian Krog Tamnes 12 Dec '16

12 Dec '16

Dear Juan and FreeSurfer team, We are trying to test out the longitudinal hippocampus subfield segmentation pipeline, but can't seem to run/find the script (longHippoSubfieldsT1.sh). We have done the standard processing in v5.3 and have the following dev version: freesurfer-Linux-centos6_x86_64-dev-20160914-bdac8bc. Sorry for the basic question, but do we simply need a later dev build? Best regards, Christian

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