Freesurfer February 2017

freesurfer@nmr.mgh.harvard.edu

162 participants
277 discussions

Contrast percent map
by Seung-Goo KIM 03 Feb '17

03 Feb '17

Hi Doug, Thank you so much for clarification. Probably there is an issue with the mailing list, I only received the digest list, and now I saw your reply. In fact, I found it by myself while looking through fast_selxavg3.m: the baseline being defined by the overall offset. and yes, I was thinking something else.. because contrast=(baseline+contrast)-baseline, so it’s just contrast/offset*100 Thanks! -SG > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] [FSFAST] Contrast percent map > Date: 1 February 2017 at 17:38:35 GMT+1 > To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > > you have the right idea, but it is > > cespct = 100*contrast/baseline > > The baseline is the mean offset of the fMRI, the contrast is the deviation from baseline > > > On 2/1/17 4:49 AM, Seung-Goo KIM wrote: >> Dear all, >> >> I wish to know how “cespct.nii.gz” is computed in selxavg3-sess. I thought it computes something like a relative change like: >> >> cespct = (contrast-baseline)/baseline*100, >> >> but I cannot figure out what was taken for the baseline. I thought it could be mean beta for constant terms (0-th polynomial) for each run, but my calculation was different from cespct. >> >> I would take average intensity for each voxel I would greatly appreciate a detailed explanation how the program computes it. >> >> Best regards, >> -- >> Seung-Goo KIM -- Seung-Goo KIM

1 0

How to check recon-all finished without any error
by shi yao wang 03 Feb '17

03 Feb '17

Dear FS experts: How to check recon-all finished without any error? Sometime, there are showing no error message, however, when I running hippocampus subfield, it does not run. thanks Lawrence Emory

3 2

Error: if: Expression Syntax.
by Anderson Napolitano 02 Feb '17

02 Feb '17

Hello Experts! I am having trouble running the following command: tkregisterfv --mov /Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm --reg /Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm --surfs as it outputs the following error: if: Expression Syntax. I've attached below the full output with the debug flag on. Any help would be greatly appreciated. Thank you in advance. Regards, Anderson?

2 1

Simple question regarding -T2 and -FLAIR flags (freesurfer v6)
by Joe Necus (PGR) 02 Feb '17

02 Feb '17

Hello, I am running recon-all on the latest version of freesurfer (Version 6) and would like to know whether there is any difference between using the -T2 -T2Pial and -Flair flags. I am currently running recon-all with a T1 and FLAIR image, but have used the -T2 -T2pial flags and would like to know whether I need to go back and instead re-run with the -FLAIR flag instead. Thanks a lot, Joe

3 2

design specification with 3 categorical predictors
by Tim Reess 02 Feb '17

02 Feb '17

Dear Freesurfer experts, I would like to set up a design matrix for a design that is not QDEC-able. I have three categorical factors: 1.disease status: 2 levels 2.gender: 2 levels 3.scan site: 4 levels The first design I set up was the following (the rows are just for illustration and don’t reflect the number of subjects that will enter the analysis): designs4_fs_mailinglist.png However, I have my doubts as to the “efficiency” of the design (in terms of number of regressors / DOF). Therefore, here is my second design: Would this design be correct for assessing the group differences for disease status while regressing out gender and scanner site? My understanding is, that in this design I can’t assess the effects of interactions regarding scanner site. However, I think it is fair to assume that the scanner site doesn’t have a differential effect on either gender or disease status. Any feedback is highly appreciated. Thanks a lot. Best regards, Tim

2 1

LGI issue/Error
by aral ahmadi 02 Feb '17

02 Feb '17

Dear experts I have a question regarding Freesurfer- LGI error I got during running LGI after all recon steps been ran with no problem. you could see the error below. *reading filled volume...* *??? undefined function or variable 'ismac'.* *error in -->load_mgh at 68* *if(strcmp(computer,'MAC') || strcmp(computer,'MAC') || ismac)* *error in -->MRIread at 87* *[mri, voi, M, mr_parms, volsz] = load_mgh (fspec, [], [], headeronly);* *error in --> make outer-surface at 24* *vol = MRIread(filled_volume);* *>> ERROR:make _outer_surface did not creat output file 'net/storage1/usr2/onrc/home/p2/Aahmadi/onrc/data/Aral-july/test/subject* *Linux compute31 2.6.32-504.12.2.e16.*86_64 #1 SMP Wed Mar11 UTC 2015 86_64 86_64 GNU/Linux* *recon-all -s S1091RPY existed with Errors at thu jan19 2017* The error is ...Undefined function or variable 'ismac' - matlab is expecting that variable to be defined (it's trying to detect the OS, whether Linux, windows/ Mac), but it isn't. I appreciate if you give me your advice on this issue. Thanks, Aral

2 1

Group connectivity maps with crazy sig values
by Rodriguez-Thompson, Anais 02 Feb '17

02 Feb '17

Hi freesurfer experts, I am running a group functional connectivity analysis following the steps from the FsFast Functional Connectivity Walkthrough. When I visualize the OSGM maps, the pattern of connectivity looks normal but there are regions of ridiculously high significance values (sig= 10,000,000,000). This problem is happening bilaterally for each seed. Attached are slides showing the OSGM map for one of my seeds (left dlPFC) at a normal threshold, and then at a threshold minimum of 100 to show the regions that have this crazy significance value. After generating my .dat files using fcseed-sess and creating nuisance regressors I run the following commands: $ mkanalysis-sess -analysis FC_{mask}_FS5.3_SIRP.lh -surface fsaverage lh -fwhm 5 -notask -taskreg {mask}.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -nuisreg global.waveform.dat 1 -mcextreg -polyfit 5 -fsd bold -rlf funlist_fc_SIRP -TR 2 -per-run -force $ selxavg3-sess -sf $SUBJECTS_DIR/Subject_Files/GDD/145_GDD_FC_SerumFolate -analysis FC_{mask}_FS5.3_SIRP.lh $ isxconcat-sess -sf $SUBJECTS_DIR/Subject_Files/GDD/145_GDD_FC_SerumFolate -analysis FC_{mask}_FS5.3_SIRP.lh -all-contrasts -hemis -o $SUBJECTS_DIR/Analyses_GDD/FC_Analyses/145_GDD_SerumFolate/bold/{mask} $ mri_glmfit --fsgd /cluster/roffman/users/fsgd/GDD/145_GDD_FC_SerumFolate_OSGM.fsgd --osgm --fwhm 6 --no-prune --y /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/FC_Analyses/145_GDD_SerumFolate/bold/lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816/FC_lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816_FS5.3_SIRP.lh/lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816/ces.nii.gz --glmdir /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/FC_Analyses/145_GDD_SerumFolate/bold/lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816/FC_lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816_FS5.3_SIRP.lh/lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816/LH_OSGM --surface fsaverage lh Am I doing something wrong in my commands that is creating these results? Is there anything I can do to troubleshoot this issue? Thank you, Anais Rodriguez-Thompson Clinical Research Coordinator Brain Genomics Laboratory Martinos Center for Biomedical Imaging Massachusetts General Hospital Phone: (617) 643-3215

2 1

ROIs in midline for cortical thickness
by Sahil Bajaj 02 Feb '17

02 Feb '17

Hi everyone, I have supplementary motor area (SMA) defined in standard MNI volume space and I would like to extract cortical thickness for this area. I have 80% of SMA in left hemisphere and 20% on right hemisphere. So I am stuck at the command mri_vol2surf before proceeding to mri_segstats. In mri_vol2surf, I am not sure what should I specify for --hemi i.e. whether its left or right hemisphere (lh or rh). If I specify e.g. lh, then would not it convert left hemisphere SMA voxels to surface and later on extract the measure from left hemisphere only and vice-versa for right hemisphere. I am not sure how would that work if portion of ROI is on both hemispheres and how can I run mri_vol2surf command? Thanks, Sahil

2 4

Cannot find CTF archive
by shi yao wang 02 Feb '17

02 Feb '17

Dear FS experts: when I running hippocampus subfield, I got error messages:" Cannot find CTF archive". I copied command and screen to you. Thank you very much! [silun.wang@node5 N01]$ *recon-all -s N01 -hippocampal-subfields-T1* Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20160611-876a0e6 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20160611-876a0e6 INFO: SUBJECTS_DIR is /data/home/silun.wang/silun_data Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r--. 1 silun.wang silun.wang 489034 Feb 2 13:43 /data/home/silun.wang/silun_data/N01/scripts/recon-all.log Linux node5.cluster 3.10.0-327.36.1.el7.x86_64 #1 SMP Sun Sep 18 13:04:29 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/data/home/silun.wang/silun_data/N01/scripts/recon-all.local-copy' #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Thu Feb 2 13:53:46 EST 2017 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 /usr/local/freesurfer N01 /data/home/silun.wang/silun_data left See log file: /data/home/silun.wang/silun_data/N01/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: Error:Cannot find CTF archive /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.ctf #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Thu Feb 2 13:53:53 EST 2017 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 /usr/local/freesurfer N01 /data/home/silun.wang/silun_data right See log file: /data/home/silun.wang/silun_data/N01/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: *Error:Cannot find CTF archive /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.ctf* Started at Thu Feb 2 13:53:41 EST 2017 Ended at Thu Feb 2 13:54:01 EST 2017 #@#%# recon-all-run-time-hours 0.006 recon-all -s N01 finished without error at Thu Feb 2 13:54:02 EST 2017 done

1 0

Freesurfer- LGI error
by aral ahmadi 02 Feb '17

02 Feb '17

Dear experts, I have a question regarding Freesurfer- LGI error I got during running LGI after all recon steps been ran with no problem. Attached you could see the error. The error is ...Undefined function or variable 'ismac' - matlab is expecting that variable to be defined (it's trying to detect the OS, whether Linux, windows/ Mac), but it isn't. I appreciate if you give me your advice on this issue. Thanks, Aral

1 0

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Freesurfer February 2017