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Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs
by Douglas Merkitch 03 Feb '17

03 Feb '17

Hello Freesurfer experts, >From your wiki page, I understand how to normalize volumes in subject diffusion space to the CVS template: mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov fa-masked.mgz \ --o fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg However, how would one take take a volume in CVS template space and reverse normalize it back to subject diffusion space? Is this possible? If so, what would that command look like and what other steps would be necessary to get the required inputs? Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu>

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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

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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

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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?

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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

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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

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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

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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

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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

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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

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