Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

long_mris_slopes sign of do-rate
by vbrunsch＠nmr.mgh.harvard.edu 05 Aug '13

05 Aug '13

Dear Freesurfer experts, I have followed the LongitudinalTutorial with two time points + two groups and now, after looking at the output of the qdec analysis, I just want to make sure I haven't made a sign error as for the control group the difference is as expected around 0 but for the experimental group I see negative values (= thinning?) all over the place which seems weird, just want to make sure I got this right: I set the time variable to 0 for the baseline scan and to 1 for the after-intervention-scan. Is it correct that for do-rate the calculation is then only <thickness of tp2> - <thickness of tp1> and not the other way around? I ask because in the long_mris_slopes -help it says that do-rate would yield the "thinning in mm/time" and if this means that a positive value stands for thinning then this would contradict what I understood from the Tutorial where it says for the rate "thick2-thick1" is calculated, so a positive value should mean "thickening". Also, how does long_mris_slopes know which one is tp1 and which one is tp2? I assume it takes the first entry in the fsid column of long.qdec.table.dat as tp1 and the second entry below as tp2? Hm, I see no other possibilities of making a sign error during the whole process, did anyone report a similar issue? Thanks for your help! Best, Vincent

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Re: [Freesurfer] TR,TE,TI,FA variability w/ mri_ca_train
by Mark Plantz 05 Aug '13

05 Aug '13

For some reason, when I run that command, I get the following output: Input volume is : seg_mov Output volume is : seg_mov_2 There are no errors, but when I check "mri_info" of the output file, the TR, TE, etc. values are still non-zero. Any ideas what could cause that to happen? Thanks! MP On Mon, Aug 5, 2013 at 11:35 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > yes, I think so > > On Mon, 5 Aug 2013, Mark Plantz wrote: > > thank you. Would the command simply be something like this: mri_modify >> -tr 0 -te 0 -ti 0 -fa 0 <input.mgz> <output.mgz> ? >> >> >> On Thu, Aug 1, 2013 at 1:41 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Mark >> >> the formatting got messed up so I can't parse your table. You can >> get around this using mri_modify, and just setting >> everything to 0. As for the effects, look at the images and see >> what you think. >> >> cheers >> Bruce >> >> On Thu, 1 Aug 2013, Mark Plantz wrote: >> >> Hello freesurfers, >> I currently have a series of images with various >> TR,TE,TI,FA values. I >> would like to use mri_ca_train to create a .gca atlas based >> on these >> segmented volumes. Unfortunately, they all have slightly >> different control >> parameters (TR,TE,TI,FA). Is there any way around this >> problem, or would it >> be best to break the subjects into multiple groups with the >> same control >> parameters? >> >> Here are the various parameters: [each row is a subject] >> >> TR >> TE >> TI >> flip angle >> 9.38 >> 3.86 >> 450 >> 12 >> 9.34 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.34 >> 3.86 >> 450 >> 12 >> 9.44 >> 3.87 >> 450 >> 12 >> 9.39 >> 3.86 >> 450 >> 12 >> 2065.98 >> 7.61 >> 886.92 >> 90 >> 9.45 >> 3.89 >> 450 >> 12 >> 9.41 >> 3.87 >> 450 >> 12 >> 9.41 >> 3.87 >> 450 >> 12 >> 9.42 >> 3.91 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.44 >> 3.86 >> 450 >> 12 >> 9.44 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.34 >> 3.86 >> 450 >> 12 >> 9.34 >> 3.86 >> 450 >> 12 >> 9.39 >> 3.86 >> 450 >> 12 >> 1900 >> 2.6 >> 900 >> 9 >> 1900 >> 2.6 >> 900 >> 9 >> 1900 >> 2.6 >> 900 >> 9 >> 9.41 >> 3.87 >> 450 >> 12 >> 9.41 >> 3.87 >> 450 >> 12 >> 9.41 >> 3.87 >> 450 >> 12 >> 1900 >> 2.6 >> 900 >> 9 >> 9.41 >> 3.87 >> 450 >> 12 >> 1900 >> 2.6 >> 900 >> 9 >> 1900 >> 2.6 >> 900 >> 9 >> >> Thank you in advance. >> >> -Mark >> >> >> >> >> >> 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<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. >> >> >> >>

2 3

hemispheric masks?
by John Richey 05 Aug '13

05 Aug '13

Dear freesurfer experts, I was wondering whether there is an existing mask for the left and right hemispheres for fsaverage. I can't seem to find any documentation of this, but perhaps I am missing something? Thanks in advance, John.

2 1

Fwd: TR,TE,TI,FA variability w/ mri_ca_train
by Mark Plantz 05 Aug '13

05 Aug '13

---------- Forwarded message ---------- From: Mark Plantz <markplantz2016(a)u.northwestern.edu> Date: Mon, Aug 5, 2013 at 11:32 AM Subject: Re: [Freesurfer] TR,TE,TI,FA variability w/ mri_ca_train To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> thank you. Would the command simply be something like this: mri_modify -tr 0 -te 0 -ti 0 -fa 0 <input.mgz> <output.mgz> ? On Thu, Aug 1, 2013 at 1:41 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Mark > > the formatting got messed up so I can't parse your table. You can get > around this using mri_modify, and just setting everything to 0. As for the > effects, look at the images and see what you think. > > cheers > Bruce > > > On Thu, 1 Aug 2013, Mark Plantz wrote: > > Hello freesurfers, >> I currently have a series of images with various TR,TE,TI,FA values. I >> would like to use mri_ca_train to create a .gca atlas based on these >> segmented volumes. Unfortunately, they all have slightly different control >> parameters (TR,TE,TI,FA). Is there any way around this problem, or would >> it >> be best to break the subjects into multiple groups with the same control >> parameters? >> >> Here are the various parameters: [each row is a subject] >> >> TR >> TE >> TI >> flip angle >> 9.38 >> 3.86 >> 450 >> 12 >> 9.34 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.34 >> 3.86 >> 450 >> 12 >> 9.44 >> 3.87 >> 450 >> 12 >> 9.39 >> 3.86 >> 450 >> 12 >> 2065.98 >> 7.61 >> 886.92 >> 90 >> 9.45 >> 3.89 >> 450 >> 12 >> 9.41 >> 3.87 >> 450 >> 12 >> 9.41 >> 3.87 >> 450 >> 12 >> 9.42 >> 3.91 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.44 >> 3.86 >> 450 >> 12 >> 9.44 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.34 >> 3.86 >> 450 >> 12 >> 9.34 >> 3.86 >> 450 >> 12 >> 9.39 >> 3.86 >> 450 >> 12 >> 1900 >> 2.6 >> 900 >> 9 >> 1900 >> 2.6 >> 900 >> 9 >> 1900 >> 2.6 >> 900 >> 9 >> 9.41 >> 3.87 >> 450 >> 12 >> 9.41 >> 3.87 >> 450 >> 12 >> 9.41 >> 3.87 >> 450 >> 12 >> 1900 >> 2.6 >> 900 >> 9 >> 9.41 >> 3.87 >> 450 >> 12 >> 1900 >> 2.6 >> 900 >> 9 >> 1900 >> 2.6 >> 900 >> 9 >> >> Thank you in advance. >> >> -Mark >> >> >> >> > > 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<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. >

1 0

Re: [Freesurfer] Trac-all question
by Anastasia Yendiki 05 Aug '13

05 Aug '13

Hi Alan - On the tutorial page you need to follow the directions under "If you are not at an organized course", and $TUTORIAL_DATA is whatever directory you have downloaded the tutorial data in. Please address questions to the list and not to me personally, as other people may have the same issue and this way the answers get archived. Thanks, a.y On Mon, 5 Aug 2013, Alan Francis wrote: > Hi Anastasia: > > Sorry about being a pest. One more question. I am running the Tutorial data > to get a better understanding of Tracula. When I type $TUTORIAL_DATA, it > keeps saying Undefined variable. Could you please help me. > > Thanks, > > Alan > > csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D > ATA/diffusion_recons] : setenv FREESURFER_HOME > /usr/local/freesurfer/stable5_3_0/ > csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D > ATA/diffusion_recons] : source $FREESURFER_HOME/Set > SetUpFreeSurfer.csh* SetUpFreeSurfer.sh* > csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D > ATA/diffusion_recons] : source $FREESURFER_HOME/SetUpFreeSurfer.csh > -------- freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer/stable5_3_0/ > FSFAST_HOME /usr/local/freesurfer/stable5_3_0//fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer/stable5_3_0//subjects > MNI_DIR /usr/local/freesurfer/stable5_3_0//mni > FSL_DIR /usr/pubsw/packages/fsl/current > csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D > ATA/diffusion_recons] : setenv SUBJECTS_DIR $TUTORIAL_DATA/d > $TUTORIAL_DATA/ not found > > csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D > ATA/diffusion_recons] : setenv SUBJECTS_DIR /autofs/space/d > dali_001/ dali_002/ dali_003/ > csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D > ATA/diffusion_recons] : setenv SUBJECTS_DIR/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_DA > TA/diffusion_recons/ > csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D > ATA/diffusion_recons] : gedit > $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial & > TUTORIAL_DATA: Undefined variable. > csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D > ATA/diffusion_recons] : gedit > /TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial & > [1] 32742 > csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D > ATA/diffusion_recons] : trac-all -prep -c > $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial > TUTORIAL_DATA: Undefined variable. > > > > On Fri, Aug 2, 2013 at 7:16 PM, Alan Francis <alandarkenergy(a)gmail.com> > wrote: > thanks again. > > > On Fri, Aug 2, 2013 at 3:51 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > It can have any name you want. You just have to type the > right name next to the "-c ..." > > On Fri, 2 Aug 2013, Alan Francis wrote: > > Sorry. I have another question. Should I name > the config file dmrirc.txt or > is there any other name? > thank you so much, > > Alan > > > On Fri, Aug 2, 2013 at 2:45 PM, Alan Francis > <alandarkenergy(a)gmail.com> > wrote: > Thanks Anastasia. > > > On Fri, Aug 2, 2013 at 2:26 PM, Anastasia > Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Alan - All the "set ..." commands for > tracula need to > be in a configuration file. You then > pass that > configuration file as an argument to the > "-c" option of > trac-all. See tutorial: > > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula > > Hope this helps, > a.y > > On Fri, 2 Aug 2013, Alan Francis wrote: > > Hi Anastasia and others: > I have been trying to run Trac all on > five brains. > It keeps giving me the > error message: > > ERROR: run list is longer than subject > list > > My run list is equal to the subject > list: Here is > the environment: > > Thanks for your help, > > Alan > Martinos Center for Biomedical Imaging > > > __________________________________________________________________ > > -------- > > freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 > -------- > > Setting up environment for > FreeSurfer/FS-FAST (and > FSL) > FREESURFER_HOME > /usr/local/freesurfer/stable5_3_0/ > FSFAST_HOME > > /usr/local/freesurfer/stable5_3_0//fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR > > /usr/local/freesurfer/stable5_3_0//subjects > MNI_DIR > /usr/local/freesurfer/stable5_3_0//mni > FSL_DIR > /usr/pubsw/packages/fsl/current > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : setenv SUBJECTS_DIR > /autofs/space/d > dali_001/ dali_002/ dali_003/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] :setenvSUBJECTS_DIR/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5. > 3_Data > /diffusion_r > econs/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set dtroot = /autofs/space/d > dali_001/ dali_002/ dali_003/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : setdtroot=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diff > usion_ > r > econs/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set subjlist = (101/ 102/ 103/ > 104/ 105/) > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set dcmroot = /autofs/space/d > dali_001/ dali_002/ dali_003/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : setdcmroot=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/dif > fusion_ > r > econs/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : setdcmlist=(101/Diffusion_Recons/20080424_182054563000-000012-000001DTIValeras > 012a001 > . > nii \ > ?102/Diffusion_Recons/20080911_101015358000-000010-000001DIFFUSIONHighResva > > l > erabi1002s010a001.nii \ > ?103/Diffusion_Recons/20080911_140753578000-000010-000001DIFFUSIONHighResva > > l > eraBI1003s010a001.nii \ > ?104/Diffusion_Recons/20080915_160812745000-000010-000001DIFFUSIONHighResVa > > l > eraBI104s010a001.nii \ > ?105/Diffusion_Recons/20080917_190940899000-000016-000001DIFFUSIONHighResVa > > l > eraBI105s016a001.nii \ > ? ) > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set runlist = (101/ 102/ 103/ 104/ > bem/ mri/ stats/ > > touch/ > Diffusion_Recons/ scripts/ surf/ > > trash/ > label/ src/ tmp/ > > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set runlist = (101/ 102/ 103/ 104/ > 105/) > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set bvecfile = > /autofs/space/dbvecs.txt > dali_001/ dali_002/ dali_003/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : setbvecfile=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/di > ffusion_ > r > econs/bvecs.txt > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : setbvalfile=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/di > ffusion_ > r > econs/bvals.txt > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set doeddy = 1 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set dorotbvecs = 1 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set usemaskanat = 1 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set thrbet = 0.3 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set doregflt = 0 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set doregbbr = 1 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set doregmni = 1 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set doregcvs = 0 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set mnitemp = > $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set cvstemp = cvs_avg35 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set cvstempdir = > $FREESURFER_HOME/subjects > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set pathlist = ( lh.cst_AS rh.cst_AS > \ > ? lh.ilf_AS rh.ilf_AS \ > ? lh.unc_AS rh.unc_AS \ > ? fmajor_PP fminor_PP \ > ? lh.atr_PP rh.atr_PP \ > ? lh.cab_PP rh.cab_PP \ > ? lh.ccg_PP rh.ccg_PP \ > ? lh.slfp_PP rh.slfp_PP \ > ? lh.slft_PP rh.slft_PP ) > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 > 4 4 5 5 5 > 5) > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : trac-all -prep -c /autofs/space/d > dali_001/ dali_002/ dali_003/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > > Data/diffusion_ > recons] : trac-all-prep-c/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diff > usion > _r > econs/ > > ERROR: run list is longer than subject list > > > > > > 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. > > > > > > > >

1 0

tksurfer problem - annotation of vertices
by Sinead Kelly 05 Aug '13

05 Aug '13

Dear freesurfer users, I am having a problem visualizing results using tksurfer using the following command: tksurfer fsaverage lh inflated -annot lh.MIR137_area.glmdir/MIR137_test/mc-z.abs.sig.ocn.annot -fthresh 2 -curv -gray & Please also see the terminal output stating that the vertices do not have an annotation. I do not have much experience with freesurfer - is there a way to resolve this? Thank you for your help! Sinead [kellys37@tcin-n01 Freesurfer_data]$ setting fthresh to 2.0000 subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /projects/pi-donoghug/HPC_11_00168/Freesurfer_data/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /projects/pi-donoghug/HPC_11_00168/Freesurfer_data checking for nofix files in 'inflated' Reading image info (/projects/pi-donoghug/HPC_11_00168/Freesurfer_data//fsaverage) Reading /projects/pi-donoghug/HPC_11_00168/Freesurfer_data//fsaverage/mri/orig.mgz surfer: Reading header info from /projects/pi-donoghug/HPC_11_00168/Freesurfer_data//fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 surfer: curvature read: min=-0.673989 max=0.540227 reading colortable from annotation file... colortable with 12 entries read (originally none) Found embedded color table in annotation. 149719 vertices did not have an annotation! surfer: single buffered window surfer: tkoInitWindow(fsaverage) surfer: using interface /home/support/tcin/apps/freesurfer/5.2.0/tktools/tksurfer.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/tktools/tkm_common.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/tktools/tkm_wrappers.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/lib/tcl/fsgdfPlot.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

2 1

issues with registering MNI 152 to fsaverage on the right hemisphere
by Yune Lee 04 Aug '13

04 Aug '13

Hello freesurfer users -- I noticed an issue with registering MNI template to freesurfer surface, whereby a cluster located on the right hemisphere does not appear at all in the fsaverage rh.inflated template while the left cluster was clearly seen. [image: Inline image 1] The map was generated in SPM8, which indeed does not use MNI152 template. However, as far as I'm concerned, it should be more or less similar to MNI 152 template, so I can rule out the possibility of using a different template image instead of MNI152. Any way, I'd be grateful if you guys let me know any thoughts on this issue. -ysl fyi) below is the command line that I used. ----------- #for LH mri_vol2surf --mov rad4_regions.img --reg /usr/local/freesurfer/centos4_x86_64-stable-pub-v5.1.0/average/mni152.register.dat --trgsubject fsaverage --hemi lh --projfrac 0.5 --o rad4_lh.mgh #for RH mri_vol2surf --mov rad4_regions.img --reg /usr/local/freesurfer/centos4_x86_64-stable-pub-v5.1.0/average/mni152.register.dat --trgsubject fsaverage --hemi rh --projfrac 0.5 --o rad4_rh.mgh

3 2

Statistical concerns
by stdp82＠virgilio.it 04 Aug '13

04 Aug '13

Hi list,I have some questions please. 1- I have carried out Monte Carlo Simulation to assess the difference among three groups (23, 24 and 32 subjects). Main results were confirmed also by FDR, but I prefer to shown the Monte Carlo becouse it better describes my thesis.Recently I have submitted my paper but a referee asked me "Why use cluster based Monte Carlo methods for correction of multiple comparisons instead of the more conventional vertex-wise FDR correction? I suspect the former is much less conservative than the latter. It would be interesting to know the results for FDR corrected thresholds (p<0.05), and whether the present results would remain statistically 'active'.Now, I'm looking literature and I'm noting that several recent articles published on top journals used Monte Carlo Simulation (Ehrlich et al., 2013 Schizophr Bull.; Sasamoto et al., 2013 Schizophr Bull).What do you think about it? How do you advise to reply to the referee? I'd like to show Monte Carlo results. 2- I should do also correlation analysis. I'm using QDEC as recommanded in guideliness (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freev…) In one group, after fsgd creation, I'm performing correlation analysis between thickness and neuropsychiatric test scores (it has been put in covariete windows-it should be dipendent factor). I'm also putting some nuisance factors (they should be dipendent factor in the regression analysis) to exclude the their effect on data.a- Is this procedure corrected?b- Is corrected to talk regression analysis in the text of my manuscript? c- Is corrected whether I explain this correlation analysis as reported in the description performed above? Thank you very much, Stefano

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Re: [Freesurfer] GLM Analysis: ROI (--label)
by Rachel Jonas 04 Aug '13

04 Aug '13

Hi Doug, Thanks for the response. Here is my glmfit command: mri_glmfit \ --y lh.22q_age.thickness.10.mgh \ --fsgd 22q_age.fsgd dods\ --C 22q_age_2.mtx \ --surf fsaverage lh \ --label lh.orbitofrontal.label --cortex \ --glmdir lh.22q_age_OFC.glmdir And here is the error message: gdfReadHeader: reading 22q_age.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 12.7292 Class Means of each Continuous Variable 1 HC 12.8261 2 22Q 12.6400 INFO: gd2mtx_method is dods Reading source surface /u/home/FMRI/cbearden/data/22q/Analyses/sMRI/fsaverage/surf/lh.white ERROR: must specify GLM output dir [racheljo@login3 sMRI]$ --cortex \ ? --glmdir lh.22q_age_OFC.glmdir --cortex: Command not found. Thanks! Rachel

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identify the centroid of a volume
by John Richey 04 Aug '13

04 Aug '13

Dear freesurfer experts: I have a few MNI labels, and I need to identify the centroid of the volume in MNI coordinate space. These are binary files in compressed nifti format. At first, i thought could use mri_volcluster, and simply set the minimum to 0.01, which would capture the remaining voxels and then compute a centroid. However, this seems not to be the case. The coordinates refer only to the edge of the volume which is not correct. Has anyone done this before? Thanks in advance, John

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