Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

specifying random effects in LME (Linear Mixed Effects models)
by Lalonde, Francois (NIH/NIMH) [E] 29 Mar '13

29 Mar '13

I am following the wiki page for LME analysis and I have a quick question. The Mass-univariate example near the bottom of the page proposes an initial model that contains intercept, linear and quadratic terms as random effects. However, the examples just below for lme_mass_fit_EM_init(), lme_mass_fit_EM_Rgw() only have [1 2] as selected random effects. Should the vector Zcols contain [1 2 3] as selected random effects in order to test the proposed model? Thanks, Francois François Lalonde, Ph.D. Child Psychiatry Branch NIMH / NIH 10 Center Drive, Room 3N202 Bethesda, MD 20892

2 5

Set up data for longitudinal processing
by Lukas.Scheef＠ukb.uni-bonn.de 29 Mar '13

29 Mar '13

Hi folks, sorry it's me again with a very basic question. What is the best way to import longitudinal data? recon-all -i /path/T1A.nii -i /path/T1B.nii FIRSTSUBJECT or recon-all -i /path/T1A.nii FIRSTSUBJECT_A recon-all -i /path/T1A.nii FIRSTSUBJECT_B I tend to use the second choice because otherwise I would have no idea how to distinguish between SUBJECT-ID and TimepointID later on in the processing stream. Best whises, Luke

3 2

FS5.2: selxavg3-sess error
by tapsya＠nmr.mgh.harvard.edu 29 Mar '13

29 Mar '13

Dear Doug, I am trying to analyze fMRI data where TR = 1.2 secs. For several subjects the analysis works as expected, but for about half of the subjects when I try to execute the command selxavg3-sess terminates with the following error: "OLS Beta Pass run 1 t= 0.0 ERROR: TR mismatch between analysis and data analysis TR = 1.2, data TR = 1.56" I checked the *nii header information and all indicate TR = 1.2 sec. I am not sure why I get the error. Please advise. Thanks! Wishes, Tapsya FS-FAST version: 5.2 Machine: adapt

1 0

slice timing
by Meryem Ayse Yucel 29 Mar '13

29 Mar '13

Hi, I am running a pASL sequence with a TR = 3 sec and TI2 = 1.8. I am wondering when I do slice time correction does that move all slices to the mid of TR that is 1.5 s prior in time or, it moves them to the timing of the mid slice, which would be the mid of image acquisition aorund 0.6 sec prior in time with respect to the end of TR. Thank you, Meryem

3 2

Use a SPM roi to extract thickness measurements
by McMains, Stephanie 29 Mar '13

29 Mar '13

Hi all, I have been trying to take an SPM volume and extract FS thickness measurements. I think I successfully took my spm volume from mni152 to fsaverage space (mni305) via the command line: mri_vol2vol --mov $FREESURFER_HOME/subjects/fsaverage/mri.2mm/mni305.cor.mgz --targ RTPJ_9mm_001_10_64_-54_16.img --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --inv --o $SUBJECTS_DIR/2506/mri/RTPJ_mni305_9mm_001_10_64_-54_16.nii.gz Then I turned it into an ROI: mri_binarize --i $SUBJECTS_DIR/2506/mri/RTPJ_mni305_9mm_001_10_64_-54_16.nii.gz --o $SUBJECTS_DIR/2506/mri/RTPJ_mni305_roi_9mm_001_10_64_-54_16.nii.gz --min .0000000001 > From here I figured I could map it to the fsaverage surface (mri_vol2surf) and extract thickness measurements (mri_segstats using rh.thickness.fsaverage.mgh) as suggested in the volume roi cortical thickness workflow. However, some of my ROIs don't show up after I transform them. From what I can tell, this is because they don't intersect with the fsaverage surface. My thinking was that it might be better to stay within the individual subject space. So I would: 1. transform ROI to subject space 2. extract thickness values from rh.thickness However, I am struggling to get the roi into single subject space. I feel like this transform (or the inverse of it) should exist because I put all my subjects into fsaverage space via the -qcache flag, but i couldn't tell what to use. So I tried: fslregister --s 2506 --mov $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --reg $SUBJECTS_DIR/2506/fsaverage_to_indiv.dat But the registration doesn't look all that good. I am not sure if this is because the fsaverage is 'smoothed' or what. And then I am at a loss for how to put my roi into individual space and then extract thickness, or even if this is the right approach. Thanks, Stephanie

2 1

FS version of Colin27
by ZhiLiangLong 29 Mar '13

29 Mar '13

Hi FS experts: I am trying to map AAL template onto FS surface to create surface-based AAL template. Several days ago, i asked this question, and Garikoitz Lerma gave me some suggestions. Possibly, i think the process is like as folllows: 1. downloa the Colin27 subject in Surfrend page, and transform it to the latest FS version (5.2 currently). 2. obtain register.dat between Colin27 subject and single_subj_T1.nii under the canonical directory in SPM8 using bbregister. bbregister --s Colin27_subject --mov single_subj_T1.nii --reg register.dat --init-fsl --t1 3. transfrom each AAL ROI to the surface file with register.dat file obtained above using mri_vol2surf. mri_vol2surf --mov AAL_ROI.nii --reg register.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh \ --out lh.Colin27_AALROI.mgh --reshape 4. use mri_label2label or mri_segstat to obtain the cortical thickness of each ROI for individual subject. My question is about the first step. How to transform the Colin27 subject to FS version 5.2? that is to say how can i get the FS version of Colin27 template instead of fsaverage template? Hope someone gives me some suggetions. Besh wishes.

2 1

selxavg3-sess problem with -per-run flag
by SHAHIN NASR 29 Mar '13

29 Mar '13

Hi, I used to run my mkanalysis-sess without indicating -per-run or -per-session, assuming that when I have pre-processed my files with -per-run flag then selxavg3-sess will do the same. But when I checked the analysis.info I noticed "PerSession 1" which I think it means system will use per-session preprocessing. So, this time I explicitly used -per-run in my mkanalysis-sess as below: preproc-sess -s <SubjId> -per-run -fwhm 5 -fsd bold -fwhm 5 -surf self rhlh mkanalysis-sess -analysis Reward.rh -surface self rh -native -fwhm 5 -paradigm Conds.par -event-related -polyfit 2 -gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 7 -refeventdur .10 -fsd bold -per-run -force This time when I ran selxavg3-sess command I faced this error: ERROR: cannot determine format of /autofs/cluster/tootell/pitcairn/1/shahin/Reward/Subjects/limi1/bold/004/fmcpr.sm5 (MRIread) Error in flac_customize (line 87) mri = MRIread(fstem,1); Error in fast_selxavg3 (line 65) flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n As I checked my subjects directory I had these files in /bold/004/ directory: fmcpr.nii.gz fmcpr.sm5.self.rh.nii.gz fmcpr.sm5.self.lh.nii.gz Notably, if I drop that -per-run flag from my mkanalysis-sess then system works without any problem. But then I am not sure whether I have processed my data in per-run or per-session mode. Any help will be appreciated Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Re: [Freesurfer] bbr problem run
by Anastasia Yendiki 29 Mar '13

29 Mar '13

Hi Sal - Would it be possible for you to run the bbregister command that fails (you can find the command line in trac-all.log) using both the 5.1 and 5.2 version of bbregister and see if one of them works on your system? a.y On Fri, 29 Mar 2013, Salil Soman wrote: > Hi Anastasia, > > Because I did not have a compatible older version of fsl on the SGE, I was not able to > run tracula with 5.1. > > Thank you, > > Sal > > > On Fri, Mar 29, 2013 at 8:32 AM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > wrote: > > Hi Sal - Had you ever tried running this in 5.1? Just trying to figure out > if it's 5.2-specific. > > Thanks, > a.y > > On Thu, 28 Mar 2013, Salil Soman wrote: > > Thank you for your response. > I tried re-running Tracula using bbr in a subject I had > successfully run using flt. > trac-all prep and bedp worked without an error. Bedpostx sent > me an email confirming > bedpost completed without problem. However, when I try to run > trac-all paths, I get > the following error: > > Loading atlas reference volumefrom/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr > _end > 1_dil.nii.$ > niiRead(): error openingfile/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr > _end > 1_dil.nii.gz > ERROR: Could notread/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr > _end > 1_dil.nii.gz > > recon-all did finish without error. > > Best wishes, > > -S > > > On Thu, Mar 28, 2013 at 8:43 AM, Anastasia > Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Sal, > > 1. I have no experience with the sun grid engine, > perhaps someone else on > the list can help with that. > > 2. The -bedp step needs the outputs from the -corr and > -masks steps. The > -path step needs the outputs from the -bedp step. The > output files from > each part are listed here: > > http://www.freesurfer.net/fswiki/trac-all#Outputdirectoriesandfiles > > 3. Checking the aparc+aseg should be enough for tracula > purposes as well, > since that's the freesurfer output that tracula uses. > Keep in mind that > DWI resolution is usually lower than T1 resolution, > so tiny changes in > the aparc+aseg might not affect tracula at all. > > 4. Yes, I do recommend using bbregister. It's not > surprising that it would > give better results since it uses the additional > information of the > surfaces. If I remember correctly, Doug didn't manage > to replicate your > bbregister error, right? I'd check if you get the > same error with the > 5.1 version of bbregister. > > Hope this helps, > a.y > > On Wed, 27 Mar 2013, Salil Soman wrote: > > Hi, > I have been able to implement FS 5.2 on our Sun > Grid Engine > Cluster using the CentOS 6 > distribution. After modifying the fsl_sub_mgh file > to work > with out cluster queue > names and to modify the email notifications, I am > able to run > the entire processing > pipeline using FLT. (Everytime I try bbr I get > errors. I had > email doug about this but > have not heard any response). > > I am submitting the jobs to the cluster as follows > > recon-all -i ./*.nii -s WCA_0202_T1_FS > -nuintensitycor-3T > -nocanorm -openmp 50 > -hippo-subfields -all > trac-all -prep -no-isrunning -c > /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc > trac-all -bedp -no-isrunning -c > /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc > trac-all -path -no-isrunning -c > > /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc > > There are a few issues I am trying to sort out: > > 1) how should one conifigure the openmp flag for > the Sun Grid > Engine? the flag I used > did not change processing time, and each subject > is still > taking ~24 hrs? > > 2) once the script starts bedpost, bedpost has > controller code > which paralelizes all > of the slices (which has been great going from 12 > hrs of > processing to 1.5 hrs). > However, my original script goes on to execute > trace-all -path > ... before bepost is > done, generating errors. I have gotten around this > by running > the trace-all -path > command again after bedpost sends me an email > confirming > completion. Is there a way to > more cleanly do this (some kind of hold command I > can do based > on output from > bedpost)? > > 3) In your experience, how important is quality > control of > freesurfer on tracula > results? We have come to the compromise for > freesurfer output > to manually check the > segmentation of aparc+aseg.mgz using free view, > only > correcting and rerunning steps of > freesurfer when there are specific structures we > want the > volumes of (eg hippocampus). > > 4) have you found a significant benefit of bbr > over flt? If > so, any suggestions on > things I may need to check to get bbr to work > (given flt > works)? > > Best wishes, > > Sal > > > > > > > > > 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. > > > > > >

2 1

mris_preproc with --xhemi
by Ejoe Yizhou Ma 29 Mar '13

29 Mar '13

Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the "--xhemi" flag do in the "mris_preproc" command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for "--paired-diff", and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry

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Re: [Freesurfer] bbr problem run
by Salil Soman 29 Mar '13

29 Mar '13

Thank you for your response. I tried re-running Tracula using bbr in a subject I had successfully run using flt. trac-all prep and bedp worked without an error. Bedpostx sent me an email confirming bedpost completed without problem. However, when I try to run trac-all paths, I get the following error: Loading atlas reference volume from /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.$ niiRead(): error opening file /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz ERROR: Could not read /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz recon-all did finish without error. Best wishes, -S On Thu, Mar 28, 2013 at 8:43 AM, Anastasia Yendiki < ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Sal, > > 1. I have no experience with the sun grid engine, perhaps someone else on > the list can help with that. > > 2. The -bedp step needs the outputs from the -corr and -masks steps. The > -path step needs the outputs from the -bedp step. The output files from > each part are listed here: > http://www.freesurfer.net/**fswiki/trac-all#**Outputdirectoriesandfiles<http://www.freesurfer.net/fswiki/trac-all#Outputdirectoriesandfiles> > > 3. Checking the aparc+aseg should be enough for tracula purposes as well, > since that's the freesurfer output that tracula uses. Keep in mind that > DWI resolution is usually lower than T1 resolution, so tiny changes in > the aparc+aseg might not affect tracula at all. > > 4. Yes, I do recommend using bbregister. It's not surprising that it would > give better results since it uses the additional information of the > surfaces. If I remember correctly, Doug didn't manage to replicate your > bbregister error, right? I'd check if you get the same error with the > 5.1 version of bbregister. > > Hope this helps, > a.y > > > On Wed, 27 Mar 2013, Salil Soman wrote: > > Hi, >> I have been able to implement FS 5.2 on our Sun Grid Engine Cluster using >> the CentOS 6 >> distribution. After modifying the fsl_sub_mgh file to work with out >> cluster queue >> names and to modify the email notifications, I am able to run the entire >> processing >> pipeline using FLT. (Everytime I try bbr I get errors. I had email doug >> about this but >> have not heard any response). >> >> I am submitting the jobs to the cluster as follows >> >> recon-all -i ./*.nii -s WCA_0202_T1_FS -nuintensitycor-3T -nocanorm >> -openmp 50 >> -hippo-subfields -all >> trac-all -prep -no-isrunning -c /mnt/glusterfs/salsoman/SRC/** >> WCA_0202_T1/DTI/dmrirc >> trac-all -bedp -no-isrunning -c /mnt/glusterfs/salsoman/SRC/** >> WCA_0202_T1/DTI/dmrirc >> trac-all -path -no-isrunning -c /mnt/glusterfs/salsoman/SRC/** >> WCA_0202_T1/DTI/dmrirc >> >> There are a few issues I am trying to sort out: >> >> 1) how should one conifigure the openmp flag for the Sun Grid Engine? the >> flag I used >> did not change processing time, and each subject is still taking ~24 hrs? >> >> 2) once the script starts bedpost, bedpost has controller code which >> paralelizes all >> of the slices (which has been great going from 12 hrs of processing to >> 1.5 hrs). >> However, my original script goes on to execute trace-all -path ... before >> bepost is >> done, generating errors. I have gotten around this by running the >> trace-all -path >> command again after bedpost sends me an email confirming completion. Is >> there a way to >> more cleanly do this (some kind of hold command I can do based on output >> from >> bedpost)? >> >> 3) In your experience, how important is quality control of freesurfer on >> tracula >> results? We have come to the compromise for freesurfer output to manually >> check the >> segmentation of aparc+aseg.mgz using free view, only correcting and >> rerunning steps of >> freesurfer when there are specific structures we want the volumes of (eg >> hippocampus). >> >> 4) have you found a significant benefit of bbr over flt? If so, any >> suggestions on >> things I may need to check to get bbr to work (given flt works)? >> >> Best wishes, >> >> Sal >> >> >> >> >> >> >> > > 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. >

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Freesurfer March 2013