Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

is there a flag for updating recon-all output from 5.0 to 5.3?
by Ruth Carper 18 Oct '13

18 Oct '13

I have about 100 subjects that have been run on 5.0 and I'd like to update them to 5.3. Is there a flag for recon-all that just runs the steps that would be affected by the version change? I seem to recall seeing a flag on the wiki but can't find it now. Maybe it was just for small patches? Thanks.

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Re: [Freesurfer] medial wall crossing the surface
by silver47＠gmx.com 18 Oct '13

18 Oct '13

Not always, but yes, in some instances the aseg crosses. > ----- Original Message ----- > From: Bruce Fischl > Sent: 10/18/13 01:22 PM > To: silver47(a)gmx.com > Subject: Re: [Freesurfer] medial wall crossing the surface > > Does the aseg cross as well? > > > > On Oct 17, 2013, at 10:07 PM, "silver47(a)gmx.com" <silver47(a)gmx.com> wrote: > > > Dear All, > > > > I too am seeing the medial pial surfaces crossing hemispheres in some subjects. > > > > The approach that appears to be working for me involves making copies of brainmask.mgz and aseg.mgz > > For the left hemisphere crossing into the right, edit brainmask.mgz and aseg.mgz to delete voxels at the crossing belonging to the right hemisphere. > > I then run recon-all -autorecon-pial -hemi lh -subjid subject > > followed by returning the brainmask.mgz and aseg.mgz back to their original copy. > > > > This is similarly repeated for the right hemisphere crossing into the left. > > > > Are there any issues or concerns with this approach particularly in regard to thickness or the segmentations? > > > > Thanks, > > > > Paul > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > 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.

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Comparison between fsaverage and a template created from scratch
by Sophie Maingault 18 Oct '13

18 Oct '13

Hello Experts, I did the procedure to create a template from scratch by following the steps explaining in this page : http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates The objective was to create a template to use it in the command recon-all qcache target my template. So, after creating mytemp2.tif I did mris_register for the subjects used for the template (80 subjects) and then I used make_average_subject --subjects <80 subjects> --out mytemplate. Finally I ran recon-all -qcache target mytemplate in order to visualize my analyzes in QDEC. This procedure seems correct to you because when I just visually compared your template (fsaverage) with mine it looks like very different, as if mine was more smoothed (cf ppt file) ? What do you think ? Best regards. Sophie Maingault

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FS-FAST between-conditions analysis
by Susan Ruiz 18 Oct '13

18 Oct '13

Hi all, When running a functional analysis and comparing two experimental conditions, we observed that there are some voxels/vertices where both condition A and condition B have a positive % signal change from baseline, and condition A has greater activity than condition B. In other regions, both condition A and condition B have negative % signal change from baseline, but condition B has a greater absolute value % signal change (thus relative to baseline condition B has more "deactivation"--a term I am using since you all know what I mean even if the term itself is imperfect). Since, in both cases, the % signal change is technically condition A > condition B, the between-conditions maps do not distinguish these two scenarios. FS-FAST sees these as being the same. Is there a way to tell FS-FAST to cluster these scenarios separately? Is there a compelling reason why I should not consider these different situations? It seems to me that the interpretation of what's taking place in these two scenarios is not identical. Agree or disagree? Can FS-FAST distinguish these with a flag I don't know about? Thank you, ~Sue -- * * ** *** ***** ******** ************* Susan Mosher Ruiz, Ph.D. Research Scientist Boston University School of Medicine Laboratory of Neuropsychology VA Boston Healthcare System smosher(a)bu.edu * * ** *** ***** ******** *************

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medial wall crossing the surface
by silver47＠gmx.com 17 Oct '13

17 Oct '13

Dear All, I too am seeing the medial pial surfaces crossing hemispheres in some subjects. The approach that appears to be working for me involves making copies of brainmask.mgz and aseg.mgz For the left hemisphere crossing into the right, edit brainmask.mgz and aseg.mgz to delete voxels at the crossing belonging to the right hemisphere. I then run recon-all -autorecon-pial -hemi lh -subjid subject followed by returning the brainmask.mgz and aseg.mgz back to their original copy. This is similarly repeated for the right hemisphere crossing into the left. Are there any issues or concerns with this approach particularly in regard to thickness or the segmentations? Thanks, Paul

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aparcstats2table error
by Corinna Bauer 17 Oct '13

17 Oct '13

Hi; I want to put cortical thickness in a table format and am getting an error. command: aparcstats2table --subjectsfile symmetry_subjects.txt --hemi lh --meas thickness --tablefile symm_aparc_stats_rh.txt error: ERROR: The stats file /media/working_tb_drive/symmetry/MMT_08292013/stats/lh.aparc.stats is not found or is too small to be a valid statsfile The statsfile is there and is not empty. Subject names are all in this format ABC_12345678 Any suggestions? Thanks Corinna

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mri_fill failure in macaque
by Soyoung Park 17 Oct '13

17 Oct '13

Dear FreeSurfer experts, I'm attempting to make cortical surfaces for a macaque brain, and am having trouble getting mri_fill to work. The command has worked without any errors for a different macaque dataset in the past, and I can't seem to figure out why it isn't working this time. I am using v. 5.3 for Mac Snow Leopard, and I used the command (I have confirmed on tkmedit that the CC and pons seed coordinates are correct): *mri_fill -CV 125 119 147 -PV 125 103 65 wm.mgz fill.mgz* The log from running the command is as follows: -------------------------------------------------------------------------------------------------------- using voxel position (125, 119, 147) as corpus callosum seed point using voxel position (125, 103, 65) as pons seed point reading input volume...done. searching for cutting planes...INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Calculated talairach cc position (125.00, 119.00, 147.00) Using the seed to calculate the cutting plane find_cutting_plane:seed point not in structure! Searching neighborhood... Looking for area (min, max) = (350, 1400) area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75) need search nearby using seed (125, 119, 147), TAL = (125.0, 119.0, 147.0) talairach voxel to voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; talairach cc position changed to (125.00, 119.00, 147.00) Using voxel pons seed point, calculated talairach pons position (125.00, 103.00, 65.00) find_cutting_plane:seed point not in structure! Searching neighborhood... Looking for area (min, max) = (350, 790) area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20) need search nearby using seed (125, 103, 65), TAL = (125.0, 103.0, 65.0) talairach voxel to voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(143.00, 119.00, 147.00) SRC: (143.00, 119.00, 147.00) could not find rh seed point around (143, 119, 147) ------------------------------------------------------------------------------------------------------------ Any help with this would be greatly appreciated. Best, Soyoung

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inferior horn of lateral ventricle
by Nawaf Yassi 17 Oct '13

17 Oct '13

Hi I would like to ask a question about the segmentation of the inferior horn of the lateral ventricle using freesurfer. I have noticed that the inferior horn is usually not filled in the wm.mgz file and excluded from the surface reconstruction (as demonstrated in the attachment). However, it is correctly labelled in the aseg file. Will I need to correct the wm.mgz manually and rerun recon-all or is this expected? Regards Nawaf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

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Re: [Freesurfer] Tracula configuration error
by Anastasia Yendiki 17 Oct '13

17 Oct '13

Hi Mike - Good to know. This would make perfect sense b/c in 5.1 trac-all required a variable to be defined that isn't used any more in 5.3. a.y On Tue, 15 Oct 2013, Michael Datko wrote: > Hi Anastasia,I updated freesurfer from 5.1 to 5.3 and that fixed the > problem! Thanks for taking a look at my file. > > Mike > > > > On Tue, Oct 15, 2013 at 1:49 PM, Michael Datko <mikedatko(a)gmail.com> wrote: > I tried making the subjects directory line in the configuration > file point to somewhere that didn't actually exist. I got the > same error as you, where it says that SUBJECTS_DIR doesn't > exist. Then I changed it to point to the real folder, and I am > back at the "set: variable name must begin with a letter" error. > I have now tried this on two different computers with similar > but not identical setups, and get the same error. I am using > freesurfer 5.1 now, but the original data was processed with > version 5.0, if that makes a difference. > Mike > > > > On Mon, Oct 14, 2013 at 6:04 PM, Michael Datko <mikedatko(a)gmail.com> > wrote: > Very strange...I'm running this on a 2009 macbook pro, > with OSX 10.6.8 (Snow Leopard). I've never had this sort > of problem with command-line programs like AFNI or > freesurfer. > > > On Mon, Oct 14, 2013 at 2:37 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Michael - It doesn't look like the configuration > file is the problem, or at least I cannot replicate > it. I ran "trac-all -c dmrirc.txt -prep" on a mac > and a linux machine and the only error I got was > that the SUBJECTS_DIR doesn't exist (as expected > since I don't have your directory structure). What > system are you running this on? > > a.y > > On Mon, 14 Oct 2013, Michael Datko wrote: > > Hi Anastasia,No log files were created, > it seems like the program does not even > begin to run. I get that > error immediately upon calling trac-all. > I pasted the entire configuration file > into the original > message, but I attach it here as well. > > Thanks, > Mike > > > > > On Mon, Oct 14, 2013 at 1:55 PM, > Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Michael - It's hard to tell at > which point it fails. Is there any > output, is there a > trac-all.log? If so, can you > please attach the entire file, as well > as the entire > configuration file? > > Thanks, > a.y > > On Sat, 12 Oct 2013, Michael Datko > wrote: > > Hello,I have been trying to > set up a working Tracula configuration > file and I keep > getting an error: > > set: Variable name must > begin with a letter > I have searched previous > message board questions and it seems > that others have > seen this same error. I > have tried implementing some > of their solutions, as well as searching > my code for > a problem, but I cannot > find the source. Any > advice? I am trying to get this working > for a single > subject for now. I used the > dmrirc.example file as a > template. I am calling trac-all from > the tcsh command > line with the following: > trac-all -c dmrirc.example > -prep > > The contents of my dmrirc > file are below, I have deleted most of > the options for > which I am just using the > default, to make things > simpler. > > Thank you, > Mike > > # FreeSurfer SUBJECTS_DIR > # T1 images and FreeSurfer > segmentations are expected to be found > here > # > setenv SUBJECTS_DIR > /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer > > # Output directory where > trac-all results will be saved > # Default: Same as > SUBJECTS_DIR > # > set dtroot = > /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer > > # Subject IDs > # > set subjlist = (a226A) > > # In case you want to > analyze only Huey and Louie > # Default: Run analysis on > all subjects > # > set runlist = (1) > > # Input diffusion DICOMs > (file names relative to dcmroot) > # If original DICOMs don't > exist, these can be in other image > format > # but then bvecfile and > bvalfile must be specified (see below) > # > set dcmroot = > /Users/mdatko/Desktop/tracula_tutorial/data/dti > set dcmlist = > (a226A/226A/data.nii.gz) > > # Diffusion gradient table > # Must be specified if > inputs are not MGH DICOMs > # Three-column format, one > row for each volume in the diffusion > data set > # Default: Read from DICOM > header > # > set bvecfile = > > /Users/mdatko/Desktop/tracula_tutorial/data/dti/a226A/226A/bvecs.txt > > # Diffusion b-value table > # Must be specified if > inputs are not MGH DICOMs > # Single-column format, one > value for each volume in the diffusion > data set > # Default: Read from DICOM > header > # > set bvalfile = > > /Users/mdatko/Desktop/tracula_tutorial/data/dti/a226A/226A/bvals.txt > > # Perform registration-based > eddy-current compensation? > # Default: 1 (yes) > # > set doeddy = 0 > > # Perform diffusion-to-T1 > registration by bbregister? > # Default: 1 (yes) > # > set doregbbr = 1 > > # Perform registration of T1 > to MNI template? > # Default: 1 (yes) > # > set doregmni = 1 > > # Use brain mask extracted > from T1 image instead of low-b diffusion > image? > # Has no effect if there is > no T1 data > # Default: 1 (yes) > # > set usemaskanat = 1 > > # Paths to reconstruct > # Default: All paths in the > atlas > # > set pathlist = ( lh.cst_AS > rh.cst_AS \ > lh.unc_AS > rh.unc_AS \ > lh.ilf_AS > rh.ilf_AS \ > fmajor_PP > fminor_PP \ > lh.atr_PP > rh.atr_PP \ > lh.ccg_PP > rh.ccg_PP \ > lh.cab_PP > rh.cab_PP \ > lh.slfp_PP > rh.slfp_PP \ > lh.slft_PP > rh.slft_PP ) > > # Number of path control > points > # It can be a single number > for all paths or a different number for > each of the > # paths specified in > pathlist > # Default: 7 for the forceps > major, 6 for the corticospinal tract, > # 4 for the angular > bundle, and 5 for all other paths > # > set ncpts = ( 6 6 5 5 5 5 7 > 5 5 5 5 5 4 4 5 5 5 5 ) > > # List of training subjects > # This text file lists the > locations of training subject > directories > # Default: > $FREESURFER_HOME/trctrain/trainlist.txt > # > set trainfile = > $FREESURFER_HOME/trctrain/trainlist.txt > > # Number of "sticks" > (anisotropic diffusion compartments) in > the bedpostx > # ball-and-stick model > # Default: 2 > # > set nstick = 2 > > # Number of MCMC burn-in > iterations > # (Path samples drawn > initially by MCMC algorithm and > discarded) > # Default: 200 > # > set nburnin = 200 > > # Number of MCMC iterations > # (Path samples drawn by > MCMC algorithm and used to estimate path > distribution) > # Default: 7500 > # > set nsample = 7500 > > # Frequency with which MCMC > path samples are retained for path > distribution > # Default: 5 (keep every 5th > sample) > # > set nkeep = 5 > > > > > > 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. > > > > > > > >

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mri_binarize to mask and include only positively activated voxels
by Maya Rosen 17 Oct '13

17 Oct '13

Hi Doug/freesurfers, I am now trying to make a mask that includes only positively activated voxels for one conditon versus passive viewing (ConditionAvspassive). Using the inputs that you suggested, I ran the following command: mri_binarize --i ./output_23subjects/fsavg_lh_sm3_nopace_exoltm/ConditionAvpassive/ces.nii.gz --o ./output_23subjects/fsavg_lh_sm3_nopace_exoltm/ConditionAvpassive_mask.ces.nii.gz --mask-thresh 0.00001 --min 0.00001 So my understanding of what this should be doing is making a mask that only includes positively activated voxels compared to passive viewing. However, if you see the attached images of both the mask that this command creates, and the activation maps of ConditionAvpassive (set at a very low threshold for visualization purposes), you can see that there are several regions that are included in the mask that are in fact deactivated compared to passive viewing. Is there something wrong with the command that I'm running that is causing this to happen? Thank you for any insight! Maya

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