Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30087 discussions

Re: [Freesurfer] Pial surface area
by Anita van Loenhoud 21 Mar '14

21 Mar '14

Hi Bruce, The wm.mgz was created a while ago with an older version, by another student. At the moment I use v5.3.0. Should I recreate wm.mgz with this more recent version, or is there another option? Thank you, Anita

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mri_convert .tar.gz files of dicoms?
by Nate Vack 21 Mar '14

21 Mar '14

Hi, I'm testing mri_convert for our dicom conversion needs; one thing that would be fantastic is to be able to feed it a .tar.gz (or .zip) containing a dicom series we'd like to convert. Is there a way to do that? Alternately, if there were a way to make it use stdin, I could just pipe the output of tar to it. Thanks! -Nate

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Re: [Freesurfer] Pial surface area
by Anita van Loenhoud 21 Mar '14

21 Mar '14

Hi Bruce, See below. Thank you! Anita First I tried: *aloenhoud@somerenserver:/data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050$ *mris_anatomical_stats -mgz -f stats/lh.aparc.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab 0050 lh pial INFO: assuming MGZ format for volumes. computing statistics for each annotation in label/lh.aparc.annot. reading volume /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/mri/wm.mgz... znzTAGskip: tag=1818326118, failed to calloc 541878272 bytes! Cannot allocate memory Then I tried the following: *aloenhoud@somerenserver:/data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050$*recon-all -autorecon3 -subjid 0050 mris_anatomical_stats -mgz -f stats/lh.aparc.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab 0050 lh pial ERROR: Flag mris_anatomical_stats unrecognized. -autorecon3 -subjid 0050 mris_anatomical_stats -mgz -f stats/lh.aparc.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab 0050 lh pial Linux somerenserver.herseninstituut.knaw.nl 2.6.32-431.5.1.el6.x86_64 #1 SMP Wed Feb 12 00:41:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 0050 exited with ERRORS at Fri Mar 21 14:49:53 CET 2014

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combine FEAT data with inflated ANATOMY to measure distances
by Milde, Christopher 21 Mar '14

21 Mar '14

Dear Surfers, At moment I'm dealing with a huge dataset, preprocessed (with and without smoothing) and statistically analyzed in FSL FEAT. I used the reg-feat2anat to project functional EPI on inflated MPRAGE (recon-all). Because I'm interested in measuring Euclidian distances between peak voxels, I want to project FEAT EPI-data on cortical flat maps (mris_flatten) or spherical surfaces. è Is it possible to project FEAT-data on flat_maps? è Does mris_pmake* works equally fine on different projections of the EPI to ANATOMY (sphere, flat map) to measure peak/vertex distances? *https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017866.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-April/017866.html> I'm a quite Surfer-newby. So sorry for that maybe stupid question... Thank you in advance, Christopher Christopher Milde, M.Sc. Biol. Institute for Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J 5 68159 Mannheim, Germany Phone: +49-621-1703-6313 E-mail: christopher.milde(a)zi-mannheim.de Homepage: http://www.zi-mannheim.de/ Office: Forschungs- und Verwaltungsgebäude, Room 230

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Pial surface area
by Anita van Loenhoud 21 Mar '14

21 Mar '14

Hi mailinglist, I want to obtain aparc.stats for pial instead of white matter surface area. I read that I therefore should adjust mris_anatomical_stats. However, when I run this command separately, the following error occurs: cannot allocate memory Then I tried to put autorecon3 -parcstats in front in this command, but now it says: Flag mris_anatomical_stats unrecognized. Any help would be greatly appreciated, Anita

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LME advice
by Eric Cunningham 20 Mar '14

20 Mar '14

Hello Freesurfer experts, I am getting some unusual results with the lme pipeline, and I would appreciate help with identifying the most likely step in which the problem may have originated. Running lme_fit_FS.m on a single vertex, followed by lme_F on the output of that (stats) yields a p-value of 0. This is because the fcdf function in matlab rounds to 1 if the F-value is big enough (in our case it rounds at about 80, and our F-value is 123). This being the case, we are trying to determine whether this is (1) a problem with the data, (2) a problem with the script somewhere, or (3) a system setting I don't know about. I'm not sure if you have enough information, but can you tell me if the F-values and Beta values look possible (reasonable?)? Thanks for any advice you can provide. -E Starting Fisher scoring iterations Likelihood at FS iteration 1 : 484.5267 Gradient norm: 53.7987 Likelihood at FS iteration 2 : 484.5984 Gradient norm: 1.3858 Likelihood at FS iteration 3 : 484.5985 Gradient norm: 0.022222 Likelihood at FS iteration 4 : 484.5985 Gradient norm: 0.00056884 Total elapsed time is 0.24038 seconds stats = Bhat: [7x1 double] CovBhat: [7x7 double] bihat: [1x93 double] Covbihat: [93x1 double] phisqhat: 0.0110 SIGMA: [345x5 double] W: [345x5 double] Dhat: 0.0213 X: [345x7 double] Zcols: 1 re: [345x1 double] ni: [93x1 double] lreml: 484.5985 st = 1 K>> stats.Bhat ans = 3.1531 -0.0559 0.0148 -0.0154 -0.0309 -0.0767 -0.0229 K>> -0.0559 K>> fstats = lme_F(stats,contrastmatrix) fstats = F: 123.4649 pval: 0 sgn: -1 df: [1 284.0811]

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Overinclusion of brain volume during segmentation - Question
by Christina Chen 20 Mar '14

20 Mar '14

Hi! If the cortical surface outlines are fine, but there is an overinclusion of brain volume during segmentation, how should I fix this? Can we calculate brain volume based on the cortical surface outlines -- if so, how? Thanks! Christina

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Recon process
by Lin, Amy (NIH/NIMH) [F] 20 Mar '14

20 Mar '14

Hello all, I think this is a fairly simple question, but I could not find an existing answer online. If I close out the terminal window while recon is running, will the process end? I've had the issue in the past where my computer has gone to sleep and the process ends up exiting with error. Also, is it possible to rerun a recon command after a previous failed attempt without being prompted to delete the older files that had already been made? I know that usually if you attempt to rerun a recon command after you have already tried, you're usually prompted to remove the older files. This time around, I wasn't ever prompted to do that but the scripts show that the last time recon-all ran, it completed without error. Thanks very much!

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Sample bert information
by Saurabh Thakur 20 Mar '14

20 Mar '14

Hello Freesurfer Expert, Can you share the freesurfer sample named *bert* information such as age,M/F and other details. Thanks in advance, cheers Saurabh Thakur,

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Extracting Mean Diffusivity values
by Rotem Saar 20 Mar '14

20 Mar '14

Dear Doug, I'm now working with freesurfer 5.3, for this example, subject is "Anatomy0981". A while ago I wrote to the list trying to extract the MD values for each ROI as in the diffusion analysis that ends with the FA value for each ROI (for each subject). I wrote my FA script, and asked u to advise on how to convert it to my needs (MD instead of FA), u wrote - > Use mri_label2vol to transfer the wmparc.mgz into the DTI space, then > use mri_segstats with --seg-erode 1 to compute summaries of the MD in > each region (steps below for FA values ended fine) - this is what I did - 1) dt_recon --i /usr/local/freesurfer/ subjects/Anatomy0981/DTI/I160.dcm --s Anatomy0981 --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvals.bval /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvecs.bvec 2) mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0981/DTI/lowb.nii \ --targ /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz \ --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz \ --reg /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --no-save-reg 3) mri_label2vol --mov /usr/local/freesurfer/subjects/Anatomy0981/DTI/lowb.nii \ --targ /usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg.mgz \ --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg2diff.mgz \ --reg /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --no-save-reg 4) mri_segstats --seg-erode 1 /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/Anatomy0981/DTI/fa-masked.mgz --sum /usr/local/freesurfer/subjects/Anatomy0981/stats/all_stats_MD-masked error after step 3: ERROR: Option --mov unknown Trying to use vol2vol instead of label2vol ended successfully, but then when trying to perform step 4, it failed again - ERROR: Option /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz unknown Can u advise on what am I doing wrong ? Thanks !! Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel

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