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V6 beta freeview - stopped loading remaining files when one is missing
by Antonin Skoch 04 Jan '17

04 Jan '17

Dear experts, with V6 beta version of freeview I encountered, that when some input file specified in command line is missing, the loading of remaining files is stopped. This was not the case with 5.3 version. I found this feature handy. Do you think that it would be good to implement this behavior also for V6 version of freeview? Regards, Antonin Skoch

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mri_convert error message
by Wujek, Robert 04 Jan '17

04 Jan '17

I'm trying to convert a group of .dcm files to .nii.gz, but I've been getting the following output with an error at the end... mri_convert IM-0020-0001.dcm example.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from IM-0020-0001.dcm... Starting DICOMRead2() dcmfile = /Users/Desktop/example/IM-0020-0001.dcm dcmdir = /Users/Desktop/example Ref Series No = 23 Found 482 files, checking for dicoms Found 480 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 3 Vs: 0 0 1 Second Sorting Counting frames nframes = 6 nslices = 80 ndcmfiles = 480 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=7584.00, TE=11.10, TI=1500.00, flip angle=111.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to example.nii.gz... niiWrite(): error opening file example.nii.gz ERROR: failure writing example.nii.gz? I'm wondering how I should interpret this error. I have disk space, and proper permissions. I also have experience using mri_convert with other projects, so generally speaking, I am capable with this script. I would appreciate any suggestions. Thank you. -Robert Wujek?

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freeview V6beta - reposition surface option
by Antonin Skoch 04 Jan '17

04 Jan '17

Dear experts, I have several questions regarding "reposition surface" tool in freeview (V6beta): 1. Are here any documentation how to use "reposition surface" tool? I would especially velcome the explanation of significance of "sigma", "size" and "gradient direction" parameter. I tried to play with the parameters by trial and error, but I could not get satisfactory results. 2. It seems to me that the selection of the active volume (i.e. the volume according to that the surface is repositioned) does not reflect the currently highlighted volume. It seems to always use the volume on top of the list of the volumes, but I am not sure given the unpredictive behaviour of this tool I got so far. 3. It would be maybe handy to include special flag to recon-all to rerun remaining recon-all pipeline after the reposition of the surface in freeview have been used. What do you think? 4. Do you think there is a chance to implement recon-all to preserve part of the surface which has been repositioned by this tool in case of recon-all rerun (similarly like it is done with other edits)? Regards, Antonin Skoch

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Fwd: pial surface errors - V6beta - repost
by Antonin Skoch 04 Jan '17

04 Jan '17

Dear experts, I did not receive response to this post, therefore I am reposting. Also, probably due to the attachment size, my previous post did not get archived by mail archive. Regards, Antonin Skoch From: Antonin Skoch <ansk(a)ikem.cz> To: <freesurfer(a)nmr.mgh.harvard.edu> Sent: 12/21/2016 1:41 AM Subject: pial surface errors - V6beta Dear experts, in my data I quite often encounter errors in pial surface which is probably induced by errors of white surface, in some cases caused by juxtacortical lesions (even in healthy subjects). See screenshots for examples. I have tested this on freesurfer V6 beta but it is commonly also found in older versions. I have uploaded the subject pial_errors.tar.gz to your server. The error showed pial_error1.png in probably caused by small error in white surface shape in 18,-18,63 (RAS). Another similar problem is in 15,10,53 (RAS). This is probably caused by juxtacortical lesion. Another problematic spot with juxtacortical lesion is on -7,18,47 (RAS). I have observed such kind of errors in quite a large number of subjects, these are either healthy controls or subjects with psychiatric ilnesses, therefore no particular apparent macroscopic pathology should be present in these subjects. Do you think that there could be some improvement in the mris_make_surfaces code to prevent this kind of behaviour (i.e. very small error in white has gross effect on pial), or it is necessary in all these cases to manually intervene ? Especially, I do not see any particular problem in image in case of pial_error1.png. And, in case of editing of problems errors by juxtacortical lesions I find fastest way to edit wm (due to the fact that I can constrain the brush not to draw to existing wm) in contrast to editing aseg (i.e. label the spot as a lesion). Do you think that aseg editing in contrast to wm editing has some benefit in this case? Regards, Antonin Skoch

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mri_glmfit-sim cannot determine file for mask after mri_glmfit --no-prune
by Dowling, Kevin Francis 04 Jan '17

04 Jan '17

Hello Freesurfer Experts, My apologies if this is a rather simple/obvious question. I am trying to run 3 Monte Carlos using mri_glmfit-sim with the following commands: Left hemisphere surface: mri_glmfit-sim --glmdir $SUBJECTS_DIR/.../LH_7vFix/ --sim mc-z 10000 1.3 mcz10000_1.3 --sim-sign abs -cwpvalthresh .01 Right Hemisphere surface: mri_glmfit-sim --glmdir $SUBJECTS_DIR/.../RH_7vFix/ --sim mc-z 10000 1.3 mcz10000_1.3 --sim-sign abs -cwpvalthresh .01 Volume: mri_glmfit-sim --glmdir $SUBJECTS_DIR/.../MNI305_7vFix/ --sim mc-z 10000 1.3 mcz10000_1.3 --sim-sign abs -cwpvalthresh .01 I'm running this command after my mri_glmfit that includes the --no-prune flag (command below). While the Monte Carlos for the surface ran without problems, there is an error when I try to run the volume based analysis: Error: could not determine file for /cluster/roffman/.../MNI305_7vFix//mask I believe this error refers to the absence of a mask.mgh file. In my analysis the mask.mgh file is only generated for the fsaverage lh and rh surface analyses after mri_glmfit (when the --no-prune is included), while no mask file is generated for the volume. When I re-run the mri_glmfit command with --prune, the mask.mgh file is generated for the volume and the Monte Carlo appears to run. I don't know if this matters but we run our current volume analyses in the mni305 standard space (constructed via mkanalysis-sess with -mni305 2 and not the -native flag). I'm a bit confused why a mask.mgh file isn't generated for the --no-prune volume analyses but is generated for the --no-prune surface analyses. If my mri_glmfit-sim error is referencing the lack of a mask.mgh file, is there a way that I could create a substitute mask.mgh file to feed into the Monte Carlo? Alternatively might there be another better way to work around the no mask error? My mri_glmfit command for the volume is the following: mri_glmfit --y $SUBJECTS_DIR/.../SIRP_Stable5.3_121316_sm5_mni305/7vFix/ces.nii.gz --fsgd /cluster/.../152_GDD_7vFix_Covary_Continuous_Serum_Folate_Linear_Nuis_GenderClass_Age_RT.fsgd --C /cluster/.../TwoGroups1CovariateRegressOut2covariates.mtx --glmdir /cluster/.../MNI305_7vFix/ --fwhm 6 --no-prune I am running a Linux using Release 6.7 (Santiago) and Freesurfer 5.3 (nmr-stable53-env). I would be most grateful for any suggestions or troubleshooting insights you might have! Best wishes, Kevin Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.2479

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Structural analysis
by Silas 04 Jan '17

04 Jan '17

Dear FreeSurfer team, I'm currently doing a structural FS analysis with 50 Multiple Sclerosis (MS) patients and 25 Healthy Controls (HC). FLAIR-lesions were drawn onto the aseg.mgz as White Matter Hypointensities (=77). I've finished the analysis, but have some questions regarding my results. Results: HC (n=25) MS (n=50) p-value Mean TIV (SD) [ml] 1594.9 (154.7) 1559.5 (140.1) > 0.05 Mean WMV (SD) [ml] 503.6 (57.3) 485.2 (59.5) > 0.05 Mean GMV (SD) [ml] 657.2 (69.9) 635.1 (47.9) > 0.05 Mean WMHV (SD) [ml] 1.12 (0.4) 5.97 (5.7) 0.0000677 1) Does these results look correct? WMV < GMV? 2) What is the difference between WMV+GMV and TIV? CSF? Ventricles? 3) I find no atrophy in the MS patients; are there reported any problems with FS and MS patients? 4) What is White Matter Hypointensities comprised of in HC? Best, Silas

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freesurfer multithread
by Li,Tengfei 04 Jan '17

04 Jan '17

Hello, Is there some way to use multithread in recon-all to speed up? I searched the freesurfer website and try using recon-all -autorecon-all -itkthreads 8 -subjid SUBID It simply gives an error message " ERROR: Flag -itkthreads unrecognized. " Thanks! Best Tengfei The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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drawing circle around vertex on surface
by Song, Daniel 04 Jan '17

04 Jan '17

Hi all, I'm trying to create a label by making a circle with a fixed radius around a defined vertex. I'm trying to use the method described here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg44098.html I made the initial surface overlay with my vertex of interest having a value of 1 and 0 everywhere else with: mri_volsynth --pdf delta --delta-crsf 108555 0 0 0 --o pBECTS007_spike.mgh --template rh.thickness Then I smoothed with fwhm: mri_surf2surf --s pBECTS007 --hemi rh --sval pBECTS007_spike.mgh --fwhm 10 --tval ./pBECTS007_spike_fwhm.mgh My question is, is there an easy way to divide all vertices by the value of my vertex of interest after smoothing in tksurfer? If not, is there a command that will allow me to extract the vertex values and indices to do so? Thank you! Dan Song Clinical Research Coordinator Massachusetts General Hospital Neurology Department

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R: Re: Use CA and other subfields as seed for FS-FAST
by stdp82＠virgilio.it 04 Jan '17

04 Jan '17

Dear Eugenio,thank you very much.How can I obtain the beta version 6.0?Moreover, given that we are planning to analyze a big sample, I wonder when will be approximately released the stable's 6.0?Thanks Kind regards Stefano ----Messaggio originale---- Da: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> Data: 3-gen-2017 19.41 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Use CA and other subfields as seed for FS-FAST Ciao, Stefano, Several things: 1. In 5.3, each subfield has a probability map in an independent file, so you don’t need the codes. 2. Having said that: you should probably use the new subfields in 6.0beta. Then, you can use the codes in the range 200-226. Kind regards, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 2 Jan 2017, at 10:47, stdp82(a)virgilio.it wrote: Hi list, I would like to obtain the functional connectivity maps of CA1, CA2/3... by using FS-FAST (VERSION 5.3). Which are the codes in FreeSurferColorLUT.txt, that I should use, please? The ranges from 500 - 508 and from 550 - 558 are useful by using 5.3? Thanks Kind regards, Stefano Delli Pizzi _______________________________________________ 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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aseg error - ventricle mislabeled, negative values in aparc.a2009s+aseg
by Antonin Skoch 04 Jan '17

04 Jan '17

Dear experts, while testing V6beta version I encountered problem with aseg. In one subject (with quite large ventricles) posterior part of right lateral ventricle is not labeled as brain at all and part is labeled as WM-hypointensities and nonWM-hypointensities. Moreover, in aparc.a2009s+aseg there are periventricular regions with value -1 (not present in aseg.presurf). These negative values I observed in one more subject. I am uploading the problematic subject named aseg_error.tar.gz to your server. Linear Talairach registration seems OK in this subject. Could you please comment on, how to correct this error? My second question, is it possible to check non-linear Talairach registration, i.e. talairach.m3z? Regards, Antonin Skoch

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