Freesurfer April 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
217 discussions

MRIread (load_nifti)- Out of memory
by Ilaria Sani 07 Apr '17

07 Apr '17

Dear All, I'm trying to load a pretty big diffusion MRI dataset (320x320x260x122). I'm running matlab 2015a 64bit on a linux machine. I'm using MRIread, which in turn calls load_nifti. I'm getting the following error: Error using + Out of memory. Type HELP MEMORY for your options. Error in load_nifti (line 158) hdr.vol = hdr.vol * hdr.scl_slope + hdr.scl_inter; Error in MRIread (line 158) hdr = load_nifti(fspec,headeronly); When I load half dataset (320x320x260x61) it works ok. I tried to increase the Maximum array size in Matalb (default 1,000 - now 10,000), but I'm still getting the error. I tried to change machine (which runs matlab 2013a on linux) and it worked fine. I think this is due to some matlab settings. Can anyone help? Thanks a lot, Ilaria ------------------------------------------- Ilaria Sani, PhD Postdoctoral Fellow, Freiwald Lab The Rockefeller University 1230 York Ave., New York, NY 10065. Phone: (212) 327 7699 Fax: (212) 327 7698 Email: isani01(a)rockefeller.edu<https://rumail.rockefeller.edu/owa/redir.aspx?C=Kqhy3ohui0OLc6NBHS0gx_jC9yH…>

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Analyzing xhemi results
by Marissa Pifer 07 Apr '17

07 Apr '17

Hi free surfers, I have run the xhemi process on the subjects for my study. The study is on stroke patients and their lesions are a mix of left and right hemispheres. In analyzing the results, we want to look at correlations between fmri activation in M1 and the cortical thickness of M1 ipsilesional and contralesional. To do so, I followed instructions written out in response to a question about xhemi on the mailing list: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-December/026823.… My question, is there a way when running the analysis step: *# Analyze *>* mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir *>* glm.lh.lh-rh.thickness.sm05 \ *>* --osgm --surf fsaverage_sym lh *> Can I modify this command line to include my fmri data and run that correlation also? Thank you, Marissa

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How to segment subnuclei of thalamus?
by Shane S 07 Apr '17

07 Apr '17

Hello Experts, I am interested to do a segmentation of the thalamus subnuclei based on T1 data. Is there any atlas that I could use for this? Best Wishes, S

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Hippocampal subfield segmentation, file content
by Nina Jacobsen 07 Apr '17

07 Apr '17

Hi All, I have made a hippocampal subfield segmentation using FreeSurfer version 6.0 with multispectral segmentation settings, and have both labels for the right and left hippocampus. The segmentations look very nice when viewed with freeview, so all good. Now, my problem is the file content. I would like a segmentation file, which labels all subfields with a single value (all voxels in CA1 would for example be with value 1, all voxels in CA2 would be with value 2 and so on). Does anyone know how i can gain this file? Is it in some way possible to convert the label files (lh.hippoSfLabel.v10.mgz) into such a "simple" segmentation file? Currently, the content of the label files (lh.hippoSfLabel.v10.mgz) is values in the range 0-226, which I guess origin from the RGB encoding - I opened the file with matlab. Hope my question is clear. Thanks, Nina Jacobsen.

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Multiple Comparisons Correction thresh error
by teodora petrova 07 Apr '17

07 Apr '17

Hello, I would like to correct my glm_fit results for multiple comparisons. I am using the following commands, similar to the one in the group analysis tutorial: mri_glmfit-sim --glmdir lh.index.glmdir --cache 1.3 abs --cwp 0.05 --2spacesmri_glmfit-sim --glmdir lh.index.glmdir --cache 2.0 pos --cwp 0.05 --2spaces And receive the following errors: ERROR:thresh=1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 ERROR:thresh=2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 I am sure I am typing a point, but it is read as a comma. Any ideas why? Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Platform: Ubuntu MATE 16.04 Thank you very much! Regards,Teodora

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QA Tools v1.2 and future release
by Yong Li 07 Apr '17

07 Apr '17

Dear Freesurfer Experts, As one of the new freesurfers, I really appreciate the excellent work of authors as well as great support of users' forum. A good guess of mine is that authors, e.g., Vasanth or Louis etc., are busy updating QA tools after the FSv6 release since the QA Tools v1.2 was written for FSv5.3. If so, is it possible to provide an estimated release date please so as to adjust my plan? Thanks for understanding! In case, it might take a while to release the next QA Tool, may I dare to provide my attempts of code updating of some functions in QA Tools? The following are the brief list of code adapting steps: 1. modified codes for generating file order list in recon_checker; 2. modified codes for matching segment names for instance from DefaultAsegMeans.txt in gparcmean_from_table; 3. adapted default_FOF and default_status_log for FSv6. After these adaptation, QA Tools ran through and I only encountered some 'syntax error' in terminal for 2 segments, 5th-Ventricle and WM-hypointensities, that I have to ask the experts to guide me through this point if it's of your interests. To ensure the QA Tools functioning well, I tested 116 elderly patients and detected reasonable outliers per patient. Therefore, I would like to double that my code updating based on my general understanding of QA Tool still fit to the basic purpose of authors by asking the following theoretical questions: 1. SNR and segments outliers detection are measures of quality assessment in QA Tools. Have other factors such as subject's motion, image bias, resolution etc. been considered in QA Tools or future release? The default SNR threshold is 16 based on any reference? The max SNR of my patients so far is 32. Any idea of scores of healthy elderly controls? 2. The QA Tools v1.2 analyzes aseg.stats output. Is it possible to include output of brainstem substructures and HippocampalSubfields of FSv6? If yes, I would like to adapt the codes and provide you some feedback if you think that I can help bit. 3. Future directions mentioned in QA Tools wiki site are interesting and thoughtful. Are other features like 'Detect outliers in aparc and aparc2009 volumes' on the way? 4. Is there a function to summarize all QA measures to csv files, like the quantifyBrainstemStructures.sh in brainstem substructures? Thank you in advance! Kind regards, Yong Li, PhD _________________________ Department of Neurology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany

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long mri_ca_register error
by Chris Adamson 06 Apr '17

06 Apr '17

Freesurfer devs, In freesurfer 6 stable I'm having a problem at the careg stage of the long. The relevant recon-all log is pasted below. Could you point me to where to debug this problem? Cheers, Chris. mri_ca_register -rusage 136_S_0426_20070604.long.136_S_0426/touch/rusage.mri_ca_register.dat -bigventricles -smoothness 0.5 -levels 2 -A 1 -l *base*/transforms/talairach.m3z identity.nofile -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z handling expanded ventricles... l_smoothness = 0.50 levels = 2 smoothing gradient with 1 averages... reading previously computed atlas xform /isilon/data/addo/ADNI3T/freesurfer6/136_S_0426/mri/transforms/talairach.m3z and applying inverse registration identity.nofile renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 2 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) TransformSample: gcam has not been inverted! freeing gibbs priors...done. average std[0] = 5.0 setting orig areas to linear transform determinant scaled 8.40 writing talairach.invalid.mgz writing talairach.status.mgz registering ventricular system... using threshold 45.0 from atlas ventricle (20.1 +- 5.0) and caudate (70.0 +- 5.0) distributions for initial ventricular estimate No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Custom registration template
by Linda Zhang 06 Apr '17

06 Apr '17

Dear all, I've been following the instructions for building a custom registration template as written here ( http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) and here ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html ). I'm now at the mris_preproc stage and according to the instructions, the command should be: # Get thickness values in the newtemplate space for GLM analysis mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ... I put my subject list into a text file and replaced --s with --f [subjlist] but kept everything else the same. I got two errors for no source hemi specified and no output specified, so I added --hemi lh and --out lh.surfreg.newtemplate.thick --meas thickness. Am I supposed to do this, and will the output file be used for anything else down the line, i.e., should it be named something more specific? I see that the next step is to rerun the make_average_subject, but I don't see where the output from the mris_preproc step would figure in. On a (maybe) separate issue, when I finally ran my command line: mris_preproc --surfreg sphere.reg.newtemplate --f subjlist --hemi lh --out lh.surfreg.newtemplate.thick --meas thickness I got the following error: nsubjects=100 tmpdir is ./tmp.mris_preproc.25619 /home/fsuser/data set: Variable name must contain alphanumeric characters. I'm not sure where the problem might be here. I'm running FreeSurfer v.5.3 in Virtualbox, and I haven't had any problems while running recon-all on the subjects previously. Any insight would be greatly appreciated, thank you! Cheers, Linda

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R: Re: R: R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis
by stdp82＠virgilio.it 06 Apr '17

06 Apr '17

Thanks.The file could not be open by fslview.I presume that it is inflated.How can I do to transform it?Stefano ----Messaggio originale---- Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> Data: 6-apr-2017 17.56 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis It will be in the space that you analyzed it in. If you want the native space, then use -native when running preproc-sess and mkanalysis On 4/6/17 2:34 AM, stdp82(a)virgilio.it wrote: Furthermore, the res-001.nii which is produce in produced in the res folder in not the same dimension of f.nii. I would do the whole FAST preprocessing on f.nii., maintaining the same dimension and open it with FSL. Thanks Stefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 5-apr-2017 23.39 A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis Hi, as you advise I have run selxavg3-sess with the -svres option. I found a folder called "res" which contain "res-001.nii". Is it the f.nii fully processed? Thanks Stefano ----Messaggio originale---- Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> Data: 14-mar-2017 17.38 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: Whole preprocessing with FAST without to perform a seed based analysis You can't on either occasion just using preproc-sess. You can create an analysis with those components, then run selxavg3-sess with the -svres option. This will create a folder called eres with volumes that have had all the nuisance variables and low freqeuncies regressed out On 3/14/17 12:32 PM, stdp82(a)virgilio.it wrote: Thanks. 1- By using only preproc-sess, how can I perform "band pass filtering"? 2- And how can I take in account the nuisance variables: the CSF from which the top 5 principle components, the white matter from which the top 5 principle components, motion correction parameters (-mcextreg), 5th order polynomial. How can I eliminate the first 4 time points? Regards Stefano ----Messaggio originale---- Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> Data: 14-mar-2017 16.14 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Whole preprocessing with FAST without to perform a seed based analysis just use preproc-sess On 3/14/17 10:45 AM, stdp82(a)virgilio.it wrote: Hi list, in FS-FAST, on rs-fMRI data, is possible to run selxavg3-sess without -a option? I would use whole the FS-FAST to preprocess my data. I would include the mkanalysis-sess step but I would not perform a seed-based analysis. Thanks Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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QDEC-volume, thickness and area
by Lim, Lena 06 Apr '17

06 Apr '17

Dear Freesurfer Experts, 1) I have 2 groups (A & B), which do not differ in terms of gender ratio. If there were no significant regions for Group-Gender interaction in mean cortical thickness in the QDEC analysis, can I conclude that gender does not influence the effect of group on thickness? The differences between A and B on mean thickness is not affected by Gender? Is this valid or do I need to add Gender as a covariate even though the group do not differ on gender ratio? 2) A reviewer pointed that it is not right to test for group differences in volume once I have tested for thickness and area, especially when there is a cluster where A and B do not differ significantly in thickness and area but they differ significantly in volume...Is this right? Please kindly advise. Many thanks, Lena

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Freesurfer April 2017