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30070 discussions

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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QDEC and ROI drawing
by Arnaud Boré 06 Apr '17

06 Apr '17

Dear Freesurfer's experts, I draw a specific region on fsaverage using QDEC, then I mapped this label on each subject using mri_label2label. I looked at these registered labels using freeview. Most of them are perfect but for some of them I would like to correct the segmentation. I would like to modify it using QDEC but when I overlay this label on the surface of my subject it has been shifted. I think this shift is because QDEC is using fsaverage as the standard space. I try opening QDEC using the "average" option and use the subject I want but I still get this shift. am I missing something ? Thank you in advance for your help. Arnaud Bore

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General QDEC clarification queastions
by Veggeberg, Rosanna 06 Apr '17

06 Apr '17

Hello, I am using QDEC to analyze cortical structural data and am looking for some clarification on some questions that have come up. 1. Design tab: In the "Measure" drop-down selection, I understand what we are getting when looking at thickness but the other measurements I am unclear on. Is there information or publications on the other 12 possible measures (how they are measured, what they mean, applications for using them). In particular, I am interested in learning more about area, area.pial, volume, sulc, and curv but would like to understand what the others mean as well to determine if they would be applicable to our study questions. 2. Design tab: I am a little unclear on why the model factors are labeled the way they are and wanted to see if I am using them correctly. -Discrete (Fixed Factors): this is pretty straight forward to be used as independent categorical variables, correct? -Continuous (Covariate): even though it says covariate, should these variables just be treated as independent continuous varaibles? -Nuisance Factors: should these just be treated as the covariates we wish to control for? 3. Results: When I am doing a group comparison (i.e. disease vs. control), does QDEC run the comparison based off of which order the labels appear in the table: disease vs. control, or does it run the comparison based off of which label comes first alphabetically: control vs. disease? 4. Results: When viewing the results in freeview, if I click on a significant cluster, in the bottom panel, does a negative value next to the mc-z.abs.th13.sig.cluster.mgh label indicate a decrease in cortical thickness (i.e. disease vs. control: negative value indicates control is greater than disease)? 5. Finally, once you have closed QDEC, is it possible to reopen the files again in the Gui? Or would you have to rerun the analysis? Thank you for help and please let me know if you need any further clarification.

2 1

Custom color maps
by Senften, Peter 06 Apr '17

06 Apr '17

Hello, I am wondering if it is possible to create a custom color map that will be visible in freeview using the 3D viewer - not the coronal, axial, or sagital views. I created a copy of the LUT file and then replaced the RGB values the ones I wanted but haven't been able to get it to load at all. In the end I am trying to make pretty 3D pictures to see our regions of interest better for our data. I am open to other ways of doing this. Thanks, Peter

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ROI seed size
by ERIK JAHNER 06 Apr '17

06 Apr '17

What is the appropriate size for a surface based seed? I am referencing a study with volumetric based seeds with spheres with a radius of 3mm (in fMRI data). I would like to do a similar study using surface based representations. In a volumetric based analysis folding may actually increase the amount of cortical surface represented in a sphere. Using a circle on the surface with a 3 mm radius therefore would not be the same. But…. is the difference so minimal and variable across the cortex that it is not worth considering especially since the seeds are derived from published work and not using a localizer? Do you know of any published guidelines on generating seed sizes in surface based models, not based on a localizer. Or is this the completely wrong approach? Should I be using the tal coordinates to locate which parcellation of the available atlases that the seed was located in? (for example i have a fusiform face area seed which I have set as a circle 3mm radius) many thanks for your continued help Erik

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Selxavg3-sess Looking for (and can't find) "fmc.sm0"
by Taylor, Johnmark 06 Apr '17

06 Apr '17

Hello, I am getting an odd bug on selxavg3-sess. I am getting the error message, *ERROR: cannot find [rest of file path]/fmc.sm0* I am indicating zero smoothing in mkanalysis-sess ("-fwhm 0"). I am confused because the output of preproc-sess for no smoothing is fmc.nii.gz, *NOT *fmc.sm0.nii.gz when doing analyses in native volume space, so I am not sure why selxavg-sess is looking for the wrong file path. For reference, here is my call to mkanalysis-sess: mkanalysis-sess -analysis analysis_name -fsd bold -runlistfile runlist.txt -native -nuisreg mcextreg 3 -fwhm 0 -event-related -nconditions 8 -paradigm spiralpara.par -spmhrf 0 -refeventdur 12 -TR 1.5 -polyfit 2 -nskip 8 I am using Freesurfer 5.3, if that helps. The analysis works fine when I apply 3mm smoothing (I've done preprocessing for both the 0mm and 3mm options). Thank you very much, and cheers, JohnMark

2 1

First-level GLM on externally-preprocessed functionals
by Christopher Markiewicz 06 Apr '17

06 Apr '17

Hi list, We're working on making a preprocessing stream that will be generally accessible to different analysis streams, including FreeSurfer. One component of this is sampling functional volumes to FreeSurfer meshes, and I want to test this component by running a simple first-level GLM in FreeSurfer. I've always done this through the FSFAST pipeline, but that may be a bit much, given that I'm starting from surface time series (the equivalent of `$FUNCTIONALS_DIR/$SESS_ID/bold/$RUN/fmcpr.sm0.fsaverage.lh.nii.gz`, but as a GIFTI file). Supposing I have a paradigm file and the files described above, what's the best way to do a basic GLM? Would it be to `mri_surf2surf` our GIFTI surfaces into `fmcpr.sm0.fsaverage.lh.nii.gz` files in a FSFAST directory structure, and pick up at `mkanalysis-sess`? Or is there a more straightforward way to just get a simple set of contrasts to compare with a volumetric analysis? Thanks in advance, Chris Markiewicz

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