Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

GLM significance table
by Caroline Beelen 26 Jul '16

26 Jul '16

Dear FS team, I tried to run GLM-analysis using aparc stats files. At first I created these files for a few subjects of interest (e.g. aparc_rh_thickness_stats.txt) and checked whether they looked ok, which they did (values were pretty similar). Then I used the following command (for example): Mri_glmfit -- table aparc_rh_thickness_stats.txt -- fsgd gender_dys.fsgd (see attached; example of a fsgd-file) -- C Int.mtx -- C Dys.mtx -- C Gender.mtx -- glmdir roi.gender_dyslect.rh.thickness.glmdir The file was created and it contained a sig.table.dat folder. However, the values in this folder are all quite low. According to information found on your website they should correspond to (-)log10(p) values. I found mainly values between -1 and 1, but even of -0.03, which would correspond to a p-value of 1.5 (non-existing). Could you please explain to me what I did wrong? Thank you very much! Kind regards, Caroline

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How to apply ACPC alignment to Freesurfer output
by Sandra Hanekamp 26 Jul '16

26 Jul '16

Dear Freesurfer community, I would like to apply ACPC alignment to Freesurfer output. Data was previously segmented with recon -all and a lot of manual editing using ITK. Unfortunately, the data was not aligned to ACPC and this causes errors in my pipeline (I am using the labels and white matter mask from Freesurfer for my DTI analysis). Re-doing the segmentation plus necessary edits would be very time-consuming due to a poor contrast between white and grey matter and the number of scans that I have, so I would prefer to align the current output to ACPC. Does anyone know a solution that does not involve re-doing the segmentation? How can I apply ACPC alignment to Freesurfer output? Thank you so much for any thoughts or recommendations you might be able to provide. Sandra Hanekamp Laboratory for Experimental Ophthalmology University Medical Center Groningen

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mri_ca_label with high resolution data
by Falk Lüsebrink 26 Jul '16

26 Jul '16

Hi all, I'm currently processing a 250 µm MPRAGE with a dev build from mid of May. Running recon-all with default parameters ran flawlessly. Afterwards I added the -hires flag to process the data without conformation. However, since Saturday morning it is kind of stuck at mri_ca_label stating: saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt while consuming around 30 GB of memory. I ran something similar before and processing works, it's just terribly slow. Maybe this particular stage is just not very efficient as it does take a few minutes on 1 mm data only? Would it help to add the openmp flag in that case? Best, Falk ---------------------------------------- Falk Lüsebrink, M. Sc. Otto-von-Guericke-Universität Magdeburg Forschungscampus STIMULATE http://www.forschungscampus-stimulate.de/ Universitätsplatz 2 39106 Magdeburg Raum: ExFa - 4.06 Telefon: 0391-67-19366 Fax: 0391-67-19347

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Hippocampal subfields total volume differences
by Mojmír Vinkler 26 Jul '16

26 Jul '16

Hi experts, I'm using Freesurfer 6.0 dev version (Mac) to perform hippocampal subfields segmentation. I only need to measure total hippocampus volume, but measurements from basic `recon-all` were too volatile and I was hoping that using subfields with T2 modality would reduce variance. However, volume measured by hippocampal subfields is significantly different from volume in aseg.stats. Here are volumes for right hippocampus from various methods: aseg.stats - 3312.8 rh.hippoSfVolumes-T1.v10.txt (Mode A - only T1 used) - 2883.8 rh.hippoSfVolumes-T2.v10.txt (Mode B - using only additional scan) - 2503.97 rh.hippoSfVolumes-T1-T1T2.v10.txt (Mode B - Multispectral segmentation) - 2596.09 I checked labeling visually and there were no obvious problems. Is such a large difference common? Am I missing something? What number should be most trusted? Thanks for any hints! Mojmir

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Running Several Versions of fsfast GLM In Parallel Leads to "Stale File Handles"
by Taylor, Johnmark 25 Jul '16

25 Jul '16

Hello, I have been trying to run several versions of the same GLM analysis, trying out different parameters to see if they affect the results. For instance, I am running the GLM with different levels of smoothing, per-session versus per-run motion correction, etc. To speed this up, I am trying to do these GLMs in parallel. However, when I do this, I run into a "stale file handle" problem. As near as I can tell, this occurs because the analyses try to read and write to the same log files at the same time. A typical error message is "/net/rcss2/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/fpoinfips01/scripts/glm/log/preproc-160718_xu_loc01_sub02-bold.log: Stale file handle". I have tried putting "-nolog" in the call to selxavg3-sess, but this doesn't prevent the creation of log files when it makes the sub-calls to the various pre-processing functions. Is there any way around this? It would be rather slow to try to run the GLMs sequentially, so I am wondering if anybody has figured out a way around this problem. Much obliged, JohnMark

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Error with mri_glmfit_sim (dev version f)
by Nicola Toschi 25 Jul '16

25 Jul '16

Hi List, I am getting a couple of strange error when running a 3-group F-test. WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin WARNING: 251446 NaNs found in volume analysis/Ftest/cache.th20.pos.sig.cluster.mgh... And as a result, I consistently get huge clusters: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 inf 0 63247.45 -38.8 -19.0 66.9 0.00010 0.00000 0.00020 98722 inf precentral However, this doesn't happen when running t-tests on the same data. Still, I think my F-contrast is correct (see below). Thanks in advance for any advice! Nicola PS: my F-contrast looks like this: 1 -1 0 0 0 0 1 0 -1 0 0 0 and my design matrix looks like this: 0 0 1 1 179 110 0 0 1 1 193 103 0 0 1 1 176 108 0 0 1 1 198 94 0 1 0 1 186 87 0 1 0 1 217 83 ..... and my versions are # $Id: mri_surfcluster.c,v 1.57 2014/03/06 17:02:46 greve Exp $ # $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $

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ERROR: dimension mismatch between input volume and seg
by Kari Parsons 25 Jul '16

25 Jul '16

Hi, I'm trying to get some cortical thickness volumes for an ROI that I have (I'm pretty much following the instructions at https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness verbatim), but for some of my subjects I'm getting errors that look like this when I run mdi_segstats: ERROR: dimension mismatch between input volume and seg input 1 1 145283 seg 145283 1 1 Does anyone have any thoughts on how to trouble-shoot this one? Thanks!

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Re: [Freesurfer] Checking segmentations with aseg.mgz
by Reema Jayakar 25 Jul '16

25 Jul '16

Hi Dr. Fischl, Thank you for clarifying that about norm.mgz for checking segmentations. Good to know that brain and brainmask wash out low contrast borders. Cheers, Reema -- *Reema Jayakar, M.A.* Doctoral Candidate - Clinical Neuropsychology Health Resources and Services Administration (HRSA) Fellow Department of Psychology Georgia State University Email: rjayakar1(a)student.gsu.edu On Mon, Jul 18, 2016 at 4:42 PM, Reema Jayakar <reemajayakar(a)gmail.com> wrote: > Hello FS Listserv members, > > With regard to checking amygdala segmentation, is it appropriate to > overlay the aseg.mgz file on the brainmask.mgz? Or should I be overlaying > aseg.mgz on norm.mgz? I am aware of the general rule of thumb that > editing the subcortical segmentations generally is not recommended. > > Also, where can I find documentation on the Freeview options "Resample to > standard RAS space" and > > "Apply registration file". I am trying to understand whether or not it is necessary for me to use any of these options for what I am doing with the subcortical segmentations. > > > Thanks in advance for your help! > > Reema > > > > -- > *Reema Jayakar, M.A.* > Doctoral Candidate - Clinical Neuropsychology > Health Resources and Services Administration (HRSA) Fellow > Department of Psychology > Georgia State University > Email: rjayakar1(a)student.gsu.edu > >

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mri_label2label volume registration problem
by Agoston Mihalik 25 Jul '16

25 Jul '16

Hi Freesurfer Developers, I would like to ask for your expertise in the following problem I encountered: I want to create subject specific labels based on a label I created in fsaverage. The transformation needs to be based on Talairach intermediate registration, since my label was drawn based on Talairach coordinates. I ran the following command: mri_label2label --srclabel test.label --srcsubject fsaverage --trglabel lh.test2.label --trgsubject subj222 --regmethod volume The problem is that the output label is scattered and all around the place when I look at it in tksurfer - see the image attached (lh.regmethod_volume.tif). When I did the registration based on surface, it worked fine (see the image also attached - lh.regmethod_volume.tif), however, it resulted in 0-4 mm misalignment when I looked at the Talairach coordinates of the label borders. I guess it is due to the surface registration that optimises the surfaces to be aligned, not the Talairach coordinates. Please find some information attached in case it is any help - content of files, output etc. Here is my freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 Your help would be really appreciated. Thanks and best, Agoston

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ERROR: cannot find volume matching
by Erik Jahner 25 Jul '16

25 Jul '16

Dear Free Surfer experts I am attempting to run a functional connectivity analysis on some resting state data. However, I keep getting stuck in this final step of the online Functional Connectivity Pathway. I have made a change based on discussion boards, but it do not help. CHANGE: in the mkanalysis step, I changed the "-taskreg L_Posteriorcingulate.dat 1" to "-taskreg L_Posteriorcingulate 1². This did not solve the problem. My mkanalysis lines are as follows: mkanalysis-sess -analysis fc.lpccseed.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg L_Posteriorcingulate 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd rest -TR TR2 -hpf .01 -force -per-run mkanalysis-sess -analysis fc.lpccseed.surf.rh -surface fsaverage rh -fwhm 5 -notask -taskreg L_Posteriorcingulate 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd rest -TR TR2 -hpf .01 -force -per-run mkanalysis-sess -analysis fc.lpccseed.surf.mni305 -mni305 -fwhm 5 -notask -taskreg L_Posteriorcingulate 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd rest -TR TR2 -hpf .01 -force -per-run I then run the following: selxavg3-sess -s 401 -a fc.lpccseed.surf.lh -overwrite and the error that is produced is as follows: (what does "cannot find volume ² mean? and how might I fix this) /Applications/freesurfer/LagStructure/413 ------------------------- $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m /Applications/freesurfer/matlab/MRIread.m ------------------------- outtop = /Applications/freesurfer/LagStructure Extension format = nii.gz ERROR: cannot find volume matching /Applications/freesurfer/LagStructure/413/rest/001/L_Posteriorcingulate ERROR: loading nonpar reg /Applications/freesurfer/LagStructure/413/rest/001/L_Posteriorcingulate ------------------------------------------ ERROR: fast_selxavg3() failed\n

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