Freesurfer

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30080 discussions

normalizing in fsgd
by miracle ozzoude 26 Jul '16

26 Jul '16

Hello freesurfer experts, I am trying to normalize my continuous variables in my fsgd file. Is this the correct term to add to my fsgd file in order for mri_glmfit to normalize it? GroupDescriptorFile 1 Title PCS Class group1 Class group2 Normalize 1 Variables Age Education Scoreone Scoretwo Input 053 group1 47 18 3.4 5.6 Input 054 group2 50 16 5.3 2.8 Thank you, Paul

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Projecting AAL atlas to fsaverage
by Salim Arslan 26 Jul '16

26 Jul '16

Hi, We are trying to project the AAL labels from volume to surface in order to be able to include the AAL atlas to our surface-based experiments. What we have done so far is that we projected the volume labels to the fsaverage white surface using mri_vol2surf function in the following setting: mri_vol2surf --mov ROI_MNI_V5.nii --mni152reg --hemi lh --surf white --o $OUT_FOLDER/lh.fsaverage.white.ROI_MNI_V5.asc.w --out_type paint --trgsubject fsaverage where ROI_MNI_V5.nii corresponds to the ALL atlas in MNI space. After converting the output asc.w file first to a FreeSurfer-compatible format, and then to gifti, we realized that the result was garbage (Please see Fig. 1). Following a suggestion from a member of our research group, we applied dilation to the input atlas (ROI_MNI_V5.nii) and re-ran the function with the same setting as above. This way, the final cortical parcellation was not perfect but still seemed to be usable (Please see Fig. 2). The problem here is that, as you may have also noticed, some of the cortical parcellation boundaries do not follow the folding patterns across the surface. Besides, some parcels just do not seem to be right (see the arrows in the motor area). Having said that, I have the following questions:1- Why is not possible to properly project the labels onto the surface without first dilating the input atlas?2- If dilation is not a big issue, how would the experts in the mailing list interpret the distortions, especially in the motor area? Is it kind of a side effect we should expect after such process between volume and surface? >From the archive I can see that similar questions have been posted a few years back (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27586.html, https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg23761.html) Although these messages are highly useful, apparently there is still not a standard solution to this problem. Please accept my sincere apologies if this is still considered as re-posting. Any feedback is greatly appreciated. Thanks for your attention. Kind regards,Salim

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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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GLM significance table
by Caroline Beelen 26 Jul '16

26 Jul '16

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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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