Freesurfer April 2018

freesurfer@nmr.mgh.harvard.edu

118 participants
177 discussions

Creating average surface for fMRI subjects and extracting cortical thickness
by Arsenije Subotic 11 Apr '18

11 Apr '18

Dear experts, I would like to create an average surface template of fMRI activation for two groups, and then determine areas of low cerebrovascular reactivity in my disease group, create a ROI, and extract the cortical thickness in this region and see how it compares to a control group by translating this ROI onto the control surface template. Do you have any tips or suggestions on how this workflow should be done? I've currently been able to create an average surface for both groups, and I know how to create labels using tksurfer and to extract cortical thickness using mri_anatomical_stats. Is it possible however to create an ROI by only considering areas of low CVR/low activation in my disease group and calculating cortical thickness for this area, and then visualize it somehow and then translate this label onto the control group and doing the same? I know it's a lot of questions, but going through the tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_tk…) it seems that I wasn't able to find exactly what I'm looking for. Thank you for your help, Arsenije

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mri_surf2surf results in large area with zero values
by Frauke Beyer 11 Apr '18

11 Apr '18

Dear experts, I have an issue with mri_surf2surf (i suspect). I have resampled T1-values to the fsaverage template using mri_vol2surf and a --projfrac of 0.25 with the default white matter surface. Then I loaded these values in Matlab using MRIread, inverted them and saved them back into a file using MRIwrite. In Matlab, there were no suspicious data points (e.g. the range of R1 values excluded 0, minimum was 0.25). This was also true when loading the R1values as an overlay in Freeview. Now I wanted to smooth this image using mri_surf2surf with target and source subject being identical to fsaverage and fwhm of 10mm. exact command was: mri_surf2surf --srcsubject fsaverage --trgsubject fsaverage --hemi lh --sval /nobackup/aventurin4/data_fbeyer/flica_myelin/flica_inputs/round2/t1maps/lh.t1map.proj0.25.fsavg_inv.mgh --tval /nobackup/aventurin4/data_fbeyer/flica_myelin/flica_inputs/round2/t1maps/lh.t1map.proj0.25.fsavg_inv_smoothed10mm.mgh --fwhm-trg 10 But now, while it worked fine for some subjects in the 4D file for others large areas of 0 emerged in the smoothed file. Those were mostly found in inferior temporal/orbitofrontal lobe. Does anybody have an idea what could cause this strange behaviour? Thank you so much for your help, Frauke

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Running matlab-based components of freesurfer on windows 10 linux shell
by Savio Wong 11 Apr '18

11 Apr '18

Hi everyone, I have installed freesurfer on windows 10 linux shell following this link: http://nuclear-imaging.info/site_content/2016/09/12/installing-running-free… Recon-all and freeview run perfectly on the system. However, when I tried to run mkcontrast, I encountered the following error: An Error has occurred while trying to initialize the MCR. The error is: Fatal error loading library /usr/local/freesurfer/MCRv83/bin/glnxa64/libmwmclbase.so Error: libmwblas.so: cannot enable executable stack as shared object requires: Invalid argument Error:mclmcr initialization failed ERROR running mkcontrast It seems that the windows 10 linux shell lacks some libraries to run the matlab: https://www.mathworks.com/matlabcentral/answers/308911- can-i-install-matlab-in-bash-on-ubuntu-on-windows Does anyone have any experience in this error? is there any solution for that? Any advice is much appreciated. best..................savio

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Re: [Freesurfer] Surface label to volume and then back to surface
by David Beeler 11 Apr '18

11 Apr '18

Hi Doug, thanks for the response! So it looks like my initial transform from surface label to anatomical volume wasn't working because my template.nii.gz and brainmask were in a different space than the functional data I was processing. This happened because I was taking the raw f.nii.gz, doing some transformations first, and saving it to a file called f_reg.nii.gz. I was then trying to run preproc-sess using the -i flag to specify this f_reg.nii.gz, but when preproc runs mktemplate-sess it still uses f.nii.gz to make the template, regardless of what the -i or -mcin flags say. I just added a line in the if($DoTemplate) section of preproc-sess to have the option of adding a -funcstem and it worked fine. I have now updated my preprocessing to run all the commands individually instead of using preproc-sess at all, and I'm probably going to send another message to this list later making sure I'm doing that correctly. Additionally, Re: "I think you could do it with a single call to mri_label2vol using --regheader and specifying the func template." This works great! Thanks for the shortcut. I got the surface label direct to functional volume transform working with: mri_vol2vol --regheader --mov $OUTPUTDIR/rh.MT.volume.anat.nii.gz --targ $MEANFUNCDIR/meanfunc.nii.gz --o $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz --nearest But I'm still not entirely sure exactly what information is contained in regheader (or where I can view this information). The reason I have been using regheader instead of register.dof6.lta is that my functional data is aligned to the anatomical prior to running preprocessing, and my understanding was that using regheader would just downsample (similar to mri_convert) and I wouldn't need to specify a registration file. Is this a flawed understanding of regheader? So transforming to functional space seems to be okay now, but transforming back to the surface is still not perfect. I tried mri_vol2surf --mov $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz --regheader $SUBJID --projfrac 0.5 --interp nearest --hemi rh --o $OUTPUTDIR/regheadersurface.nii.gz and also bbregister --s $SUBJID --reg $OUTPUTDIR/testreg.lta --mov $MEANFUNCDIR/meanfunc.nii.gz --init-fsl --bold mri_vol2surf --mov $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz --reg $OUTPUTDIR/testreg.lta --projfrac 0.5 --interp nearest --hemi rh --o $OUTPUTDIR/testregsurface.nii.gz Which both give essentially the same result: Original Label: http://web.mit.edu/dsbeeler/www/images/MTlabel.png Back to Surface Overlay: http://web.mit.edu/dsbeeler/www/images/MTpatchy.png This is actually much better than it was, but is there a way to get rid of the patchiness? Again, thanks for all the useful info! David ______________________________ Hi David, I've tried to answer your questions below. doug On 03/30/2018 01:48 PM, David Beeler wrote: > Hi all, > Sorry in advance, this is a bit of an annoying one! > > I am trying to use freesurfer's automatically generated MT label as a > parcel to constrain activity measured during a functional MT > localizer. I am currently doing my analysis in the volume and I'd like > to transform the MT surface label into the subject's volume functional > space (i.e. the same space as the sig.nii.gz for a particular > contrast), take the voxels in sig.nii.gz that are within the MT label, > and project them back onto the surface (preferably to be viewed as an > overlay with freeview). I will eventually run the analysis on the > surface as well (making this much less roundabout, but I also use > volume parcels so understanding how to correctly go between the volume > and surface is important to me). > > In my pipeline I start off by running preproc-sess, then I register > and transform my preprocessed functional data (fmcpr.nii.gz) to the > subject's anatomical (without upsampling). After doing mkanalysis and > mkcontrast, I run selxavg on this volume. So the functional data is > aligned with the anatomical, but still has low res dimensions. > > If it's not too much to ask, would it be possible to provide the > specific commands to do all these transformations properly? I'll > provide some of the commands I've tried below so you can see where I'm > going wrong: > > First I want to transform the MT label to the functional volume. I've > tried: > > mri_label2vol --subject $SUBJID --label > $SUBJECTS_DIR/$SUBJID/label/rh.MT.label --o > $OUTPUTDIR/rh.MT.volume.anat.nii.gz --temp > $SUBJECTS_DIR/$SUBJID/mri/orig.mgz --identity --fill-ribbon --hemi rh > > ...which I would expect to put the label in high resolution anatomical > volume space (orig.mgz), but it doesn't fill the graymatter ribbon > nicely at all. I would have expected this to work. Can you send a pic? I just ran it myself, and it seemed to do ok. > > I then use mri_vol2vol to transform to functional/sig.nii.gz space (I > could also just downsample with mri_convert since I've already aligned > my sig.nii.gz to my anatomical, this gives me the same result). I am > using regheader here, is this okay? > > mri_vol2vol --regheader --mov $OUTPUTDIR.rh.MT.volume.anat.nii.gz > --targ meanfunc.nii.gz --o rh.MT.volume.func.nii.gz --nearest > > ...and this works pretty well, but it's a little sparse so I may need > to dilate it with mri_morphology. I think this step is fine. Why do this extra step? I think you could do it with a single call to mri_label2vol using --regheader and specifying the func template. Why are you using --regheader here instead of the register.dof6.lta? > > Next I use matlab to take the voxels in sig.nii.gz that are also in > rh.MT.volume.func.nii.gz and I save that as a new volume, say > constrainedsig.nii.gz. You can do this with mri_mask sig.nii.gz rh.MT.volume.func.nii.gz constrainedsig.nii.gz > Now I want to transform constrainedsig.nii.gz to the surface. I have > tried going directly using the register.dof6.lta generated from > preproc-sess: > > mri_vol2surf --mov constrainedsig.nii.gz --reg register.dof6.lta > --projfrac 0.5 --interp nearest --hemi rh --o > $OUTPUTDIR/constrainedsig_surface.nii.gz This should have worked. Try doing directly on the rh.MT.volume.func.nii.gz > > ... and this is in the right area, but its shape doesn't match the > shape of the original label. So I've also tried backtracking and doing > another vol2vol and then vol2surf with regheader: > > mri_vol2vol --regheader --mov constrainedsig.nii.gz --targ > $SUBJECTS_DIR/$SUBJID/mri/orig.mgz --o > $OUTPUTDIR/constainedsig_anatvolume.nii.gz > > mri_vol2surf --mov constrainedsig_anatvolume.nii.gz --hemi rh > --regheader S02 --o $OUTPUTDIR/constrainedsig_anatsurface > > ...and while this ends up in the right place, it is really patchy > (looking kind of like twisty zebra stripes). Seems to me like it has > the wrong dimensions or something, but mri_info says it's the same > dimensions as the volume I originally created with mri_label2vol. > > Any help is much appreciated, thanks! > David > > > _______________________________________________ > 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 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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Canonical HRF shape generated by FSFAST
by Sarah Cole 11 Apr '18

11 Apr '18

Hi Doug, At the end of my FSFAST analysis, I would like to plot the Canonical HRF shape generated by FSFAST for my events. I have found this thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-July/031902.html but I am not sure if I understand this line: "plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf)" Could you please clarify how to plot the Canonical HRF that was generated by FSFAST? Thank you, Sarah

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Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)
by Anna Daniels 11 Apr '18

11 Apr '18

Hi Bruce, thank you for the quick reply! Ubuntu 16.04 LTS 64-bit freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Please let me know how to incorporate the new version into the installation. Thank you very much and best, Anna Hi Anna no attachments :< Srishti's issue stemmed from control points outside of the head. The current (dev) version of mri_normalize detects and removes them. Can you grab a new version of mri_normalize and see if it fixes your problem? Let us know your hardware/software environment and we will get it to you cheers Bruce On Fri, 6 Apr 2018, Anna Daniels wrote: > Hi Bruce, hi Srishti, > > I have exactly the same problem with several subjects rerunning recon-all > and there was sufficient memory available. I also tried out the last command > directly which resulted in the same error log. > > ?mri_normalize -f/home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_ cross_edits_transfer/rrer > uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg > aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz > > Attached you can find the input file. > > Thank you and best, > Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE]

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-make all error
by Carissa Nicole Weis 11 Apr '18

11 Apr '18

Hello, I am running recon-all for several subjects’ 7T data using Freesurfer version 6.0 and currently trying to ensure appropriate skull stripping and pial/wm surface generation. For a few participants that needed some control points added and for which I reran them through the –autorecon2-cp option, I was unable to open the pial surfaces for review. I’ve seen on some of the other posts that you guys recommend running “recon-all –make all” to rebuild the files. I’ve tried to run the -make all command but have been running into the same error in the “Jacobian white lh” step: #@# Jacobian white lh Wed Apr 4 12:07:37 CDT 2018 /bigraid-03/LS/Data/7T_fall2017/6315/6315_fs/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc… mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn’t match ../surf/lh.white.preaparc No such file or directory mrisReadTriangleFile failed. No such file or directory mris_jacobian: could not read target surface ../surf/lh.sphere.reg No such file or directory recon-all –s 6315_fs exited with ERRORS at Wed Apr 4 12:07:40 CDT 2018 All of the output in the log file up until this point appears to have finished without error. I can now open the surfaces for review, but am wondering what is affected by –make all not finishing completely. Carissa N. Weis, B.S. Graduate Student Affective Neuroscience Laboratory University of Wisconsin-Milwaukee cnweis(a)uwm.edu

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Subparcellation Problem
by Connor Garris 11 Apr '18

11 Apr '18

Hello, I'm running into a problem when subparcellating my regions of interest where after subparcellating there are some sublcusters that are labelled identically by freesurfer even though they are distinct subclusters. More specifically, I ran one iteration of mris_divide_parcellation passing it 400mm subclustering size and then ran a second iteration passing it 200mm (I did this because I want subclusters that are square-ish in shape as opposed to long bands). On the first iteration there is no problem, the second iteration however produces the problem I described where distinct subclusters are considered to be the same by freesurfer. I have attached a picture of exactly the problem since this explanation is a little convoluted. Any help would be greatly appreciated. Thank you, -Connor

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DICOM input to recon-all
by Karin Westin 11 Apr '18

11 Apr '18

Hi everybody! I'm very new to freesurfer and I'm trying to perform a reconstruction using recon-all. My problem is I don't see how I can access a single file to input to recon-all. I've run dcmunpack -src <path to mri-file> but the only output I get is Found 2 unique series: 4 401 Subject (name of subject) Date (date of examination) Time 110000 Institution (place of acqusition) 4 3DBRAVO+Gd 3.344 8.724 13 0.9375 ROW 195.312 ./EE975AF8 401 refSAGBRAVO+gd 3.344 8.724 13 0.46875 unknown 195.312 ./EEF3A407 <freesurfer(a)nmr.mgh.harvard.edu> How do I access the actual files of these series? Best, Karin

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how to control for head size differences when measuring global atrophy?
by Maria Gloria Rossetti 10 Apr '18

10 Apr '18

Dear freesurfers my study aims to measure volumetric differences between patients X and controls. As dependent variables, I have (i) a-priori ROIs and (ii) global brain measures (total gm, total wm and CFS). In the ROIs analysis, I use eTVI to control for for head size variability. Now my question is: should I control for head size when measuring overall brain atrophy? Theoretically speaking I'm not sure . Practically speaking there is a high positive correlation (as expected) between global brain measures and eTVI in my sample so I think it wouldn't be correct to use eTVI. But still, is global atrophy affected by head size? should I control for it? Second quick question: I'm planning to replicate the analysis measuring thickness differences. Should I control for tot mean thickness then? Thanks in advance for your help. Gloria

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Freesurfer April 2018