Freesurfer October 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
170 discussions

Getting combined bvals/bvecs
by Marissa Pifer 21 Nov '16

21 Nov '16

Hello freesurfer experts, I am trying to run tracula on subjects that have separate AP/PA direction DTI files. We combined the data into one using topup, and would now like to run tracula on the subject. The problem is, the combined file doesn't have a bvals/bvecs file. When I try to use the original bval/bvec files, I get the error that the bvals and bvecs don't match up. I have tried combining the files into one, and then running a dicom to nifty conversion to get a combined bvals/bvecs output, but that results again in two separate bvals/bvecs files as well. I then tried just have two specified bvals and bvecs. This did not give us an error message, but trac-prep took only a few seconds and did not complete the steps it was supposed to to create the directories for trac-bedp to complete. I have attached our dmrirc.example file and the log for the trac-prep step for your reference. The questions then are; is there a way to get one bvals/bvecs file that has the correct parameters for the AP and PA combined file. Or, if not, is there a way to run tracula with two sets of bvals and bvecs (one for the AP and one for the PA direction)? In case you need this information, the process is being run with freesurfer 5.3, on a macbook pro OS X version 10.9.5. Thank you in advance, Marissa

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fsaverage_sym LR-flipchecks
by James Roe 20 Nov '16

20 Nov '16

? Hi Freesurfer experts I have an ultimate goal of performing direct LH v RH comparisons using the fsaverage_sym template, so these pre-analysis steps are aiming to assess the symmetry of the template. I have performed a first-level fMRI analysis on a subject and am using this to compare the output with the exact same analysis performed on the same subject with LR-flipped data (anatomical, BOLD runs and B0 maps). I then ran recon-all on this flipped subject (treating flipped subject as new subject). Attached is a screenshot showing the different analysis outputs. In the top left image, analyses have been performed and smoothed on fsaverage_sym (RH shows LH flipped anat and BOLD data). As you can see, agreement is generally high, but there are also marked differences, most notably in postcentral/precentral regions. The bottom left shows this output resampled onto the individual surface (for comparison purposes for the next analysis). The top right image shows the output when analyses were performed on the individual surfaces of the original and flipped subject. Here, agreement seems much higher, also in postcentral/precentral regions (although still not symmetrical). The bottom right image shows this output resampled onto fsaverage_sym, and agreement remains very high. So it seems that performing the analysis on fsaverage_sym itself may be affecting the expected symmetry of the output. Originally I aimed to perform a comparison of the vectors of B-values in order to prove symmetry, although I am not sure whether this is a viable option anymore. Do you have any advice as to how I could proceed with this? Finally, it appears that also in the fsaverage_sym template the L/R vertices do not correspond to one another. So will it be possible to flip the analysis values and template in order to perform LH v RH comparisons at the group level? System: Linux CentOS 6 x86_64 (64b) stable v5.3.0 Thank you for your time James

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Re: [Freesurfer] Two Stage Longitudinal Model
by Timothy Hendrickson 18 Nov '16

18 Nov '16

Hi Martin, Thank you for your reply. I am glad to hear that I am doing that correctly. I am running into an error when I attempted to run my GLM. I have looked at my fsgd and qdec files for errors, however I cannot seem to find anything. The error is in the attached .txt file named illCondMatrix_twoStage_years_10_31_16.txt. Additionally I've included my fsgd file for stage two and my qdec file for stage one. Any assistance would be extremely helpful, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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Longitudinal analysis
by Jaiashre Sridhar 18 Nov '16

18 Nov '16

Hi FreeSurfer Team, We are doing a longitudinal analysis with three time points which are six months apart. The subjects at any time point were scanned on either one of the two scanners (both Siemens 3T TIM TRIO) and we used FreeSurfer v5.1 for our analysis. Most of the subjects show decrease in cortical volume over time except a few of them, who show a huge increase in volume at their 6th-month visit (or at their 12th-month in a couple of cases). When we tried to look at the reconstructed surfaces of the long brains in Freeview, the gray matter and white matter boundaries of the 6th-month were bigger overall than the boundaries of the baseline and 12th-month. Could you share with us your thoughts on what factors (with MPRAGE/Scanner/FreeSurfer) might have caused this problem? Thank you, Jaiashre.

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'Invalid' license file
by Lee.Reid＠csiro.au 16 Nov '16

16 Nov '16

Hi, Our IT department have recently upgraded our cluster OS and now Freesurfer complains that its license is invalid. I have tried rebuilding, and acquiring a new license, but these do not fix the problem. The license file I am using works in my Ubuntu 12.04 computer - it has been copied across as a file, not via a text editor - and used to work on an older version of the same OS. Do you know of any solution to this issue? I've tried everything I have seen on the mailing list, including naming it .license and license.txt, checking for whitespace, etc. Our OS is now SUSE Linux Enterprise Server 12 SP1 (x86_64). Many thanks, Lee

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Mean intensity with mri_segstats : different results with .annot or .label
by Matthieu Vanhoutte 11 Nov '16

11 Nov '16

Dear experts, I am in trouble with two ways of computing mean intensity with mri_segstats. First I have used on .annot files with three different labels inside (SegId 1 to 3) : *mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum* which give me those results: # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 1 27805 14182.6 cluster-001 8.8194 1.4351 6.2105 14.2947 8.0842 2 2 2321 1047.3 cluster-002 10.3661 1.0848 8.8375 12.9317 4.0942 3 3 552 313.1 cluster3 10.3365 0.4711 9.3719 11.8694 2.4975 Second I have created on .label files containing the three segmented labels (SegId 1 to 3) and used this label with mri_segstats: *mri_segstats --slabel fsaverage lh lh.th23.cluster.thresh1.3.label --i lh.PET.fsaverage.sm10.mgh --excludeid 0 --sum lh.pet.label.sum * which give me those results: *# ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range * * 1 1 30678 15542.9 Seg0001 8.9637 1.4701 6.2105 14.2947 8.0842 * I verified if I obtained the same results with the two ways (.annot or .label) and everything is fine comparing NVertices, Area_mm2 but Mean in first way gives me (8.8194+10.3661+10.3365)/3 = 9.84066 and with .label file Mean = 8.9637. Did I have miss anything and how is computed mean intensity ? Many thanks in advance. Best regards, Matthieu

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mri_average vs mri_concat
by Trisanna Sprung-Much 10 Nov '16

10 Nov '16

Hi Doug I spoke with you at the Freesurfer tutorial last week about using mri_average to average my sulcal labels and get a probability map on fsaverage. You had suggested using "mri_concat" instead, which is a newer command. So, I performed the following command: *mri_concat all files --o output.mgz --mean --keep-datatype* I had to put --keep-datatype or else it tried to create an annot file. This worked just fine. My question then is concerning *the min and max values *when this average is overlayed in Freeview. See the snapshot attached. The values seem to be based on 256 instead of percentage and this is what happens when I used "mri_average" without specifying the "-p". Is there a way to illustrate the values in percentage in a similar way with mri_concat? Many thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Manual pial and white matter corrections cause irregularities
by Cleo Vandervost 10 Nov '16

10 Nov '16

Hi Bruce, As you asked, I uploaded the recon-all log-file for that subject, edited and unedited. We're using version 5.3. How can you check for sure that the WM significantly gets >110? I also uploaded the pictures once again. Thanks, Cleo ________________________________________ Van: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> namens Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Verzonden: vrijdag 21 oktober 2016 02:14 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Manual pial and white matter corrections cause irregularities Hi Cleo can you upload a subject before and after editing so we can replicate what you are seeing? And what version of FreeSurfer are you using? Does the WM after editing get signifcantly >110? If so, you may have accidentally placed a control point in a gray matter voxel cheers Bruce On Thu, 20 Oct 2016, Cleo Vandervost wrote: > > Hello Freesurfer team, > > > For my thesis I'm researching the differences in grey and white matter and cortical thickness between > children with and without dyslexia. My supervisor advised me to manually edit the Freesurfer-generated > data. I've been editing my data as follows: > > - adding control points to (larger) WM-areas that FS did not include > > - manually editing (smaller) WM-areas through recon-editing > > - correcting the pial surface through recon-editing > > > After finishing and saving my edits I reran recon-all with this command: recon-all -autorecon2-cp > -autorecon -subjid (subject number). When I opened my data again in Freesurfer to check my edits, I saw > that there were two big problems: > > - 'distortions' in the pial surface > > - sometimes large areas of WM suddenly were excluded, even when I didn't make any edits in that area > > It makes the edited data look much worse than the original data, which is weird I suppose. > > > I've included some pictures so you can see what I mean. > > - Picture (a) is the original unedited version. > > - Picture (b) is the edited version: control points and WM edits. You can see that there's a large area > in the left hemisfere excluded from the original WM area > > - Picture (c) is the re-edited version of (b), control points added in that large area. This time it's > included but the pial surface shows a lot of irregularities. > > > Me and my supervisor tried a couple of times with other data, but we still had the same results. We also > tried by only adding control points and editing manually, without the pial-corrections. > > > Do you have any idea of what's going wrong in the editing proces? > > > Thank you very much, > > > Kind regards > > > Cleo Vandervost > > 1st master speech and language therapy > > Katholieke Universiteit Leuven > > > > >

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recon-all steps question
by miracle ozzoude 08 Nov '16

08 Nov '16

Hello Freesurfer, I have couple of questions. While going through the frequently asked questions on your page http://freesurfer.net/fswiki/UserContributions/FAQ I came across a question regarding how to integrate a skull stripped from another problem into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid ----> create a symbolic link from T1.mgz to brainmask.auto.mgz and another like from brainmask.auto.mgz to brainmask.mgz ------> after run the finall stages of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created during skull stripping? why are they present if I included the "-no skullstrip" flag? Second question, where do I insert my already skull stripped data in the symbolic link? Last question, the final stages of recon-all doesn't include skull stripping, how can I be sure my skull stripped data was incorporated into the freesurfer recon-all process? Best, Paul

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mapping ROI to surface space
by Andrews, Derek 04 Nov '16

04 Nov '16

Hello Freesurfer Developers and Community, I am looking to map a ROI.nii based on the MNI152 template to the fsaverage pial surface. I have used the following commands Bbregister -s fsaverage -mov MNI152.nii -reg register.dat -init-fsl -12 -t1 Then mri_vol2surf -src ROI.nii -out ROI.mgh -srcreg register.dat -hemi lh The ROI appears to be in the right place however is very blotchy. Have I missed a step? Or is this correct? See bellow a picture of the ROI highlighted in FSL and in tksurfer after mapped using the above. Thank you for your support, Best, Derek [cid:20AF047A-6501-433B-9BE0-F5410F5ED296] ________________________________ Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews(a)kcl.ac.uk

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Freesurfer October 2016