Freesurfer December 2017

freesurfer@nmr.mgh.harvard.edu

107 participants
172 discussions

mri_nlfilter
by John Anderson 14 Dec '17

14 Dec '17

Dear Dr Bruce, Kindly, I have question regarding the command "mri_nlfilter". I am sorry if my questions is simple, but I highly appreciate any explanation to improve my understanding. I see in the man list of the command "mri_nlfilter" that it can apply Gaussian filtering and blurring kernell. What is the difference between Gaussian smoothing and blurring. For example in PET images we used to smooth the images to improve SNR. Does blurring apply something similar and can be helpful to improve SNR. Thanks for any clarification! J

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Correlation between CTh and Clinical Data
by Shatil, Anwar Shahadat 14 Dec '17

14 Dec '17

Dear Experts: I am very new to freesurfer glmfit and this post may seem dumb. I wanted to find the correlation between Cth and Education for each of HC and RRMS group regressing out the effect of gender and (demeaned) age. My fsgd file is something like below. GroupDescriptorFile 1 Title Group-Edu-Correlation MeasurementName thickness Class FemaleHC Class FemaleRRMS Class MaleHC Class MaleRRMS Variables Age Education Input 1 FemaleRRMS -7.97 0.243 Input 2 MaleRRMS -2.97 -1.300 Input 3 FemaleHC -12.97 -0.914 Input 5 Male HC 4.03 -1.686 ………………….. I used DODS method. For HC, I set the correlation matrix as: 0 0 0 0 0 0 0 0 0.5 0 0.5 0 And for RRMS, I set the matrix as: 0 0 0 0 0 0 0 0 0 0.5 0 0.5 1. I am wondering, if my DODS contrasts are correct. 2. To get better DOF, should I create two different FSGD file for each group (i.e. one for HC and one for RRMS)? 3. If I create two different FSGD file for each group then can I use DOSS method and use the contrast: 0 0 0 1 ? Thanks, Anwar This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.

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A note about the Freesurfer license file
by Z K 14 Dec '17

14 Dec '17

Hello All, Users on newer linux distributions who upgrade from Freesurfer version 5.3 to version 6.0 may get the following error message: -------------------------------------------------------------------------- GNU libc version: 2.17 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html -------------------------------------------------------------------------- This is a known issue, and as the message says, it is resolved by downloading a newly formatted license file from our registration page: http://surfer.nmr.mgh.harvard.edu/registration.html Simply overwrite the old license file with the newly formatted one. Sorry for any inconvenience this may have caused. -The Freesurfer team

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mri_surf2surf on edited subjects
by Defenderfer, Matthew K 14 Dec '17

14 Dec '17

Hi all, I am trying to transfer a surface file from fsaverage_sym space to a recently edited individual subject's hemisphere. I previously ran recon-all on the subject and then edited the wm, brainmask, etc. to fix some defects I had found. Before the edits, I could transfer the surface and load it on the subject's hemisphere as an overlay perfectly fine. After editing and rerunning the subject through recon-all and the xhemi pipeline, I tried to transfer and load the overlay again using the following command, same as originally: mri_surf2surf --srcsubject fsaverage_sym --srcsurfreg sphere.reg --trgsubject subj001 --trgsurfreg fsaverage_sym.sphere.reg --hemi lh --sval template.sym.mgh --tval subj001/surf/template.sym.mgh The command completes, but the resulting overlay does not have the same number of vertices as the surface. It does however, have the same number of vertices as the original surface from before rerunning the recon-all command. So it seems like it's still transferring the overlay to original surface. My SUBJECTS_DIR does not have the subjects' original recon-all data in it either, just the data from the edited recon-all. Any help on this would be appreciated. Thank you! -Matt Defenderfer Matthew K. Defenderfer B.S. | Graduate Research Assistant Graduate Biomedical Sciences | Neuroscience UAB | The University of Alabama at Birmingham Laboratory of Kristina Visscher, PhD Department of Neurobiology CIRC 111 | C: (865) 805-6389

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Re: [Freesurfer] free surfer v5 & 6
by Lilla Zollei 14 Dec '17

14 Dec '17

Hi Gianluca, > I am working with data coming from two different versions of Freesurfer, v5.1 and v6. > As measurements looks different (an excerpt below from aseg.stats files), I am trying to see if that difference is statistically relevant. > Could you anticipate something with this respect? We do not advise you to include data processed with different versions in the same study as there are differences between our releases. > One more question is about voxel counting and their volume. aseg.stats prints out that # VoxelVolume_mm3 1 > but volumes from v.6 seems to be sometimes greater sometimes lower than the voxel number, > while in v. 5.1 they correspond. > Could you give me some clarification? I do not understand your question. Are you asking about the volume differences between the two versions? Lilla > > v.6 > > # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange > 1 4 5424 5779.6 Left-Lateral-Ventricle 22.1768 15.6303 0.0000 81.0000 81.0000 > 2 5 198 225.9 Left-Inf-Lat-Vent 43.8838 14.0865 6.0000 77.0000 71.0000 > 3 7 17444 18248.8 Left-Cerebellum-White-Matter 80.5691 8.7322 20.0000 133.0000 113.0000 > 4 8 69258 69340.7 Left-Cerebellum-Cortex 49.2701 12.9332 0.0000 128.0000 128.0000 > 5 10 8758 8432.7 Left-Thalamus-Proper 81.4639 10.8500 37.0000 123.0000 86.0000 > > v. 5.1 > > # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange > 1 4 5013 5013.0 Left-Lateral-Ventricle 16.7825 16.6860 0.0000 82.0000 82.0000 > 2 5 161 161.0 Left-Inf-Lat-Vent 39.9084 12.2446 7.0000 73.0000 66.0000 > 3 7 19250 19250.0 Left-Cerebellum-White-Matter 83.1263 8.1640 41.0000 110.0000 69.0000 > 4 8 60246 60246.0 Left-Cerebellum-Cortex 50.8222 10.7915 5.0000 93.0000 88.0000 > 5 10 7911 7911.0 Left-Thalamus-Proper 88.1600 10.4226 43.0000 134.0000 91.0000 > > > > >

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Re: [Freesurfer] Qdec Table Loading Error
by Douglas N Greve 14 Dec '17

14 Dec '17

there are lots of strange characters in that file (as revealed with the od octal dump program). Maybe run dos2unix on the file or create it from scratch. On 12/14/2017 12:00 PM, Arsenije Subotic wrote: > > Hi Douglas, > > > I tried doing that but it seems that the issue is that when I open > Qdec it does not recognize any of the files in the folder as a data > file (.dat). > > > Thanks, > > Arsenije > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *Sent:* Thursday, December 14, 2017 9:47:54 AM > *To:* Arsenije Subotic > *Subject:* Re: [Freesurfer] Qdec Table Loading Error > The table is not quite the right format. Your first line is > > > lh.aparc.thickness lh_MeanThickness_thickness > BrainSegVolNotVent eTIV gender age > > > but it should be > > > fsid lh.aparc.thickness lh_MeanThickness_thickness > BrainSegVolNotVent eTIV gender age > > try that > > > On 12/12/2017 02:21 PM, Arsenije Subotic wrote: > > > > Hi Douglas, > > > > > > Here is the text file I am trying to convert. > > > > > > Thanks, > > > > Arsenije > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > > *Sent:* Tuesday, December 12, 2017 11:52:41 AM > > *To:* Arsenije Subotic > > *Subject:* Re: [Freesurfer] Qdec Table Loading Error > > yes > > > > > > > > On 12/12/2017 01:48 PM, Arsenije Subotic wrote: > > > Hi Douglas, > > > > > > Is it ok if I can send you the table to your email? I tried > > uploading my file using the FTP File Exchange but it doesn’t seem to > > work for me under the put.filename.txt command. > > > > > > Thanks, > > > Arsenije > > > > > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > FileDrop v2.0 - Martinos Center for Biomedical Imaging > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > gate.nmr.mgh.harvard.edu > > Filedrop is for sending files work-related files up to 2GiB; For files > > over 2GiB, please use the Accellion File Transfer from Partners; > > Filedrop is not a secure ... > > > > > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Martinos Center File Drop - nmr.mgh.harvard.edu > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > www.nmr.mgh.harvard.edu <http://www.nmr.mgh.harvard.edu> > > 11/15/2012 -- There is a new version of Filedrop. Please help us test > > it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos > > Center file drop area ... > > > > > > > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > 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. > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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JRE error in fsfast/matlab
by Yagmur Ozdemir 19 14 Dec '17

14 Dec '17

Hello FreeSurfer experts, I have been running into a matlab-related problem that I was wondering if anyone came across. I am using Matlab2017b with Freesurfer 6.0. Whenever I run selxavg-sess<https://surfer.nmr.mgh.harvard.edu/fswiki/selxavg-sess> command, the matlab tries to find the OpenGL rendering, then gives a Java fatal error with a failure to find the Java Runtime Environment and exits. (I don't have the command outputs with me right now, sorry.) I have been trying to fix it with getting a better graphics card, OpenGL, getting Octave etc but this error didn't come up when I was using an earlier version of Matlab. I would appreciate any help. Best Idil

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?h.DKTatlas100.gcs to annot
by tony han 14 Dec '17

14 Dec '17

Hi, Is it possible to get an annot file for ?h.DKTatlas100.gcs, not for individuals, but for fsaverage atlas? I want to plot the 'standard' parcellation, instead of individual ones, on the surface so that I can use as a general reference. Thanks! Tony

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LGI ERROR
by 郑凤莲 13 Dec '17

13 Dec '17

Hi professors, I am using Freesurfer 6.0 for calculating LGI. I have done 'recon-all' for it. When I ran Monte Carlo in qdec (FWHM=10), it has errors: However, when FWHM=5, It was ok. What led to this result? I don't know why. Thanks in advance ! Zheng

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Re: [Freesurfer] Dura classified as GM in brainmask
by FSL Analysis 13 Dec '17

13 Dec '17

Hi Bruce, Thank you for your reply. I am using 5.3.0 version. Do I still only correct misclassified GM voxels in the brainmask? For the subjects with brain classified as cerebral cortex in the aseg file which is outside of the pial surface (but present in the brainmask) how do I correct this: 1. If it should be GM how do I edit the pial surface? 2. If it is non-brain matter how do I remove it from the aseg file- do I erase these voxels from the brainmask even though they are not in the pial surface mask? Thanks, Ciara Hi Ciara what version are you running? I think you only need to correct voxels that cause the white and/or pial surfaces to be incorrect, as we correct the aseg with them (at least I think we do in v6) cheers Bruce On Wed, Dec 13, 2017 at 12:11 PM, FSL Analysis <fslanalysis(a)gmail.com> wrote: > Hi again, > > I realize my last question about the brainmask did not make sense. I meant > to ask if I have to either manually delete all non-brain voxels around the > eye area which is very time consuming per subject or just delete those > misclassified as GM? ( I check this through the command: tkmedit > subj_output brainmask.mgz -aux T1.mgz -surfs) > > Also for some subjects: > 1. When I open freeview and look at the aseg file there is area around the > eye misclassified as cerebral cortex for some subjects. > 2. When I load the pial surface the aseg file shows cerebral cortex in the > temporal poles and frontal lobes near the eye region outside of the pial > surface outline. How do I edit this? > > > > I look forward to your response. > > > > > Thanks > > On Tue, Dec 12, 2017 at 4:21 PM, FSL Analysis <fslanalysis(a)gmail.com> > wrote: > >> Hi all, >> >> I have processed data using freesurfer and the output for most of my >> subjects did not remove all of the eye and dura around it during skull >> stripping. When I check the brainmask there is dura (or blood vessel) in >> the frontal lobe that is classified as GM. >> >> I am wondering if I have to manually edit the skullstrip and rerun >> recon-all or do I just edit the brainmask file by deleting non-brain >> voxels? Or do I have to do both? >> >> If I only edit the brainmask file does this skip any other important >> processing steps that may affect my results? >> >> I am planning on looking at brain volumes and cortical thickness and how >> they relate to behavioral measures. >> >> >> >> >> Kind Regards, >> >> Ciara >> > >

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Freesurfer December 2017