Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

Strange background when opening brain mask
by pablo najt 24 Jul '14

24 Jul '14

FreeSurfer experts,I have a question about one of my scans after running recon-all -all. When I open the image with freeview for inspecting brain mask volume.To give you a better idea of the problem I have attached a screenshot of the T1 volume. All my other images did not show the coloured black background that observed here, so I am wondering what might be the problem.To open T1 I have used the suggested command:freeview -v pial_edits_before/mri/T1.mgz \ pial_edits_before/mri/brainmask.mgz \ -f pial_edits_before/surf/lh.white:edgecolor=yellow \ pial_edits_before/surf/lh.pial:edgecolor=red \ pial_edits_before/surf/rh.white:edgecolor=yellow \ pial_edits_before/surf/rh.pial:edgecolor=redMy scans have been processed in nifti format. Also I have previously run nu_correct for correction of artefacts in the top of the brain.I also opened this particular scan and it looks very similar to the others.Thank you in advance for your attention.Pablo

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area vs. area.pial
by Katharina Zech 24 Jul '14

24 Jul '14

Dear administrators, I've got the problem that I cannot make out the difference between "area" and "area.pial". As far as I understand "area" refers to white matter surface area while "area.pial" includes everything up to pia mater (including CSF). Unfortunately I don't know what I am exactly looking at when I run the "area.pial"-simulation. What does it tell me? Thanks a lot, Katharina

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Re: [Freesurfer] Anterior Temporal Lobe / Pial Reconstruction Troubles
by Las Blawimo 24 Jul '14

24 Jul '14

Dear Dr. Fischl, Thank you for offering to look at our data. I have used the FTP server to upload a zip archive, based on the website instructions (http://freesurfer.net/fswiki/FtpFileExchange) The file is in: transfer/incoming/1353.zip (using anonymous and my email address for the user/password) Please let us know if you have any thoughts on how we can improve our temporal lobe pial reconstruction. Sincerely, Las 2014-07-18 18:00 GMT+02:00 <freesurfer-request(a)nmr.mgh.harvard.edu>: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: mni152reg error (JacobML(a)nmr.mgh.harvard.edu) > 2. template replacement (Ilwoo Lyu) > 3. unit of each index (thickness, volume, sulc, curv) after > mri_glmfit-sim (wang kangcheng) > 4. Re: unit of each index (thickness, volume, sulc, curv) after > mri_glmfit-sim (Douglas Greve) > 5. Re: mni152reg error (Douglas Greve) > 6. Re: unit of each index (thickness, volume, sulc, curv) after > mri_glmfit-sim (wang kangcheng) > 7. Re: unit of each index (thickness, volume, sulc, curv) after > mri_glmfit-sim (Douglas Greve) > 8. Spatial smoothing in Matlab (Reza Rajimehr) > 9. Re: unit of each index (thickness, volume, sulc, curv) after > mri_glmfit-sim (wang kangcheng) > 10. Re: Anterior Temporal Lobe / Pial Reconstruc?tion Troubles - > part 1 (Las Blawimo) > 11. Re: selxavg3-sess error in ==> fast_selxavg3 at 434 > (pfannmoelj(a)uni-greifswald.de) > 12. Errors in Mapping of Brodmann Areas (pfannmoelj(a)uni-greifswald.de) > 13. Re: mni152reg error (JacobML(a)nmr.mgh.harvard.edu) > 14. Re: Errors in Mapping of Brodmann Areas (Bruce Fischl) > 15. Re: Errors in Mapping of Brodmann Areas > (pfannmoelj(a)uni-greifswald.de) > 16. Re: Anterior Temporal Lobe / Pial Reconstruc?tion Troubles - > part 1 (Bruce Fischl) > 17. Thickness measurements on longitudinal data set (Bastian Cheng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Jul 2014 13:14:43 -0400 (EDT) > From: "JacobML(a)nmr.mgh.harvard.edu" <jacobml(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mni152reg error > To: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <44065.172.20.147.36.1405617283.squirrel(a)mail.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hello again Doug, > > Thank you for sending the updated version of mri152reg. It ran without > error and generated the reg.mni152.2mm.dat registration matrix. > > Unfortunately though, when I tried to apply the transformation to the same > subject's t_000.bfloat, the registration is not correct (command below). > > mri_vol2vol --inv --targ /.../t_000.bfloat --mov > $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o > CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg > /.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat > > On a positive note, I was able to load the output image and > MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed to be > shifted too far anterior. > > With my next attempt, I used mri_convert to make the t_000.bfloat into a > .mgz and than ran mri_vol2vol, but the same misalignment occurred (see > attached photo). > > Using tkmedit, I have confirmed that this file aligns properly on this > subject's native structural image, so I am not quite sure why the > registration matrix may be off. Given that the reg.mni152.2mm.dat file > reflects the transformation of the native struc to MNI, I wonder if I need > to account for the reg file between the func data and the native struc? > > Can you please let me know what I may be doing incorrectly? > > As always, your help is very appreciated. > > Jacob > > > > > > > Yea, i fixed this problem. I've attached a new version with the fix. doug > > > > On 07/17/2014 10:35 AM, JacobML(a)nmr.mgh.harvard.edu wrote: > >> Hello Freesurfer Experts, > >> I am trying to view stats generated with FsFast in fslview/MNIspace, > and > >> in doing so I have run mni152reg to generate the registration matrix. > That said, mni152reg did not complete correctly and below I have pasted > the terminal output: > >> Thu Jul 17 09:58:10 EDT 2014 > >> setenv SUBJECTS_DIR > >> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons > >> cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons > /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s > >> CD_cerv_pat4_sess1_recon > >> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 > UTC > >> 2014 x86_64 x86_64 x86_64 GNU/Linux > >> fslregister --mov > >> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz > --s CD_cerv_pat4_sess1_recon --reg > >> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat > --dof 12 > >> mkdir: cannot create directory > >> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833': > Permission denied > >> Log file is > >> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log > Thu Jul 17 09:58:11 EDT 2014 > >> --mov > >> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz > --s CD_cerv_pat4_sess1_recon --reg > >> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat > --dof 12 > >> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ > >> purkinje > >> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 > UTC > >> 2014 x86_64 x86_64 x86_64 GNU/Linux > >> nIters 1 > >> -------------------------------------- > >> /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons > >> mri_convert > >> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz > > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > mri_convert > >> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz > > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > niiWrite(): error opening file > >> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from > >> > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz... > TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00 > >> i_ras = (-1, 0, 0) > >> j_ras = (-0, -0, -1) > >> k_ras = (0, 1, 0) > >> writing to > >> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii... > ERROR: failure writing > >> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii > I tried to run the fslregister command from within the subject's > directory > >> (in hopes to possible correct what may be a permissions issue), but > this > >> produces the same final error, "ERROR: failure writing > >> > /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii." > Lastly, probably to no surprise, the > >> /.../mri/transforms/reg.mni152.2mm.dat file was never generated. Any > ideas how I may be able to correct these errors? > >> Thank you for the help! > >> Jacob > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > 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/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Calculate average thickness mathematically?
by Dorian P. 23 Jul '14

23 Jul '14

Hi all, A while ago I asked how can I calculate the average thickness of the three lateral temporal gyri, and Bruce kindly suggested to draw the label on fsaverage and use transforms to calculate it for each subject. I may try to do that, but given my time constrains and my level of knowledge of Freesurger I thought an alternative method: Say for example I have the inferior, middle, and superior temporal gyrus with surface areas of 1000, 2000, and 3000. They also have an average thickness of 2, 3, and 4mm, respectively. Given that these thicknesses are distributed in those areas, I could weight each region accordingly and calculate the average thickness as: ( (1000*2) + (2000*3) + (3000*4) ) / (1000+2000+3000) = 20000/6000 = 3.33 Is this logic correct, and why yes or no? Thank you in advance. Dorian TJU

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Questions regarding recon-all command
by soumyabrata.dey 23 Jul '14

23 Jul '14

?Hi All, I am new to freeSurfer and need your guidance for some of the doubts I have. I have installed freeSurfer in a windows 7 machine using virtualBox. I am trying to process some of my own sMRI data using freeSurfer software. The data is skull-stripped and has cerebellum. The format of the data is NIFTI (.hdr, .img). I am having some problem with running the recon-all command on the data as I am getting the error message saying <filename>.hdr is not found (I have also tried with inputting .img file). My questions are: * ?Is recon-all compatible with .hdr .img file format? I know it should run with .dcm and .nii files. If not what are my option? * ?Do I need to set up any environment variable for the -i option of the recon-all like the SUBJECTS-DIR for -s option. I have tried inputting the full path of the input file. Also, I tried with moving to the directory of input file and run the command from there. Thanks for your help, Soumya.

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Re: [Freesurfer] question regarding control point edits
by Adam Mezher 23 Jul '14

23 Jul '14

Hi Bruce, Yeah that was my thinking as well. So, if after running 500 subjects through FS and 100 need similar edits in the anterior temporal lobes, we will have no choice but to perform manual edits for each case individually? Thanks for clarifying! Adam Mezher > > Hi Adam I don't think so as how would we don't know where the anterior temporal lobe at that stage in the process. Bruce On Tue, 22 Jul 2014, Adam Mezher wrote: > Hi FreeSurfer group, > I was wondering if there is a way to include control points in my command > line when I run recon-all. We are working with a large dataset and many of > the subjects have underestimations in the anterior temporal lobes so it > would be beneficial to expand the WM surface slightly on numerous cases > rather than doing control point edits on each case individually. > > Thank you, > Adam Mezher >

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Mapping stats into volume with mri_label2vol
by Jackie Lam 23 Jul '14

23 Jul '14

Hello all, I am trying to map polar angle and eccentricity into the voxels underneath a particular label. For each vertex in the label file, I’ve put in the respective angle in the stats column. I then used mri_label2vol with the --label-stat flag to map the angle values into the volume. Comparing the angle values for each individual voxel and each vertex, I’ve noticed that some values that are in the voxels are not present in the vertices (ie a particular voxel might have a value of 0.5 but none of the vertices have that exact value). What happens when the values are mapped from the vertex into the volume? Is there some averaging or weighting process or something? Many thanks, jack

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wm/pial surfaces from manually created surfaces
by Itamar Kahn 23 Jul '14

23 Jul '14

Greetings, I would like to use two surfaces that I created manually on the same anatomy and to create a single subject with the surfaces such that one is the pial and the other is the wm surface. Any leads on how to achieve this will be greatly appreciated. Thanks, Itamar

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qcache number of vertices error
by O'Shea,Andrew 23 Jul '14

23 Jul '14

Hello, I am running into an error when using qcache. Subjects that have had manual edits are exited with errors, while subjects that have not had edits run fine. All subjects have had –make all ran after edits and finished without errors. I have read about this problem and tried some of the solutions but am still getting errors. When I first tried running –qcache I received this error: Reading curvature file /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.volume ERROR: number of vertices in /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.volume does not match surface (128222,130849) ERROR: reading curvature file Linux c2a-s21.ufhpc 2.6.32-358.23.2.el6.x86_64 #1 SMP Sat Sep 14 05:32:37 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1492 exited with ERRORS at Wed Jul 23 10:32:24 EDT 2014 To make sure everything was ran I re-ran –make all and got make: Nothing to be done for `all’. I then ran –vno_match_check and it said everything was fine: Pass: all surfaces and surface data for subject 1492 for hemi lh have the same number of vertices. Pass: all surfaces and surface data for subject 1492 for hemi rh have the same number of vertices. I saw Doug gave this suggestion ( using –surf volume –qcache) to someone who was having the same problem this resulted in qcache getting past the volume stage but failing lh.w-g.pct.mgh Reading curvature file /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.w-g.pct.mgh ERROR: number of vertices in /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.w-g.pct.mgh does not match surface (128222,130849) ERROR: reading curvature file Linux c1a-s11.ufhpc 2.6.32-358.23.2.el6.x86_64 #1 SMP Sat Sep 14 05:32:37 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1492 exited with ERRORS at Wed Jul 23 11:07:01 EDT 2014 Any suggestions on how to address this? Any idea of the cause? I assuming it has something to do with the manual edits since unedited ppl run fine. -Andrew

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Re: [Freesurfer] recon-all error
by Cheng Peng 23 Jul '14

23 Jul '14

Hi, Bruce: I attached the file with an email and sent it to you an hour ago and received an automatic reply saying it's pending for approval due to the size of the email. Is there another way to upload my image or it's getting processed? I don't want to spam you guys since i already sent it twice and got the same result. Thanks! Cheng Peng On Wednesday, July 23, 2014 9:39 AM, Cheng Peng <pcdulaney(a)yahoo.com> wrote: Hi, Bruce, I attached the nu.mgz file with this email, i'm at home right now and would upload T1.mgz later if need to. As far as i know individual recon-all runs were completed without error (two scans on one subject, two hours apart), really appreciate the help! Cheng Peng Maryland Neuroimaging Center On Wednesday, July 23, 2014 9:32 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: Hi Cheng do the cross-sectional runs look okay? The base? If so, does the first intensity normalized images look ok (the T1.mgz and the nu.mgz)? If you can't track it down, upload the subject and we will take a look cheers Bruce On Wed, 23 Jul 2014, Cheng Peng wrote: > Hi, Freesurfer experts: > > > > I encountered an error message while i was attempting to run a longitudinal > study (following the instructions from > https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing, step 2 > under workflow summary) > > egister_mri: find_optimal_transform > find_optimal_transform: nsamples 2185, passno 0, spacing 8 > GCAhistoScaleImageIntensities: could not find wm peak > resetting wm mean[0]: 102 --> 107 > resetting gm mean[0]: 64 --> 64 > input volume #1 is the most T1-like > using real data threshold=0.0 > skull bounding box = (0, 0, 0) --> (255, 255, 255) > using (85, 85, 128) as brain centroid... > mean wm in atlas = 107, using box (53,53,96) --> (116, 116,159) to find MRI > wm > WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1, mri_peak=-1 > before smoothing, mri peak at 0 > WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1, mri_peak=-1 > after smoothing, mri peak at 0, scaling input intensities by inf > > It appears that the skull strip step has failed as brainmask.mgz is > completely blank. I tried to look up the error message online but found > little help there. I would really appreciate it if someone can explain the > problem or where to look for an explaination. I attached the recon-all error > log with this email, i would also include nu.mgz but the last email attached > with that was blocked due to the size of the image. > > Thanks! > > Best Regards, > > Cheng Peng > > Maryland Neuroimaging Center > > > > > > > > _______________________________________________ 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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Freesurfer July 2014