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30086 discussions

RA position available in Neuroimaging of Multiple Sclerosis
by Lilla Zollei 25 Jul '14

25 Jul '14

Contact Caterina Mainero, M.D. (caterina(a)nmr.mgh.harvard.edu) if interested! >>> A full-time Research Technologist (Assistant) position is available in the field of Neuroimaging of Multiple Sclerosis (MS) at the A. A. Martinos Center for Biomedical Imaging of Massachusetts General Hospital (MGH). Duties will include acquiring and analyzing positron emission tomography (PET), functional magnetic resonance imaging (fMRI), diffusion tensor imaging (DTI) and high-resolution morphometric data acquired at high-field (3T) and ultra-high-field (7T) MRI in studies of patients with MS. The central research program seeks to study brain pathology in subjects with multiple sclerosis, and to identify in vivo bio-imaging markers that could help to improve monitoring multiple sclerosis disease course and potentially response to treatments. To investigate this, our laboratory utilizes ultra-high-field MRI and a multimodal imaging acquisition approach, together with an extensive clinical and cognitive assessment of patients. We collaborate with an interdisciplinary group of clinicians, psychologists and neuroscientists to accomplish our research objectives. The responsibilities of the Research Assistant position are varied, and involve all phases of human neuroimaging research. Specifically, the position involves the collection, management and analysis of multiple modes of imaging and requires the processing of functional, structural MRI and behavioral data. Requirements Undergraduate or Master degree in Physics and/or Biomedical Engineering, Computer Science or related field. Written and oral English communication skills are required. Solid PC-based skills are needed in word processing, spreadsheet and presentation programs. Proficiency in statistics and programs such as SPSS, or R are especially desirable. The ideal candidate would also have strong experience with MATLAB and UNIX/LINUX. Candidates with prior experience in neuroimaging research will be given special consideration. The job requires a candidate who is mature, responsible and flexible with strong interpersonal skills. The candidate must have excellent organizational skills and be able to maintain accurate records. The environment can be fast-paced and calls upon the individual to independently problem-solve/trouble-shoot, prioritize multiple tasks and seek assistance when appropriate. Interested applicants should send a cover letter describing research experience, interests and goals, as well as a curriculum vitae with contact names and details of three references to: Caterina Mainero, M.D., by e-mail: caterina(a)nmr.mgh.harvard.edu. A two-year time commitment is requested and salary will be based on qualifications and experience. The Massachusetts General Hospital is an Equal Opportunity/Affirmative Action Employer.

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WM inspection with freeview
by Pablo Najt 25 Jul '14

25 Jul '14

Dear FS experts, I have a doubt about inspecting white matter with free view. I could not find any irregularities where the blue line cuts through the surface. However, I noted in a few areas that the pail border makes funny shapes and seems to close up (please see attaches). I am in doubt here whether this should be edited or not. I have checked this in the other views and the inflated surface but I could not find anything wrong with the scan (eg.. a dimple or a hole). So I wanted to enquire whether I should consider this as a potential issue for editing. Also in the last attachment I have doubts about a yellow coloured in right parietal area apron. in the border between the white and pial. I was surprised of the location of this as the ventricles are usually yellow. It might be nothing but I just wanted to double check. Thank you! Pablo

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qcache number of vertices error [fixed]
by O'Shea,Andrew 25 Jul '14

25 Jul '14

Hello all, I was able to fix my error (see below) by re-running recon-all $SUB –autorecon2 –autorecon3 –qcache . However I am unsure why –make all was not incorporating edits correctly? Is it inappropriate to use –make all after manual edits? If so, should I just use –autorecon2 –autorecon3 as a catch all (assuming no edits in the first stage) after manual edits? -Andrew ----- 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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Serious error in updating ?h.aparc.stats in FLAIR/T2pial processing pipeline
by Martijn Steenwijk 24 Jul '14

24 Jul '14

Dear all, It seems that there is a serious error in the Parcellation stats files (i.e. ?h.aparc.stats) when using the FLAIR / T2 processing pipeline of FS 5.3. starting a particular recon-all with recon-all -s ${SUBJID} -i ${DIR} -FLAIR ${DIR/t1/flair} -FLAIRpial -all and looking through the recon-all.cmd file, it appears that the Parcellation stats are computed prior to refining the pial surfs, but not updated after refining the pial surfs. For instance: #@# Parcellation Stats lh Thu May 29 14:36:50 CEST 2014 and further on: #@# Refine Pial Surfs w/ T2/FLAIR Thu May 29 15:36:58 CEST 2014 but mris_anatomical_stats is not called again after updating the pial surfs. This can also be recognized by comparing the last-modified times of lh.aparc.stats and lh.pial-files, where the time of the first is older than compared to the latter. Moreover the ?h.aparc.stats of separate freesurfer runs with and without pial surface correction are *identical*. Is this a known issue? Best, Martijn

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Deep white matter parcellated atlas
by Alshikho, Mohamad J. 24 Jul '14

24 Jul '14

Hi Dear Fs Experts, I am looking for an atlas segmented all white matter without to leave any unsegmented white matter like in WMPARC I highly appreciate your help and support Thanks Mohamad

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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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