Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Global mean FA
by Alshikho, Mohamad J. 31 Jul '14

31 Jul '14

Hi Fs Experts, In order to calculate the global white matter fractional anisotropy FA I used (wm.mgz ) the output of recon-all as a mask in the following command line mri_segstats --seg $SUBJECTS_DIR/015601/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --mask wm.mgz --i fa.anat.mgh --sum fa.stats Kindly, Is this correct? Thanks Mohamad

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Surface "resampling" for Qdec using -qcache
by "Christoph Abé" 31 Jul '14

31 Jul '14

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Re: [Freesurfer] tkmedit doesn't show lines distinguishing grey and white matter
by Talia Raney 31 Jul '14

31 Jul '14

Hi, What seems to be happening is that I insert this command: tkmedit subject_id brainmask.mgz rh.white -aux T1.mgz -aux-surface lh.white -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt it should show me the subcortical segmentation overlayed with the pial, white, and orig surface lines shown. It no longer shows me this after I made some control points in the coronal view. [image: Inline image 1] This is what should show [image: Inline image 2] Why is this? Talia On Mon, Jul 28, 2014 at 10:40 AM, Talia Raney <talia.raney(a)gmail.com> wrote: > Hi, > I'm having issues with tkmedit. I'm doing visual inspection and I checked > tkregister to be sure that the white matter is outlined in the functional > image. However, when I open tkmedit for surface and cortical segmentation, > it doesn't show up the red and green lines that distinguish the boundaries > of the grey and white matter. It had previously and I put a few control > points but now it doesn't show up at all. > Why might this be and how can it be fixed? > Thanks! > Talia > > >

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mpr2mni305 failed
by Francesco Deleo 31 Jul '14

31 Jul '14

I all! I have the same problem in about 15% of MRI scans, all made with the same scanning protocol (T1 MPRAGE in a SIEMENS Avanto 1,5 T) during the recon-all -all process. I can't recognize any difference between those scans which work correctly and those not. I have never found the same error on 3T MRI scans. I've already tried to add these flags to the recon-all -all command: -use-mritotal -talairach -use-mritotal -notalairach but I've always received an error message Thank you very much ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin pro-di-villani.besta.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 Thanks for your attention Francesco Deleo Milan, Italy --------------------------------------------------------------------- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 13.3.0 x86_64 --------------------------------------------------------------------- LAST LINES IN TALAIRACH_AVI.LOG parameters 9.0270 134.9373 110.8627 -84.3566 -7.5458 -11.3475 eta,q 0.95791 3.72402 0.0485 0.0470 0.0477 0.0513 0.0470 0.0452 0.0475 0.0471 0.0478 0.0513 0.0457 0.0435 0.0472 0.0472 0.0476 0.0428 0.0434 0.0415 0.0471 0.0471 0.0476 0.0435 0.0430 0.0415 0.0470 0.0478 0.0457 0.0525 0.0415 0.0430 0.0473 0.0511 0.0430 0.0548 0.0442 0.0453 0.0486 0.0426 0.0406 0.0672 0.0431 0.0503 niter,ni,del,rscale 7 3 12.0000 1.2000 imgrege: no voxels in register ERROR: 'imgreg_4dfp /Applications/freesurfer/average/711-2C_as_mni_average_305 /Applications/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted

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Re: [Freesurfer] NIH Staff Scientist Position available, Bethesda, MD, USA
by Xiaomin Yue 31 Jul '14

31 Jul '14

The title has been FedEx for overnight. Please let me know after getting it. Xiaomin ________________________________ From: Thomas, Adam (NIH/NIMH) [E]<mailto:adamt@nih.gov> Sent: ‎7/‎30/‎2014 6:36 AM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>; FSL - FMRIB's Software Library<mailto:FSL@JISCMAIL.AC.UK>; spm(a)jiscmail.ac.uk<mailto:spm@JISCMAIL.AC.UK>; announce(a)fmrib.ox.ac.uk<mailto:announce@fmrib.ox.ac.uk> Subject: [Freesurfer] NIH Staff Scientist Position available, Bethesda, MD, USA Posted on behalf of Dr. Judy Rapoport: Department of Health and Human Services (DHHS) National Institutes of Health (NIH) National Institute of Mental Health (NIMH) Division of Intramural Research Programs (DIRP) Section on Childhood Neuropsychiatric Disorders (SCND) Child Psychiatry Branch (CPB) Staff Scientist position available The Child Psychiatry Branch, in Bethesda, Maryland, is recruiting applicants for a Staff Scientist position. As a Staff Scientist, the primary duties will include conducting statistical analyses on clinical, neurobiological and treatment studies carried out in the Branch. This includes but is not limited to tasks such as maintaining the appropriate data sets, clearly conveying statistical results and methods both orally and in writing, reviewing and writing statistical content for manuscripts prior to submission, and working closely with and providing statistical support for all Branch members. The Staff Scientist position entails 25% time allotted to pursuing individual research interests. The Child Psychiatry Branch is a highly productive and collaborative group with a rich, multimodal dataset that seeks to understand neuro-developmental disorders, with a focus on childhood-onset schizophrenia. There is a strong scientific and statistical computing core facility in existence, which can benefit this work. For more information about the Child Psychiatry Branch, please utilize the following link: http://www.nimh.nih.gov/labs-at-nimh/research-areas/clinics-and-labs/chp/in dex.shtml Interested candidates should have a Ph.D., M.D. or equivalent doctoral degree and five years post-doctoral experience. Applicants should have a strong background in statistics as well as interests and experience in neuroimaging and behavioral research. The recruit should be adept at writing his/her own code to clean, organize, analyze, and visualize data. In addition some highly desirable skills include: experience analyzing structural MRI, functional MRI and/or MEG data; knowledge of cognitive neuroscience or clinical psychology; a solid foundation in multivariate statistics and longitudinal data analysis; proficiency in statistical programs such as R and MATLAB and visualization methods. SALARY RANGE: Salary is commensurate with experience and accomplishments. BENEFITS: The federal government offers a comprehensive benefits package including vacation, sick leave, holidays, life insurance, health benefits, and participation in the Federal Employees Retirement System. For more information go to new employee benefits at the NIH (http://hr.od.nih.gov/Benefits/permanentemployee.htm) and other employee benefits information (http://tiny.cc/saVcr) Interested applicants should send their CV and cover letter to: Dr. Judith Rapoport, NIMH, 10 Center Drive, Bldg. 10, Rm. 3N202 (MSC-1600), Bethesda, MD 20892 USA, or by email: rapoporj(a)mail.nih.gov SUBMISSION DEADLINE: September 1, 2014 NIH and DHHS are Equal Opportunity Employers. _______________________________________________ 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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Problem with Manual WM Edits not Affecting Surface Generation
by Andrew Schoen 31 Jul '14

31 Jul '14

Hi All, I am currently running freesurfer on a group of subjects, some of which have some bright areas of GM near the surface of the pial line that is getting included as WM. As per the wiki article here <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freev…> I erased the offending GM from the wm.mgz file, and reran with the command: recon-all -autorecon2-wm -autorecon3 -subjid SUBID However, despite making the edits and rerunning, the ?h.white surfaces did not seem to adjust to the revised wm.mgz file (in fact, they looked pretty much the same as before). I found an exchange on the listerv here <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-July/039002.html>, where it was suggested that Max look at the ?h.orig.nofix files, to see if the changes were recorded there. I opened the ?h.orig.nofix (yellow) up next to the ?h.white file (red), and you can see those in the attached image wmedits.png. An image with the edited wm.mgz file as a heat overlay is included (wmeditswithwm.png) I could see that the edits made to wm.mgz are being saved/read/interpreted correctly, and the nofix file was being saved correctly, but it doesn't seem to be influencing the surface file correctly. Do you have any idea what might be going on here? Thanks very much for any help you can provide, Andrew

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mni152reg
by Fan, Qiuyun 31 Jul '14

31 Jul '14

Hi Freesurfer experts, I was trying to align T1 image to MNI space by running 'mni152reg --s <subject>', and got the following error messages: mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.5197': Permission denied ... niiWrite(): error opening file /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.6610/refvol.fslregister.nii ... writing to /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.5197/refvol.fslregister.nii... ERROR: failure writing /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.5197/refvol.fslregister.nii Could somebody give me some advice on how to deal with the error? Thanks a lot! Best, Qiuyun

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Re: [Freesurfer] LocalGI error {Disarmed}
by Sarina Iwabuchi 31 Jul '14

31 Jul '14

Hi Marie, I've attached the log file. Thanks very much, Sarina Iwabuchi Hi Sarina, Can you please send me the full log of the LGI (e.g. recon-all.log) for this subject? Thanks, Marie On Jul 28, 2014, at 7:23 AM, "Sarina Iwabuchi" <Sarina.Iwabuchi at nottingham.ac.uk<mailto:Sarina.Iwabuchi at nottingham.ac.uk>> wrote: Hi all, I have been trying to run localGI and have been coming across errors. It creates the filled.mgz file and opens matlab (running 2012a) but crashes straight after with the below errors: >> reading filled volume... set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set: Variable name must begin with a letter. rm: Command not found. SWITCH expression must be a scalar or string constant. Error in load_mgh (line 158) switch type Error in MRIread (line 87) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly); Error in make_outer_surface (line 24) vol=MRIread(filled_volume); Has anyone come across this? I do have gunzip on my system. Thanks very much, Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Question with QDEC annotations and mri_convert and mri_annotation2label
by Tara Ann Miskovich 31 Jul '14

31 Jul '14

Hello, I am trying to convert my significant cluster from qdec into a .gii file, and I have a couple of questions. My mri_convert is not working, but it is my first time using it so I may be missing something, but it just keeps opening up the usage and gives no errors. mris_convert --annot mc-z.abs.th13.sig.ocn.annot mc-z.abs.th13.sig.ocn.gii Also, I was curious, how would one separate a annotation file created in qdec into separate label files with mri_annotation2label since there is no target subject which is required in he script. Thanks! Tara

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yet another newbie question (YANQ)
by Krieger, Donald N. 31 Jul '14

31 Jul '14

Thanks for the helpful responses to the previous questions, Bruce. It's great to not stay stuck for long. Here's another. I am working with voxels in the original MRI coordinate system. It appears that voxel and vertex coordinates in freesurfer are transformed to a 1 mm x 256^3 volume. Is there a tool to transform these back to MRI coordinates, preferably command line? Or is the transform itself easily found? Thanks again. Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text

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Freesurfer