Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

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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mri_binzrize (flag --wm )
by Alshikho, Mohamad J. 31 Jul '14

31 Jul '14

Hi, I have a question about the flag " -wm" in mri_binarize: The following segments IDs 8 2 41 82 251 252 253 254 255 are included in this flag (based on the summary of this command line when I run it). Kindly what is the segment ID (Right-non-WM-hypointensities) means? and why the (left-non-WM-hypointensities ) is not included in this flag? Also what is maximum number of segments IDs that I can include in this command line using the flag -match ? Thanks, Mohamad

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Error in recon-all
by stdp82＠virgilio.it 31 Jul '14

31 Jul '14

Hi list, during recon-all, I have this error in three subjects (some months ago I analyzed them with success): Loading source label.No such file or directoryERROR reading /Applications/freesurfer/subjects/subject_prova/Con13/fsaverage/label/lh.perirhinal.labelDarwin iMac-di-Stefano.local 12.5.0 Darwin Kernel Version 12.5.0: Sun Sep 29 13:33:47 PDT 2013; root:xnu-2050.48.12~1/RELEASE_X86_64 x86_64 recon-all -s SUBJECTS_DIR exited with ERRORS at Thu Jul 31 07:48:56 CEST 2014 This is the log file is attached. Thank you very much. Regards, Stefano

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freesurfer FSL installation
by mahsa abadian 31 Jul '14

31 Jul '14

I have installed freesurfer V5 on my system (ubuntu 12.4) and there is no FSL in this path /usr/local/freesurfer. I think FSL has not been installed ad I want to install FSL compeletly in ubuntu there are two questions: 1. Should I write any command in terminal before doing anything else? I have understand from mail-list that I must remove FSL but there is no FSL to remove. 2.Should I make any changes to my .tcshrc file( freesurfer environment variable) to install FSL? please guide me to install FSL. I would be very appreciate if anybody could help me. mahsa

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PostDoc Position in Network Imaging / Post-Processing for Epilepsy
by Niels Focke 31 Jul '14

31 Jul '14

We are currently seeking a Postdoctoral Researcher (Akademischer Mitarbeiter) for the AG Translational Neuroimaging, Neurological Clinic and Hertie Institute for Clinical Brain Research in Tübingen (Germany). to work on post-processing of functional and structural MRI / network analysis (graph-theory, classification algorithms, EEG-fMRI) in the context of epilepsy. For details please see the attached PDF. Informal inquiries can be done via E-Mail (niels.focke(a)uni-tuebingen.de) http://www.hih-tuebingen.de/stellenangebote/stellenangebote-fuer-wissenschaf tler/postdoc-position-translational-neuroimaging/ __________________________________________________________________________ Dr. Niels Focke Oberarzt Abt. Neurologie mit Schwerpunkt Epileptologie Universitätsklinikum Tübingen AG Translationale Bildgebung Hertie Institut für Klinische Hirnforschung Werner Reichhardt Centre for Integrative Neuroscience

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Re: [Freesurfer] question regarding control point edits
by Adam Mezher 30 Jul '14

30 Jul '14

Hi Bruce, Thanks a lot for your help thus far. I've edited, computed, and applied the average bias to the error subjects' orig.mgz files. However, I'm not sure how to re-run all autorecon steps for these cases using the newly created orig.mgz (with bias applied). Thoughts? Thanks, Adam Hi Adam it depends on the source of the bias. If it is fixed in the coordinate system of the scanner you could correct a few, then try using mri_compute_bias and mri_apply_bias to see if it helps (it computes an average bias field in scanner coords, then applies it to a new dataset) cheers Bruce On Wed, 23 Jul 2014, Adam Mezher wrote: > > 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 > > > > > _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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