Freesurfer April 2013

freesurfer@nmr.mgh.harvard.edu

131 participants
220 discussions

Problem with aseg - Other segmentations fine
by preciado＠nmr.mgh.harvard.edu 03 Apr '13

03 Apr '13

I am having a bit of a problem the aseg on this subject. (See 2013.03.22.cor108.aseg.jpg attached) It is way overestimating the white matter bilaterally. The problems are about this bad for about 20 or more slices so editing manually seems like... a less than efficient proposition. Any thoughts on how to fix this programmatically? For reference, I have a attached some other images with no segmentation and using the Desikan-Killiany atlas (aparc+aseg) and the Destrieux atlas (aparc.a2009s+aseg) which look fine. Thanks, -Ronny

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Research Coordinator Position at the University of Washington
by McLaughlin, Katie 03 Apr '13

03 Apr '13

An experienced, independent, and organized individual is sought for a full-time Research Study Coordinator position in the Stress and Development Laboratory at the University of Washington Psychology Department, run by Katie McLaughlin, PhD. The individual in this position would coordinate the operations of a child clinical psychology laboratory focused on studying the impact of trauma exposure on children’s brain and behavioral development. Principle responsibilities include developing, coordinating, and monitoring research activities for several psychophysiology and neuroimaging studies of children and adolescents; recruiting children, adolescents, and parents from community sources; conducting clinical interviews and neuropsychological tests; supervising and monitoring undergraduate research assistants; and coordinating the management of study data. This position would be an excellent fit for applicants interested in obtaining doctoral training in clinical or developmental psychology or developmental cognitive neuroscience. Specific duties include: · Assistance in the development of recruitment methods; recruitment and screening of potential participants to determine eligibility. · Assistance in the preparation of IRB applications, consent forms and progress reports for institutional review board. · Development and implementation of standardized protocols for collecting and scoring behavioral, psychophysiology, and fMRI data. · Data collection and data quality control to ensure fidelity to study protocol · Development and programming of behavioral and fMRI tasks . Recruitment, training and supervision of volunteer undergraduate and post- baccalaureate research assistants. . Administration of neuropsychological tests and clinical interviews Previous research or clinical experience with children and the ability to work in command line environments such as Unix or Linux operating systems is preferred. The position begins in August or September 2013. Please email a CV and cover letter to Katie McLaughlin at: mclaughk(a)uw.edu<mailto:mclaughk@uw.edu>. -- Katie McLaughlin, Ph.D. Director, Stress & Development Laboratory, Boston Children's Hospital Assistant Professor of Pediatrics and Psychiatry Harvard Medical School 21 Autumn Street, Boston, MA 02115 Phone: (857) 218-5598; Fax: (617) 730-0957

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Re: [Freesurfer] Error from mri_concat while using QDEC
by Tudor Popescu 03 Apr '13

03 Apr '13

Hi Doug, I'm not sure why that does not make sense, shouldn't the input of mri_concat be several to-be-concatenated files rather than a single file? Anyway, after trying out the command with only one of the files from the tutorial, *mri_concat --debug /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/subjects/qdec/y.mgh* ..the same thing happens, namely it returns to the command prompt, with no message whatsoever. What could be wrong? As I mentioned, all those MGH files are at the expected path. Thanks again for your help! Tudor On 20 December 2012 05:24, Douglas Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > That does not make sense. Try using only one input file. Also, put --debug > as the first option. > doug > > > > > > > On 12/19/12 8:32 AM, Tudor Popescu wrote: > > Hi Doug, > So the full command is > > mri_concat > /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/049/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/141/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/084/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/021/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/093/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/080/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/091/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/040/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/017/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/138/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/106/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/108/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/092/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/124/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/129/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/103/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/130/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/039/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/123/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/095/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/067/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/004/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/133/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/097/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/073/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/149/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/045/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/136/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/144/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/032/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/131/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/145/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/111/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/102/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/074/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/114/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/008/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/128/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/099/surf/lh.thickness.fwhm10.fsaverage.mgh > --o > /media/Dell/_FS/buckner_data/subjects/qdec/lh-thickness-age-fwhm10/y.mgh > --debug > > ..however, as soon as I press Enter, I'm just taken to the command prompt > again, with no output whatsoever! Am I calling mri_concat wrongly?! > > Tudor > > On 18 December 2012 17:15, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > >> Hi Tudor, >> Can you run mri_concat from the command line with the --debug option >> first. Send us the FULL command line and the full terminal output. >> doug >> >> >> >> On 12/18/2012 09:35 AM, Tudor Popescu wrote: >> > Hello everyone, >> > >> > I tried doing the QDEC group analysis tutorial, however after doing >> > everything as instructed in the tutorial, when pressing Analyze I get >> > the error message: >> > >> > /Error in Analyze: command failed: mri_concat >> > >> /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh >> > >> /media/Dell/_FS/buckner_data/subjects/049/surf/lh.thickness.fwhm10.fsaverage.mgh >> > (..)/ >> > >> > ..even though those files are all accessible there! I pasted that same >> > mri_concat manually into the terminal, however no output is produced >> > at the command prompt, nor any files are created. >> > >> > In previous attempts, I used to also get this error >> > >> > /" .ERROR: QdecProject::VerifySubjects: Couldn't find subject '032' in >> > SUBJECTS_DIR "/ >> > /Syntax error: Bad fd number"/ >> > >> > after following the sh/bash workaround from this >> > < >> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-October/008618.h… >> >previous >> > thread, I no longer get that error, however get stuck with the error >> > mentioned above. >> > >> > My SUBJECTS_DIR already contains a copy of the default subjects folder. >> > >> > Debug info below. Any help greatly appreciated! >> > Tudor >> > >> > -------- freesurfer-Linux-centos4-stable-pub-v5.1.0 -------- >> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >> > FREESURFER_HOME /home/virtualuser/freesurfer >> > FSFAST_HOME /home/virtualuser/freesurfer/fsfast >> > FSF_OUTPUT_FORMAT nii.gz >> > SUBJECTS_DIR /media/Dell/_FS/buckner_data/subjects >> > MNI_DIR /home/virtualuser/freesurfer/mni >> > >> > >> > >> > _______________________________________________ >> > 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: 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 >> >> >> 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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Re: [Freesurfer] mris_preproc with --xhemi
by Gabriel Gonzalez Escamilla 03 Apr '13

03 Apr '13

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Extract surface from volume
by Valtina Pouegue 02 Apr '13

02 Apr '13

I have a volume in mnc and nii format. I would like to extract the outer surface from those volumes to be able to use in Freesurfer. I tried 'mri_vol2surf' but I didn't have the registration file. So I try make_register to create a registration file and the system give me an error as it couldn't open the header file to configure the fctstem...Does anyone know another way for extract the surface ( even with Matlab) ? Thanks, VP

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Re: [Freesurfer] Error with .license after upgrading to 5.2
by Nicola Toschi 02 Apr '13

02 Apr '13

Hi - no luck unfortunately (I had already tried changing permissions).... On 03/22/2013 04:09 PM, Varghese Chikku wrote: > Hi Nicola, > Can you try this command,and echo the license.It may ask for > password.I have similar issues with 5.2 and this how i sorted. > sudo chmod -R a+rwX /Applications/freesurfer > then > echo each line of the licence. > Let me know > In thanks > chikku

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advice for subcortical Freesurfer processing of 2 year old brains
by Joshua Lee 02 Apr '13

02 Apr '13

The aseg has shown poor performance in my sample. Are there settings, atlases, etc, available that might improve performance? - Josh

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recon-all with multiple spgr's per subject
by Salil Soman 02 Apr '13

02 Apr '13

Dear Freesurfer experts, Could someone point me to the syntax for having recon-all use multiple T1 volumes for the same subject (which I believe it is supposed to motion correct and average). Thanks, Salil Soman, MD, MS

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preproc-sess erros
by Mario Ortega 02 Apr '13

02 Apr '13

Hi freesurfer team, I have been having intermittent problems ( Im assuming bbregister problems.) the register.dof6.dat file is not being written, and I find an error in the dat.log error is here: flirt.fsl -ref bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister.nii -in bold/011/tmp.bbregister.10308/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/011/tmp.bbregister.10308/fslregister/fslma t0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init bold/011/tmp.bbregister.10308/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for 'bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister): bad header info Error: failed to open file bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister ERROR: Could not open image bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) I do have disk space. the command that I use is preproc-sess -s FCBA05_MR1 -fsd bold -per-run -stc siemens -force -surface fsaverage rhlh -fwhm 6 Any help is appreciated as I continue tracing the error. Thanks, Mario

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R: Re: R: R: Re: R: Re: perirhinal analysis
by stdp82＠virgilio.it 02 Apr '13

02 Apr '13

Now is ok. Thank you very much!! Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 2-apr-2013 20.09 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: R: Re: R: Re: perirhinal analysis Try mri_label2label --srcsubjectsubject_prova --srclabel rh.perirhinal.label --trgsubject Con01 --trglabel Con01/label/rh.perirhinal.label --hemi rh --regmethod surface also note that if you run mri_label2label with only the --help argument, it will print out help as to what each flag means as well as examples. Reading the help is a good approach when you cannot get immediate assistant from the list. You'll also learn about how the command is supposed to work. Pretty soon, you'll be the one helping others! doug On 04/02/2013 04:37 AM, stdp82(a)virgilio.it wrote: > Dear Doug, > > I'm trying to follow your indication but, please, could you explicate > what's meaning "subjet with" and where I should put it? > Could you show me the correct command line, please? > > The wrong command line is > mri_label2label --srcsubject fsaverage --srclabel rh.perirhinal.label > --trgsubject Con01 --trglabel Con01/label/rh.perirhinal.label --hemi > rh --regmethod surface > > Many thanks, > > > Stefano > > > > > ----Messaggio originale---- > Da: greve(a)nmr.mgh.harvard.edu > Data: 28-mar-2013 18.32 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: R: Re: [Freesurfer] perirhinal analysis > > If the source subject is subject_prova then you need to spec that subjet > 2with --srcsubject (instead of fsaverage) > doug > > > On 03/28/2013 01:11 PM, stdp82(a)virgilio.it wrote: > > Yes, it is located in > > /Applications/freesurfer/subjects/subject_prova/Con01/label/rh.perirhinal.label. > > > > > > > > Stefano > > > > > > > > > > ----Messaggio originale---- > > Da: greve(a)nmr.mgh.harvard.edu > > Data: 28-mar-2013 17.46 > > A: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] perirhinal analysis > > > > It says "no such file or directory" > > does rh.perifhyinal.label exist? > > > > > > On 03/28/2013 11:55 AM, stdp82(a)virgilio.it wrote: > > > Hi list, > > > > > > I'm running perirhinal analysis with this error: > > > > > > mri_label2label --srcsubject fsaverage --srclabel rh.perirhinal.label > > > --trgsubject Con01 --trglabel Con01/label/rh.perirhinal.label --hemi > > > rh --regmethod surface > > > > > > srclabel = rh.perirhinal.label > > > srcsubject = fsaverage > > > trgsubject = Con01 > > > trglabel = Con01/label/rh.perirhinal.label > > > regmethod = surface > > > > > > srchemi = rh > > > trghemi = rh > > > trgsurface = white > > > srcsurfreg = sphere.reg > > > trgsurfreg = sphere.reg > > > usehash = 1 > > > Use ProjAbs = 0, 0 > > > Use ProjFrac = 0, 0 > > > DoPaint 0 > > > > > > SUBJECTS_DIR/Applications/freesurfer/subjects/subject_prova > > > FREESURFER_HOME /Applications/freesurfer > > > Loading source label. > > > No such file or directory > > > mri_label2label: could not open label file rh.perirhinal.label > > > No such file or directory > > > ERROR reading rh.perirhinal.label > > > > > > My $SUBJECTS_DIR=/Applications/freesurfer/subjects/subject_prova and > > > rh.perirhinal.label exist and it is located > > > in /Applications/freesurfer/subjects/subject_prova/Con01/label > > > > > > > > > Thanks, > > > > > > > > > Stefano > > > > > > > > > > > > _______________________________________________ > > > 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: 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 > > > > > > 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: 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: 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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Freesurfer April 2013