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Visually inspecting subcortical segmentations + what command should be run to apply manual fixes to aseg.mgz voxels?
by Reema Jayakar 12 Jul '16

12 Jul '16

Hello FS developers/users, I have a two part question regarding subcortical segmentation: 1) To visually inspect if segmentation accurately captures structure boundaries (e.g., amygdala) I am using the norm.mgz file and overlaying it with the aseg.mgz file in Freeview. Is this correct? Or should I be using brainmask.mgz (instead of norm.mgz)? Also, Freeview gives me some options - "Resample to standard RAS space" and "Apply registration file". Where can I find information about whether or not to use these options? 2) If I manually edit the boundaries of the amygdala (either by erasing voxels or using the color brush to add voxels), what command should I use to re-run such that the corrections are applied to my aseg.stats output? The command I found on the wiki page says to use recon-all -autorecon-2-noaseg -subjid <Subj_ID>. My understanding was that the -noaseg flag will skip all the subcortical segmentation steps and that is not what I want. What I want is for FS to re-run subcortical segmentation such that it reflects the voxel editing I did in Freeview. This is the first time I am doing something like this so any help you can provide or pointing me to the right resource would be great! Thank you! Reema -- *Reema Jayakar, M.A.* Doctoral Candidate - Clinical Neuropsychology Health Resources and Services Administration (HRSA) Fellow Department of Psychology Georgia State University Email: rjayakar1(a)student.gsu.edu

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mri_glmfit-sim
by Lauri Tuominen 12 Jul '16

12 Jul '16

Dear Freesurfers, As freesurfer mri_glmfit-sim is based on AlphaSim & FSL randomise, I would like to know if the results I’m getting are affected by recently found bugs/violations in RFT assumptions, e.g. http://www.pnas.org/content/early/2016/06/27/1602413113.full.pdf. Thank you in advance! Lauri Tuominen

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tcsh update
by shi yao wang 12 Jul '16

12 Jul '16

Dear FS experts: I am running FS in local computer and showing following error message and program stopped at recon-all WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Do I need to update tcsh? and how can I do it. thanks Lawrence

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R: Re: Recon-all error after El Capitain update
by stdp82＠virgilio.it 12 Jul '16

12 Jul '16

This is the command and the error line. Thanks. Stefano recon-all -all -i $SUBJECTS_DIR/T1_STRUCT.nii.gz -subject SUBJECTS_DIR #-------------------------------------------- INFO: fsaverage subject does not have perirhinal labels! \n cd /Applications/freesurfer/subjects/subject_prova/Control89; rm -Rf fsaverage; cd - \n INFO: Creating symlink to fsaverage subject... \n cd /Applications/freesurfer/subjects/subject_prova/Control89; ln -s /Applications/freesurfer/subjects/fsaverage; cd - \n \n mri_label2label --srcsubject fsaverage --srclabel /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh. BA1.label --trgsubject SUBJECTS_DIR --trglabel ./lh.BA1.label --hemi lh -- regmethod surface \n No such file or directory mri_label2label: could not open label file /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh. BA1.label srclabel = /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh. BA1.label srcsubject = fsaverage trgsubject = SUBJECTS_DIR trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh 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/Control89 FREESURFER_HOME /Applications/freesurfer Loading source label. No such file or directory ERROR reading /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh. BA1.label Darwin iMac-di-Stefano.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s SUBJECTS_DIR exited with ERRORS at Sat Jul 9 17:20:34 CEST 2016 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Control89/SUBJECTS_DIR/scripts/recon- all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >----Messaggio originale---- >Da: "dgw" <dgwakeman(a)gmail.com> >Data: 7-lug-2016 15.58 >A: <stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard. edu> >Ogg: Re: [Freesurfer] Recon-all error after El Capitain update > >It's hard to fully diagnose, without the command you called, but it >looks like you have your SUBJECTS_DIR and SUBJECT variable wrong, and >perhaps command syntax. Take another look at your command. > >hth >d > >On Thu, Jul 7, 2016 at 2:59 AM, <stdp82(a)virgilio.it> wrote: >> Hi list, >> >> after update with El Capitain, recon-all -all produce the error reported >> below. >> >> >> Thanks >> >> srclabel = >> /Applications/freesurfer/subjects/subject_prova/subj/fsaverage/label/lh.BA1. label >> >> srcsubject = fsaverage >> >> trgsubject = SUBJECTS_DIR >> >> trglabel = ./lh.BA1.label >> >> regmethod = surface >> >> >> srchemi = lh >> >> trghemi = lh >> >> 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/subj >> >> FREESURFER_HOME /Applications/freesurfer >> >> Loading source label. >> >> No such file or directory >> >> ERROR reading >> /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh. BA1.label >> >> Darwin iMac-di-Stefano.local 15.5.0 Darwin Kernel Version 15.5.0: >> root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 >> >> >> recon-all -s SUBJECTS_DIR exited with ERRORS >> >> >> _______________________________________________ >> 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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V3A ROI?
by Anders Hougaard 11 Jul '16

11 Jul '16

Dear experts, I am trying to find a probabilistic map of the visual cortical area V3A. I have not been able to find this particular area in the standard atlases in FSL or FreeSurfer. The Jülich Histological atlas contains a V3V ROI but not V3A. Do any of you know have this ROI as a file or do you know of an atlas which contains it? An estimation based on an experiment, e.g. an average from retinotopic maps of healthy subjects would also be very helpful. All the best, Anders

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longitudinal qdec tables
by Andrews, Derek 11 Jul '16

11 Jul '16

Dear FreeSurfer Developers and Community, I have been trying to run some commands using the -qdec-long flag (I.e. asegstats2table & mris_preproc) but am encountering errors. In the past I have used .rtf files to read in my data using the -fsgd flag but am unsure of how to go about this with longitudinal data, therefore I am using the qdec.dat file structure. I believe something must be wrong with the format of my qdec file. I'm working on MacOSx 10.9.3. I created the qdec in text editor and changed the suffix to .dat under get info (1). I also created one in gedit and saved it using a .dat suffix (2). See these qdec files attached. I receive the following errors: asegstats2table --qdec-long long.qdec.table.dat -t ./outdir/aseg.long.table SUBJECTS_DIR : /Users/dandrews/Data/MIAMRC/MIAMRC_SPGR_FS Traceback (most recent call last): File "/Applications/freesurfer/bin/asegstats2table", line 514, in <module> subj_listoftuples = assemble_inputs(options) File "/Applications/freesurfer/bin/asegstats2table", line 320, in assemble_inputs for row in reader: File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 103, in next self.fieldnames File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 90, in fieldnames self._fieldnames = self.reader.next() _csv.Error: new-line character seen in unquoted field - do you need to open the file in universal-newline mode? And mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi -lh --meas thickness --out lh.thickness.mgh ERROR: no subjects specified I imagine something silly with the qdec file must be going on. Any advice would be very appreciated. Best, Derek ________________________________ Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews(a)kcl.ac.uk

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combining -autorecon2-wm and -autorecon2-cp for segmentation correction
by Barbara Kreilkamp 11 Jul '16

11 Jul '16

Dear freesurfers, Could you please have a look at the segmentation results (attached). I ran this subject several times with control points, eventually I combined the edited wm.mgz and the control point step * and I end up with this result, which has improved segmentation, but it is still not optimal in the medial portion of the temporal lobe. * recon-all -autorecon2-wm -autorecon2-cp -autorecon3 -sd . -subjid REF033c -no-isrunning Could you please advise? Thank you so much, Best wishes, Barbara

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right hemisphere specific problem with converting labels from fsaverage to subject space
by Halbertsma, HN (ohk) 11 Jul '16

11 Jul '16

I’m having issues with the conversion of labels drawn in fsaverage to subject’s space (using mri_label2label). I’ve manually drawn labels (V1-bins) in the fsaverage brain in both the left and right hemisphere that I want to convert to a subjects brain. I’ve successfully managed to do this for the left hemisphere of all the subjects, where the V1-bins converted from the fsaverage fall perfectly within subject specific V1. However, for the right hemisphere, the bins seem slightly misaligned for all the subjects (they’re usually a bit bigger than they should be). Any idea what could have caused this?! Many thanks. Hinke Hinke N. Halbertsma, MSc PhD Student University Medical Center Groningen (UMCG) Department of Ophthalmology NeuroImaging Center (Antonius Deusinglaan 2, 9713 AW Groningen), room 124 T. (+31) 050 363 4431 E. h.n.halbertsma(a)umcg.nl<mailto:h.n.halbertsma@umcg.nl> ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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fornix segmentation using recon-all
by Hari Guragain 10 Jul '16

10 Jul '16

Dear Freesurfer Experts, I am interested to get the volume information of the structure "fornix" in the aseg.stats file. I would appreciate if there is any such argument that can be used along with the recon-all to get the volume information of the fornix like below. Till now, I have been using · *recon-all -autorecon-all -subjid **your_subject_name* Any suggestions will be appreciated. # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 4 6489 6958.2 Left-Lateral-Ventricle 34.8514 11.5767 15.0000 82.0000 67.0000 Thank you, Hari Guragain

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Question about write_surf.m
by Dulce Maria Magdaleno Arroyo 10 Jul '16

10 Jul '16

Hi freesurfers! I'm trying to run the function write_surf in matlab, as far as I understand this function is to write a surface to analyze in freesurfer from matlab data. I'm not sure if the extension of the file name has to be different, so I need your help to solve this simple (I guess) problem. The first line is what I'm trying to run and the next lines show me the error. *write_surf('prueba.nofix/', vertices, faces);* *...subtracting 1 from face indices for FreeSurfer compatibility*. *Error using fwriteInvalid file identifier. Use fopen to generate a valid file identifier.Error in fwrite3 (line 29)fwrite(fid, b1, 'uchar') ;Error in write_surf (line 38)fwrite3(fid, TRIANGLE_FILE_MAGIC_NUMBER);* thank you in advance for your help! Dulce

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