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30089 discussions

PET processing seg fault with mri_glmfit --mrtm1
by Conchy PF 25 Nov '17

25 Nov '17

Dear Douglas, I had the same problem as Jonathan described in his post "PET processing seg fault with mri_glmfit --mrtm1" ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043144.… ). In my case, I used this command: mri_glmfit --y gtmpvc/km.hb.tac.nii.gz --mrtm1 gtmpvc/km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz And I got this message: /Applications/freesurfer/bin/mri_glmfit: line 3: 27756 Segmentation fault: 11 mri_glmfit.bin "$@" Following your advice, I checked if km.hb.tac.nii.gz was all 0 using hb = fast_vol2mat( MRIread('km.hb.tac.nii.gz')); plot(hb) in matlab, but that is not the case [image: Inline image 1] I also checked the table.dat format and it was correct, and I tried using mri_glmfit.bin command insted, but it did not work. Could you give me some advice, so I can keep running the PET surfer pipeline? Thank you in advance and kind regards, CP

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Segmentation Volume to Cortical Labels
by Hengda He 25 Nov '17

25 Nov '17

Hi Freesurfer Developers, I have a manually edited segmentation of the brain cortical regions, and I want to map it to cortical parcellation labels on both white matter surface and pial surface. So I am wondering if there is any way in FreeSurfer that can map the segmentation volume to cortical labels. Something like the inverse of command mri_aparc2aseg. Thanks! All the Best, Hengda

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Error finding glmdir with mri_glmfit-sim
by Nick Corriveau-Lecavalier 25 Nov '17

25 Nov '17

Hi FS team, I ran a mri_glmfit for a 3 groups comparison and now I'm trying to run the cwp correction with mri_glmfit-sim command. When I type in my command, it says: ERROR: cannot find /Applications/freesurfer/subjects/fsgd/lh.thickness.10fhwm/ Which is exactly the emplacement of my group analysis file. The weird thing is, I ran the very same analysis a few months ago with fewer subjects and it ran well. Can you help me with this? Nick Corriveau-Lecavalier Candidat au Ph.D. recherche/intervention, option neuropsychologie clinique Président de l'Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7818

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medial wall label in Freesurfer 6
by Sofia Rodriguez Penuela 23 Nov '17

23 Nov '17

Hello, when using "make_average_subject" in Freesurfer, we have noted that the medial wall label only contains 1 vertex leading, after applying "mri_glmfit, to significant results in regions of the medial wall. This problem didn't appear in Fresurfer 5.3 Is there something different with the command "make_average_subject" in Freesurfer 6 that prevent to correctly mask the cortical surface to avoid significant results on regions of the medial wall? We would like to include only cortical vertices in our analysis. Thank you in advance. Best, Sofia -- Sofía Rodríguez Peñuela, Técnico de Laboratorio. Laboratorio de Neurociencia Funcional Departamento de Fisiología, Anatomía y Biología Celular. Universidad Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - España - Movil: 627273085 Email: srodpen(a)upo.es http://www.upo.es/neuroaging/es/

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contrasts mat file
by 박경일 23 Nov '17

23 Nov '17

Dear experts, I am trying to perform mri_glmfit to generate images indicating cortical thickness differences between groups. My data has 6 or 7 covariates such age, sex, smoking, hypertension, diabetes etc. I wonder how to make contrasts.mat files.Those are supposed to be a lot of files. FSTutorial shows only the example of two covariates. Thank you. Sincerely, Kyung

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Tilting / orienting brain slices
by Sam Norman-Haignere 23 Nov '17

23 Nov '17

I would like to tilt/rotate a brain image so that I can see multiple activations in a single slice. I don't believe this is possible in Freeview, am I'm curious if there is a brain viewer with this capability (would presumably require some type of activate interpolation)? It seems like a feature that would be quite useful. My best, Sam Norman-Haignere

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QC on CVS registration
by Mehta, Chintan 22 Nov '17

22 Nov '17

Dear FreeSurfer users, I'm using FS 6.0. I registered MRI scans to the CVS-Avg35 template (mri_cvs_register) and viewed output. While the nonlinear warp of the scan to the template looked completely fine, the warping of the automatic segmentation (aseg) did not look as "clean". Attached is a snapshot of the subject's "aseg" warped to the cvs template: "ASEG_final_CVSmorphend_tocvs-avg35.png". Also attached is a snapshot at the same slice of the ASEG of the CVS template (shipped with FS): "ASEG_template-cvs-avg35.png". This subject's "aseg" warped to CVS is typical of others in my sample. The aseg look completely fine in their respective anat spaces. The aseg warped to CVS looks splotchy. Is the splotchiness in a subject's ASEG warped to CVS template inevitable due to how registration works? With smoothing, I imagine it would look much nicer and would be almost entire in line with the ASEG of the template. As such, is it recommended that one smooth spatial maps registered to CVS template when running GLM over measures like Apparent Diffusion Coefficient (ADC) or Fractional Anisotropy (FA)? Thank you. Best, Chintan

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Re: [Freesurfer] Skullstrip commands not working {Disarmed}
by Arsenije Subotic 22 Nov '17

22 Nov '17

Hi Bruce, I performed the -autorecon-pial as a means of regenerating the surfaces as instructed on the Freesurfer skull strip tutorial. The brainmask.mgz file does not have the skull but it has some dura left over. The issue I had before was that the skull would re-appear after the subject finished processing and the surfaces would be outlined on the dura and skull. Would it be okay if I could send screenshots of the my processed subject? Thanks for your help. Arsenije ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Wednesday, November 22, 2017 11:09 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 165, Issue 35 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. Job opening: postdoc in AFNI group of NIH (P Taylor) 2. Re: Problems when loading surface and mesh showing vertices (Rosalia Dacosta Aguayo) ---------------------------------------------------------------------- Message: 1 Date: Wed, 22 Nov 2017 12:50:37 -0500 From: P Taylor <neon.taylor(a)gmail.com> Subject: [Freesurfer] Job opening: postdoc in AFNI group of NIH To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAB790KVuR-gAU__TTz0CoGSTFriKNEPCrDSSxg9wAdK3qBF+GQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello- The Scientific and Statistical Computing Core (a.k.a. the AFNI group) at the NIMH, NIH (Bethesda, MD, USA) is lookin' to hire a postdoc, particularly someone with C and/or C++ experience, with Python and OpenGL skills also being quite useful. If you like problem solving and working with a fun group of people, then check out the attached advertisement for details. (And please feel free to forward on.) --pt

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Job opening: postdoc in AFNI group of NIH
by P Taylor 22 Nov '17

22 Nov '17

Hello- The Scientific and Statistical Computing Core (a.k.a. the AFNI group) at the NIMH, NIH (Bethesda, MD, USA) is lookin' to hire a postdoc, particularly someone with C and/or C++ experience, with Python and OpenGL skills also being quite useful. If you like problem solving and working with a fun group of people, then check out the attached advertisement for details. (And please feel free to forward on.) --pt

1 0

Problems with FtpFileExchange
by Rosalia Dacosta Aguayo 22 Nov '17

22 Nov '17

Dear FreeSurfer Developers, I am having problems with FtpFileExchange. I am trying to upload a compressed file Bruce asked me to upload and it seems I am missing something in the last point of the instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange *What I have done till now*: rosalia@rosalia-Lenovo-Y520-15IKBN:~$ ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 Name (surfer.nmr.mgh.harvard.edu:rosalia): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp> cd transfer/incoming 250 Directory successfully changed. *What I do not understand* *ftp> put filename.txt* >From this *red* point I have no idea about how to include my compressed file S_001.zip. On the other hand, he asked me to rar and compress the file...I am sorry but I am stuck here and I have no idea how to fix this. Any help would be much appreciate. I have proved with Krusader and with FileZilla and it does not work either... Thank you for your time, Kind regards, Rosalia

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